1
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Gray J, Torres VVL, Goodall E, McKeand SA, Scales D, Collins C, Wetherall L, Lian ZJ, Bryant JA, Milner MT, Dunne KA, Icke C, Rooke JL, Schneiders T, Lund PA, Cunningham AF, Cole JA, Henderson IR. Transposon mutagenesis screen in Klebsiella pneumoniae identifies genetic determinants required for growth in human urine and serum. eLife 2024; 12:RP88971. [PMID: 39189918 PMCID: PMC11349299 DOI: 10.7554/elife.88971] [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: 08/28/2024] Open
Abstract
Klebsiella pneumoniae is a global public health concern due to the rising myriad of hypervirulent and multidrug-resistant clones both alarmingly associated with high mortality. The molecular mechanisms underpinning these recalcitrant K. pneumoniae infection, and how virulence is coupled with the emergence of lineages resistant to nearly all present-day clinically important antimicrobials, are unclear. In this study, we performed a genome-wide screen in K. pneumoniae ECL8, a member of the endemic K2-ST375 pathotype most often reported in Asia, to define genes essential for growth in a nutrient-rich laboratory medium (Luria-Bertani [LB] medium), human urine, and serum. Through transposon directed insertion-site sequencing (TraDIS), a total of 427 genes were identified as essential for growth on LB agar, whereas transposon insertions in 11 and 144 genes decreased fitness for growth in either urine or serum, respectively. These studies not only provide further knowledge on the genetics of this pathogen but also provide a strong impetus for discovering new antimicrobial targets to improve current therapeutic options for K. pneumoniae infections.
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Affiliation(s)
- Jessica Gray
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Von Vergel L Torres
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Emily Goodall
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Samantha A McKeand
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Danielle Scales
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Christy Collins
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Laura Wetherall
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Zheng Jie Lian
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Jack A Bryant
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Matthew T Milner
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Karl A Dunne
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Christopher Icke
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Jessica L Rooke
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Thamarai Schneiders
- Division of Infection Medicine, University of EdinburghEdinburghUnited Kingdom
| | - Peter A Lund
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Adam F Cunningham
- Institute of Immunology and Immunotherapy, University of BirminghamBirminghamUnited Kingdom
| | - Jeff A Cole
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Ian R Henderson
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
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2
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Fivenson EM, Dubois L, Bernhardt TG. Co-ordinated assembly of the multilayered cell envelope of Gram-negative bacteria. Curr Opin Microbiol 2024; 79:102479. [PMID: 38718542 DOI: 10.1016/j.mib.2024.102479] [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: 03/01/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 06/11/2024]
Abstract
Bacteria surround themselves with complex cell envelopes to maintain their integrity and protect against external insults. The envelope of Gram-negative organisms is multilayered, with two membranes sandwiching the periplasmic space that contains the peptidoglycan cell wall. Understanding how this complicated surface architecture is assembled during cell growth and division is a major fundamental problem in microbiology. Additionally, because the envelope is an important antibiotic target and determinant of intrinsic antibiotic resistance, understanding the mechanisms governing its assembly is relevant to therapeutic development. In the last several decades, most of the factors required to build the Gram-negative envelope have been identified. However, surprisingly, little is known about how the biogenesis of the different cell surface layers is co-ordinated. Here, we provide an overview of recent work that is beginning to uncover the links connecting the different envelope biosynthetic pathways and assembly machines to ensure uniform envelope growth.
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Affiliation(s)
- Elayne M Fivenson
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States
| | - Laurent Dubois
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States; Howard Hughes Medical Institute, Boston, United States.
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3
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Shu S, Tsutsui Y, Nathawat R, Mi W. Dual function of LapB (YciM) in regulating Escherichia coli lipopolysaccharide synthesis. Proc Natl Acad Sci U S A 2024; 121:e2321510121. [PMID: 38635633 PMCID: PMC11046580 DOI: 10.1073/pnas.2321510121] [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: 12/06/2023] [Accepted: 03/21/2024] [Indexed: 04/20/2024] Open
Abstract
Levels of lipopolysaccharide (LPS), an essential glycolipid on the surface of most gram-negative bacteria, are tightly controlled-making LPS synthesis a promising target for developing new antibiotics. Escherichia coli adaptor protein LapB (YciM) plays an important role in regulating LPS synthesis by promoting degradation of LpxC, a deacetylase that catalyzes the first committed step in LPS synthesis. Under conditions where LPS is abundant, LapB recruits LpxC to the AAA+ protease FtsH for degradation. LapB achieves this by simultaneously interacting with FtsH through its transmembrane helix and LpxC through its cytoplasmic domain. Here, we describe a cryo-EM structure of the complex formed between LpxC and the cytoplasmic domain of LapB (LapBcyto). The structure reveals how LapB exploits both its tetratricopeptide repeat (TPR) motifs and rubredoxin domain to interact with LpxC. Through both in vitro and in vivo analysis, we show that mutations at the LapBcyto/LpxC interface prevent LpxC degradation. Unexpectedly, binding to LapBcyto also inhibits the enzymatic activity of LpxC through allosteric effects reminiscent of LpxC activation by MurA in Pseudomonas aeruginosa. Our findings argue that LapB regulates LPS synthesis in two steps: In the first step, LapB inhibits the activity of LpxC, and in the second step, it commits LpxC to degradation by FtsH.
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Affiliation(s)
- Sheng Shu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520
| | - Yuko Tsutsui
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520
- Cancer Biology Institute, Yale University, West Haven, CT06516
| | - Rajkanwar Nathawat
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520
| | - Wei Mi
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06520
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4
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Mettlach JA, Cian MB, Chakraborty M, Dalebroux ZD. Signaling through the Salmonella PbgA-LapB regulatory complex activates LpxC proteolysis and limits lipopolysaccharide biogenesis during stationary-phase growth. J Bacteriol 2024; 206:e0030823. [PMID: 38534107 PMCID: PMC11025326 DOI: 10.1128/jb.00308-23] [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: 09/22/2023] [Accepted: 02/27/2024] [Indexed: 03/28/2024] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) controls lipopolysaccharide (LPS) biosynthesis by regulating proteolysis of LpxC, the rate-limiting enzyme and target of preclinical antibiotics. PbgA/YejM/LapC regulates LpxC levels and controls outer membrane (OM) LPS composition at the log-to-stationary phase transition. Suppressor substitutions in LPS assembly protein B (LapB/YciM) rescue the LPS and OM integrity defects of pbgA-mutant S. Typhimurium. We hypothesized that PbgA regulates LpxC proteolysis by controlling LapB's ability to bind LpxC as a function of the growth phase. According to existing models, when nutrients are abundant, PbgA binds and restricts LapB from interacting with LpxC and FtsH, which limits LpxC proteolysis. However, when nutrients are limited, there is debate whether LapB dissociates from PbgA to bind LpxC and FtsH to enhance degradation. We sought to examine these models and investigate how the structure of LapB enables salmonellae to control LpxC proteolysis and LPS biosynthesis. Salmonellae increase LapB levels during the stationary phase to promote LpxC degradation, which limits lipid A-core production and increases their survival. The deletion of lapB, resulting in unregulated lipid A-core production and LpxC overabundance, leads to bacterial growth retardation. Tetratricopeptide repeats near the cytosol-inner membrane interface are sufficient for LapB to bind LpxC, and remarkably, LapB and PbgA interact in both growth phases, yet LpxC only associates with LapB in the stationary phase. Our findings support that PbgA-LapB exists as a constitutive complex in S. Typhimurium, which differentially binds LpxC to control LpxC proteolysis and limit lipid A-core biosynthesis in response to changes in the environment.IMPORTANCEAntimicrobial resistance has been a costly setback for human health and agriculture. Continued pursuit of new antibiotics and targets is imperative, and an improved understanding of existing ones is necessary. LpxC is an essential target of preclinical trial antibiotics that can eliminate multidrug-resistant Gram-negative bacterial infections. LapB is a natural LpxC inhibitor that targets LpxC for degradation and limits lipopolysaccharide production in Enterobacteriaceae. Contrary to some studies, findings herein support that LapB remains in complex instead of dissociating from its presumed negative regulator, PbgA/YejM/LapC, under conditions where LpxC proteolysis is enhanced. Advanced comprehension of this critical protein-lipid signaling network will lead to future development and refinement of small molecules that can specifically interfere.
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Affiliation(s)
- Joshua A. Mettlach
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Melina B. Cian
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Medha Chakraborty
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Zachary D. Dalebroux
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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Maniyeri A, Wieczorek A, Ayyolath A, Sugalska W, Klein G, Raina S. Suppressors of lapC Mutation Identify New Regulators of LpxC, Which Mediates the First Committed Step in Lipopolysaccharide Biosynthesis. Int J Mol Sci 2023; 24:15174. [PMID: 37894855 PMCID: PMC10607373 DOI: 10.3390/ijms242015174] [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: 09/05/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Gram-negative bacteria, such as Escherichia coli, are characterized by an asymmetric outer membrane (OM) with lipopolysaccharide (LPS) located in the outer leaflet and phospholipids facing the inner leaflet. E. coli recruits LPS assembly proteins LapB, LapC and LapD in concert with FtsH protease to ensure a balanced biosynthesis of LPS and phospholipids. We recently reported that bacteria either lacking the periplasmic domain of the essential LapC protein (lapC190) or in the absence of LapD exhibit an elevated degradation of LpxC, which catalyzes the first committed step in LPS biosynthesis. To further understand the functions of LapC and LapD in regulating LPS biosynthesis, we show that the overproduction of the intact LapD suppresses the temperature sensitivity (Ts) of lapC190, but not when either its N-terminal transmembrane anchor or specific conserved amino acids in the C-terminal domain are mutated. Moreover, overexpression of srrA, marA, yceJ and yfgM genes can rescue the Ts phenotype of lapC190 bacteria by restoring LpxC amounts. We further show that MarA-mediated suppression requires the expression of mla genes, whose products participate in the maintenance of OM asymmetry, and the SrrA-mediated suppression requires the presence of cardiolipin synthase A.
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Affiliation(s)
| | | | | | | | - Gracjana Klein
- Laboratory of Bacterial Genetics, Gdansk University of Technology, 80-233 Gdansk, Poland; (A.M.); (A.W.); (A.A.); (W.S.)
| | - Satish Raina
- Laboratory of Bacterial Genetics, Gdansk University of Technology, 80-233 Gdansk, Poland; (A.M.); (A.W.); (A.A.); (W.S.)
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6
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Fivenson EM, Rohs PDA, Vettiger A, Sardis MF, Torres G, Forchoh A, Bernhardt TG. A role for the Gram-negative outer membrane in bacterial shape determination. Proc Natl Acad Sci U S A 2023; 120:e2301987120. [PMID: 37607228 PMCID: PMC10469335 DOI: 10.1073/pnas.2301987120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/21/2023] [Indexed: 08/24/2023] Open
Abstract
The cell envelope of Gram-negative bacteria consists of three distinct layers: the cytoplasmic membrane, a cell wall made of peptidoglycan (PG), and an asymmetric outer membrane (OM) composed of phospholipid in the inner leaflet and lipopolysaccharide (LPS) glycolipid in the outer leaflet. The PG layer has long been thought to be the major structural component of the envelope protecting cells from osmotic lysis and providing them with their characteristic shape. In recent years, the OM has also been shown to be a load-bearing layer of the cell surface that fortifies cells against internal turgor pressure. However, whether the OM also plays a role in morphogenesis has remained unclear. Here, we report that changes in LPS synthesis or modification predicted to strengthen the OM can suppress the growth and shape defects of Escherichia coli mutants with reduced activity in a conserved PG synthesis machine called the Rod complex (elongasome) that is responsible for cell elongation and shape determination. Evidence is presented that OM fortification in the shape mutants restores the ability of MreB cytoskeletal filaments to properly orient the synthesis of new cell wall material by the Rod complex. Our results are therefore consistent with a role for the OM in the propagation of rod shape during growth in addition to its well-known function as a diffusion barrier promoting the intrinsic antibiotic resistance of Gram-negative bacteria.
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Affiliation(s)
- Elayne M. Fivenson
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Patricia D. A. Rohs
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Andrea Vettiger
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Marios F. Sardis
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Grasiela Torres
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Alison Forchoh
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Thomas G. Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
- HHMI, Chevy Chase, MD20815
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7
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Raina S. Lipopolysaccharides: Regulated Biosynthesis and Structural Diversity. Int J Mol Sci 2023; 24:7498. [PMID: 37108660 PMCID: PMC10145120 DOI: 10.3390/ijms24087498] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The cell envelope of Gram-negative bacteria contains two distinct membranes, an inner (IM) and an outer (OM) membrane, separated by the periplasm, a hydrophilic compartment that includes a thin layer of peptidoglycan [...].
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Affiliation(s)
- Satish Raina
- Laboratory of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
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8
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Bogdanov M. Renovating a double fence with or without notifying the next door and across the street neighbors: why the biogenic cytoplasmic membrane of Gram-negative bacteria display asymmetry? Emerg Top Life Sci 2023; 7:137-150. [PMID: 36960750 PMCID: PMC10725183 DOI: 10.1042/etls20230042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/03/2023] [Accepted: 03/13/2023] [Indexed: 03/25/2023]
Abstract
The complex two-membrane organization of the envelope of Gram-negative bacteria imposes an unique biosynthetic and topological constraints that can affect translocation of lipids and proteins synthesized on the cytoplasm facing leaflet of the cytoplasmic (inner) membrane (IM), across the IM and between the IM and outer membrane (OM). Balanced growth of two membranes and continuous loss of phospholipids in the periplasmic leaflet of the IM as metabolic precursors for envelope components and for translocation to the OM requires a constant supply of phospholipids in the IM cytosolic leaflet. At present we have no explanation as to why the biogenic E. coli IM displays asymmetry. Lipid asymmetry is largely related to highly entropically disfavored, unequal headgroup and acyl group asymmetries which are usually actively maintained by active mechanisms. However, these mechanisms are largely unknown for bacteria. Alternatively, lipid asymmetry in biogenic IM could be metabolically controlled in order to maintain uniform bilayer growth and asymmetric transmembrane arrangement by balancing temporally the net rates of synthesis and flip-flop, inter IM and OM bidirectional flows and bilayer chemical and physical properties as spontaneous response. Does such flippase-less or 'lipid only", 'passive' mechanism of generation and maintenance of lipid asymmetry exists in the IM? The driving force for IM asymmetry can arise from the packing requirements imposed upon the bilayer system during cell division through disproportional distribution of two negatively curved phospholipids, phosphatidylethanolamine and cardiolipin, with consistent reciprocal tendency to increase and decrease lipid order in each membrane leaflet respectively.
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Affiliation(s)
- Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX 77030, U.S.A
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9
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Gao Z, Jiang S, Zhong W, Liu T, Guo J. Linalool controls the viability of Escherichia coli by regulating the synthesis and modification of lipopolysaccharide, the assembly of ribosome, and the expression of substrate transporting proteins. Food Res Int 2023; 164:112337. [PMID: 36737930 DOI: 10.1016/j.foodres.2022.112337] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/08/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
Escherichia coli (E. coli) is a Gram-negative bacterium and some pathogenic types may cause serious diseases, foods or food environments were the primary routes for its infection. Citrus aurantium L. var. amara Engl., a variety of sour orange, were used as a kind of non-conventional edible plant in China, but its antimicrobial activity and mechanisms were not well studied. Thus, in this study, EO from the flower of Citrus aurantium L. var. amara Engl. (CAEO) were studied as a kind of natural antimicrobial agent to control E. coli, our results showed that both of CAEO and its main component (linalool) exhibited strong antibacterial efficacy. Further, transcriptomic and proteomic analysis were carried out to explore cell response under linalool treatment and the main results included: (1) The synthesis and modification of lipopolysaccharide (LPS) was significantly influenced. (2) Ribosomal assembly and protein synthesis were significantly inhibited. (3) The expression of proteins related to the uptake of several essential substances was significantly changed. In all, our results would supply a theoretical basis for the proper use of CAEO and linalool as a promising antimicrobial agent to prevent and control E. coli infection in the future.
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Affiliation(s)
- Zhipeng Gao
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, Hunan Province, China.
| | - Sifan Jiang
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, Hunan Province, China
| | - Weiming Zhong
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, Hunan Province, China
| | - Ting Liu
- Hunan Agriculture Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China
| | - Jiajing Guo
- Hunan Agriculture Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China.
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10
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Yan L, Dong H, Li H, Liu X, Deng Z, Dong C, Zhang Z. Uncovering lipopolysaccharide regulation in bacteria via the critical lipid binding tunnel of YciS/YciM. iScience 2022; 25:104988. [PMID: 36093049 PMCID: PMC9460159 DOI: 10.1016/j.isci.2022.104988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/04/2022] [Accepted: 08/17/2022] [Indexed: 11/30/2022] Open
Abstract
Gram-negative bacteria contain an asymmetric outer membrane, in which the outer leaflet is composed of lipopolysaccharide (LPS). LPS, a drug target of polymyxin, plays an essential role in drug resistance, biofilm formation, and pathogenesis. An important inner membrane protein, YciM, may be responsible for the regulation of LPS biosynthesis and transport. Here, we report the crystal structure of YciM from Salmonella typhimurium in a complex with a non-specifically bond molecule, an ethylene glycol, which identified a tunnel that could bind lipids. Our in vitro assays showed that YciM could bind lipid molecules with affinity in the micromolar range, while mutagenic and functional studies confirmed that lipid-binding residues are critical for the function of YciM. Additionally, our data also showed that YciM accurately regulates LPS biosynthesis and transport with YciS, which could help to better understand the regulation mechanism of LPS. Identifying a critical lipid binding tunnel of YciS/YciM The lipid binding tunnel could bind lipid molecules Mutants of lipid binding tunnel inhibit cell growth severely
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11
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A New Factor LapD Is Required for the Regulation of LpxC Amounts and Lipopolysaccharide Trafficking. Int J Mol Sci 2022; 23:ijms23179706. [PMID: 36077106 PMCID: PMC9456370 DOI: 10.3390/ijms23179706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Lipopolysaccharide (LPS) constitutes the major component of the outer membrane and is essential for bacteria, such as Escherichia coli. Recent work has revealed the essential roles of LapB and LapC proteins in regulating LPS amounts; although, if any additional partners are involved is unknown. Examination of proteins co-purifying with LapB identified LapD as a new partner. The purification of LapD reveals that it forms a complex with several proteins involved in LPS and phospholipid biosynthesis, including FtsH-LapA/B and Fab enzymes. Loss of LapD causes a reduction in LpxC amounts and vancomycin sensitivity, which can be restored by mutations that stabilize LpxC (mutations in lapB, ftsH and lpxC genes), revealing that LapD acts upstream of LapB-FtsH in regulating LpxC amounts. Interestingly, LapD absence results in the substantial retention of LPS in the inner membranes and synthetic lethality when either the lauroyl or the myristoyl acyl transferase is absent, which can be overcome by single-amino acid suppressor mutations in LPS flippase MsbA, suggesting LPS translocation defects in ΔlapD bacteria. Several genes whose products are involved in cell envelope homeostasis, including clsA, waaC, tig and micA, become essential in LapD’s absence. Furthermore, the overproduction of acyl carrier protein AcpP or transcriptional factors DksA, SrrA can overcome certain defects of the LapD-lacking strain.
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12
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Shu S, Mi W. Regulatory mechanisms of lipopolysaccharide synthesis in Escherichia coli. Nat Commun 2022; 13:4576. [PMID: 35931690 PMCID: PMC9356133 DOI: 10.1038/s41467-022-32277-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/25/2022] [Indexed: 11/09/2022] Open
Abstract
Lipopolysaccharide (LPS) is an essential glycolipid and forms a protective permeability barrier for most Gram-negative bacteria. In E. coli, LPS levels are under feedback control, achieved by FtsH-mediated degradation of LpxC, which catalyzes the first committed step in LPS synthesis. FtsH is a membrane-bound AAA+ protease, and its protease activity toward LpxC is regulated by essential membrane proteins LapB and YejM. However, the regulatory mechanisms are elusive. We establish an in vitro assay to analyze the kinetics of LpxC degradation and demonstrate that LapB is an adaptor protein that utilizes its transmembrane helix to interact with FtsH and its cytoplasmic domains to recruit LpxC. Our YejM/LapB complex structure reveals that YejM is an anti-adaptor protein, competing with FtsH for LapB to inhibit LpxC degradation. Structural analysis unravels that LapB and LPS have overlapping binding sites in YejM. Thus, LPS levels control formation of the YejM/LapB complex to determine LpxC protein levels.
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Affiliation(s)
- Sheng Shu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Wei Mi
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA. .,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
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13
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Valvano MA. Remodelling of the Gram-negative bacterial Kdo 2-lipid A and its functional implications. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35394417 DOI: 10.1099/mic.0.001159] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The lipopolysaccharide (LPS) is a characteristic molecule of the outer leaflet of the Gram-negative bacterial outer membrane, which consists of lipid A, core oligosaccharide, and O antigen. The lipid A is embedded in outer membrane and provides an efficient permeability barrier, which is particularly important to reduce the permeability of antibiotics, toxic cationic metals, and antimicrobial peptides. LPS, an important modulator of innate immune responses ranging from localized inflammation to disseminated sepsis, displays a high level of structural and functional heterogeneity, which arise due to regulated differences in the acylation of the lipid A and the incorporation of non-stoichiometric modifications in lipid A and the core oligosaccharide. This review focuses on the current mechanistic understanding of the synthesis and assembly of the lipid A molecule and its most salient non-stoichiometric modifications.
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Affiliation(s)
- Miguel A Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, UK
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14
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Cryo-EM structure of transmembrane AAA+ protease FtsH in the ADP state. Commun Biol 2022; 5:257. [PMID: 35322207 PMCID: PMC8943139 DOI: 10.1038/s42003-022-03213-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/01/2022] [Indexed: 11/08/2022] Open
Abstract
AAA+ proteases regulate numerous physiological and cellular processes through tightly regulated proteolytic cleavage of protein substrates driven by ATP hydrolysis. FtsH is the only known family of membrane-anchored AAA+ proteases essential for membrane protein quality control. Although a spiral staircase rotation mechanism for substrate translocation across the FtsH pore has been proposed, the detailed conformational changes among various states have not been clear due to absence of FtsH structures in these states. We report here the cryo-EM structure for Thermotoga maritima FtsH (TmFtsH) in a fully ADP-bound symmetric state. Comparisons of the ADP-state structure with its apo-state and a substrate-engaged yeast YME1 structure show conformational changes in the ATPase domains, rather than the protease domains. A reconstruction of the full-length TmFtsH provides structural insights for the dynamic transmembrane and the periplasmic domains. Our structural analyses expand the understanding of conformational switches between different nucleotide states in ATP hydrolysis by FtsH.
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Checkpoints That Regulate Balanced Biosynthesis of Lipopolysaccharide and Its Essentiality in Escherichia coli. Int J Mol Sci 2021; 23:ijms23010189. [PMID: 35008618 PMCID: PMC8745692 DOI: 10.3390/ijms23010189] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/17/2021] [Accepted: 12/22/2021] [Indexed: 12/17/2022] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria, such as Escherichia coli, is essential for their viability. Lipopolysaccharide (LPS) constitutes the major component of OM, providing the permeability barrier, and a tight balance exists between LPS and phospholipids amounts as both of these essential components use a common metabolic precursor. Hence, checkpoints are in place, right from the regulation of the first committed step in LPS biosynthesis mediated by LpxC through its turnover by FtsH and HslUV proteases in coordination with LPS assembly factors LapB and LapC. After the synthesis of LPS on the inner leaflet of the inner membrane (IM), LPS is flipped by the IM-located essential ATP-dependent transporter to the periplasmic face of IM, where it is picked up by the LPS transport complex spanning all three components of the cell envelope for its delivery to OM. MsbA exerts its intrinsic hydrocarbon ruler function as another checkpoint to transport hexa-acylated LPS as compared to underacylated LPS. Additional checkpoints in LPS assembly are: LapB-assisted coupling of LPS synthesis and translocation; cardiolipin presence when LPS is underacylated; the recruitment of RfaH transcriptional factor ensuring the transcription of LPS core biosynthetic genes; and the regulated incorporation of non-stoichiometric modifications, controlled by the stress-responsive RpoE sigma factor, small RNAs and two-component systems.
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16
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Drown them in their own garbage: a new strategy to reverse polymyxin resistance? J Bacteriol 2021; 204:e0057421. [PMID: 34843378 DOI: 10.1128/jb.00574-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purcell and colleagues offer new insights into a major mechanism of polymyxin resistance in Gram-negative bacteria. Inactivating a single lipid recycling enzyme causes accumulation of waste lipid by-products that inhibit a key factor responsible for polymyxin resistance.
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Thoma J, Burmann BM. Architects of their own environment: How membrane proteins shape the Gram-negative cell envelope. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:1-34. [PMID: 35034716 DOI: 10.1016/bs.apcsb.2021.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gram-negative bacteria are surrounded by a complex multilayered cell envelope, consisting of an inner and an outer membrane, and separated by the aqueous periplasm, which contains a thin peptidoglycan cell wall. These bacteria employ an arsenal of highly specialized membrane protein machineries to ensure the correct assembly and maintenance of the membranes forming the cell envelope. Here, we review the diverse protein systems, which perform these functions in Escherichia coli, such as the folding and insertion of membrane proteins, the transport of lipoproteins and lipopolysaccharide within the cell envelope, the targeting of phospholipids, and the regulation of mistargeted envelope components. Some of these protein machineries have been known for a long time, yet still hold surprises. Others have only recently been described and some are still missing pieces or yet remain to be discovered.
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Affiliation(s)
- Johannes Thoma
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.
| | - Björn M Burmann
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
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YhdP, TamB, and YdbH Are Redundant but Essential for Growth and Lipid Homeostasis of the Gram-Negative Outer Membrane. mBio 2021; 12:e0271421. [PMID: 34781743 PMCID: PMC8593681 DOI: 10.1128/mbio.02714-21] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial cell envelope is the first line of defense and point of contact with the environment and other organisms. Envelope biogenesis is therefore crucial for the survival and physiology of bacteria and is often targeted by antimicrobials. Gram-negative bacteria have a multilayered envelope delimited by an inner and outer membrane (IM and OM, respectively). The OM is a barrier against many antimicrobials because of its asymmetric lipid structure, with phospholipids composing the inner leaflet and lipopolysaccharides (LPS) the outer leaflet. Since lipid synthesis occurs at the IM, phospholipids and LPS are transported across the cell envelope and asymmetrically assembled at the OM during growth. How phospholipids are transported to the OM remains unknown. Recently, the Escherichia coli protein YhdP has been proposed to participate in this process through an unknown mechanism. YhdP belongs to the AsmA-like clan and contains domains homologous to those found in lipid transporters. Here, we used genetics to investigate the six members of the AsmA-like clan of proteins in E. coli. Our data show that YhdP and its paralogs TamB and YdbH are redundant, but not equivalent, in performing an essential function in the cell envelope. Among the AsmA-like paralogs, only the combined loss of YhdP, TamB, and YdbH is lethal, and any of these three proteins is sufficient for growth. We also show that these proteins are required for OM lipid homeostasis and propose that they are the long-sought-after phospholipid transporters that are required for OM biogenesis.
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Conserved tandem arginines for PbgA/YejM allow Salmonella Typhimurium to regulate LpxC and control lipopolysaccharide biogenesis during infection. Infect Immun 2021; 90:e0049021. [PMID: 34780276 DOI: 10.1128/iai.00490-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterobacteriaceae use the periplasmic domain of the conserved inner membrane protein, PbgA/YejM, to regulate lipopolysaccharide (LPS) biogenesis. Salmonella enterica serovar Typhimurium (S. Typhimurium) relies on PbgA to cause systemic disease in mice and this involves functional interactions with LapB/YciM, FtsH, and LpxC. Escherichia coli PbgA interacts with LapB, an adaptor for the FtsH protease, via the transmembrane segments. LapB and FtsH control proteolysis of LpxC, the rate-limiting LPS biosynthesis enzyme. Lipid A-core, the hydrophobic anchor of LPS molecules, co-crystallizes with PbgA and interacts with residues in the basic region. The model predicts that PbgA-LapB detects periplasmic LPS molecules and prompts FtsH to degrade LpxC. However, the key residues and critical interactions are not defined. We establish that S. Typhimurium uses PbgA to regulate LpxC and define the contribution of two pairs of arginines within the basic region. PbgA R215 R216 form contacts with lipid A-core in the structure and R231 R232 exist in an adjacent alpha helix. PbgA R215 R216 are necessary for S. Typhimurium to regulate LpxC, control lipid-A core biogenesis, promote survival in macrophages, and enhance virulence in mice. In contrast, PbgA R231 R232 are not necessary to regulate LpxC or to control lipid A-core levels, nor are they necessary to promote survival in macrophages or mice. However, residues R231 R232 are critical for infection lethality, and the persistent infection phenotype requires mouse Toll-like receptor four, which detects lipid A. Therefore, S. Typhimurium relies on PbgA's tandem arginines for multiple interconnected mechanisms of LPS regulation that enhance pathogenesis.
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Luo S, Kim C. Current Understanding of Temperature Stress-Responsive Chloroplast FtsH Metalloproteases. Int J Mol Sci 2021; 22:ijms222212106. [PMID: 34829988 PMCID: PMC8622299 DOI: 10.3390/ijms222212106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 12/22/2022] Open
Abstract
Low and high temperatures are life-threatening stress factors, diminishing plant productivity. One of the earliest responses of plants to stress is a rapid burst of reactive oxygen species (ROS) in chloroplasts. Widespread efforts over the past decade shed new light on the chloroplast as an environmental sensor, translating the environmental fluctuation into varying physiological responses by utilizing distinct retrograde (chloroplast-to-nucleus) signals. Recent studies have unveiled that chloroplasts mediate a similar unfolded/misfolded/damaged protein response (cpUPR) as observed in the endoplasmic reticulum and mitochondria. Although observing cpUPR is not surprising since the chloroplast is a prime organelle producing harmful ROS, the intertwined relationship among ROS, protein damage, and chloroplast protein quality controls (cpPQCs) with retrograde signaling has recently been reported. This finding also gives rise to critical attention on chloroplast proteins involved in cpPQCs, ROS detoxifiers, transcription/translation, import of precursor proteins, and assembly/maturation, the deficiency of which compromises chloroplast protein homeostasis (proteostasis). Any perturbation in the protein may require readjustment of proteostasis by transmitting retrograde signal(s) to the nucleus, whose genome encodes most of the chloroplast proteins involved in proteostasis. This review focuses on recent findings on cpUPR and chloroplast-targeted FILAMENTOUS TEMPERATURE-SENSITIVE H proteases involved in cpPQC and retrograde signaling and their impacts on plant responses to temperature stress.
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Affiliation(s)
- Shengji Luo
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China;
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China;
- Correspondence:
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21
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Lee HB, Park SH, Lee CR. The inner membrane protein LapB is required for adaptation to cold stress in an LpxC-independent manner. J Microbiol 2021; 59:666-674. [PMID: 33990910 DOI: 10.1007/s12275-021-1130-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/08/2021] [Accepted: 04/08/2021] [Indexed: 11/29/2022]
Abstract
The inner membrane protein lipopolysaccharide assembly protein B (LapB) is an adaptor protein that activates the proteolysis of LpxC by an essential inner membrane metalloprotease, FtsH, leading to a decrease in the level of lipopolysaccharide in the membrane. In this study, we revealed the mechanism by which the essential inner membrane protein YejM regulates LapB and analyzed the role of the transmembrane domain of LapB in Escherichia coli. The transmembrane domain of YejM genetically and physically interacted with LapB and inhibited its function, which led to the accumulation of LpxC. The transmembrane domain of LapB was indispensable for both its physical interaction with YejM and its regulation of LpxC proteolysis. Notably, we found that the lapB mutant exhibited strong cold sensitivity and this phenotype was not associated with increased accumulation of LpxC. The transmembrane domain of LapB was also required for its role in adaptation to cold stress. Taken together, these results showed that LapB plays an important role in both the regulation of LpxC level, which is controlled by its interaction with the transmembrane domain of YejM, and adaptation to cold stress, which is independent of LpxC.
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Affiliation(s)
- Han Byeol Lee
- Department of Biological Sciences, Myongji University, Yongin, 17058, Republic of Korea
| | - Si Hyoung Park
- Department of Biological Sciences, Myongji University, Yongin, 17058, Republic of Korea
| | - Chang-Ro Lee
- Department of Biological Sciences, Myongji University, Yongin, 17058, Republic of Korea.
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Cardiolipin aids in lipopolysaccharide transport to the gram-negative outer membrane. Proc Natl Acad Sci U S A 2021; 118:2018329118. [PMID: 33833055 DOI: 10.1073/pnas.2018329118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In Escherichia coli, cardiolipin (CL) is the least abundant of the three major glycerophospholipids in the gram-negative cell envelope. However, E. coli harbors three distinct enzymes that synthesize CL: ClsA, ClsB, and ClsC. This redundancy suggests that CL is essential for bacterial fitness, yet CL-deficient bacteria are viable. Although multiple CL-protein interactions have been identified, the role of CL still remains unclear. To identify genes that impact fitness in the absence of CL, we analyzed high-density transposon (Tn) mutant libraries in combinatorial CL synthase mutant backgrounds. We found LpxM, which is the last enzyme in lipid A biosynthesis, the membrane anchor of lipopolysaccharide (LPS), to be critical for viability in the absence of clsA Here, we demonstrate that CL produced by ClsA enhances LPS transport. Suppressors of clsA and lpxM essentiality were identified in msbA, a gene that encodes the indispensable LPS ABC transporter. Depletion of ClsA in ∆lpxM mutants increased accumulation of LPS in the inner membrane, demonstrating that the synthetic lethal phenotype arises from improper LPS transport. Additionally, overexpression of ClsA alleviated ΔlpxM defects associated with impaired outer membrane asymmetry. Mutations that lower LPS levels, such as a YejM truncation or alteration in the fatty acid pool, were sufficient in overcoming the synthetically lethal ΔclsA ΔlpxM phenotype. Our results support a model in which CL aids in the transportation of LPS, a unique glycolipid, and adds to the growing repertoire of CL-protein interactions important for bacterial transport systems.
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Guest RL, Rutherford ST, Silhavy TJ. Border Control: Regulating LPS Biogenesis. Trends Microbiol 2021; 29:334-345. [PMID: 33036869 PMCID: PMC7969359 DOI: 10.1016/j.tim.2020.09.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/20/2022]
Abstract
The outer membrane (OM) is a defining feature of Gram-negative bacteria that serves as a permeability barrier and provides rigidity to the cell. Critical to OM function is establishing and maintaining an asymmetrical bilayer structure with phospholipids in the inner leaflet and the complex glycolipid lipopolysaccharide (LPS) in the outer leaflet. Cells ensure this asymmetry by regulating the biogenesis of lipid A, the conserved and essential anchor of LPS. Here we review the consequences of disrupting the regulatory components that control lipid A biogenesis, focusing on the rate-limiting step performed by LpxC. Dissection of these processes provides critical insights into bacterial physiology and potential new targets for antibiotics able to overcome rapidly spreading resistance mechanisms.
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Affiliation(s)
- Randi L Guest
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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Abstract
Gram-negative bacteria produce an asymmetric outer membrane (OM) that is particularly impermeant to many antibiotics and characterized by lipopolysaccharide (LPS) exclusively at the cell surface. LPS biogenesis remains an ideal target for therapeutic intervention, as disruption could kill bacteria or increase sensitivity to existing antibiotics. While it has been known that LPS synthesis is regulated by proteolytic control of LpxC, the enzyme that catalyzes the first committed step of LPS synthesis, it remains unknown which signals direct this regulation. New details have been revealed during study of a cryptic essential inner membrane protein, YejM. Multiple functions have been proposed over the years for YejM, including a controversial hypothesis that it transports cardiolipin from the inner membrane to the OM. Strong evidence now indicates that YejM senses LPS in the periplasm and directs proteolytic regulation. Here, we discuss the standing literature of YejM and highlight exciting new insights into cell envelope maintenance.
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Affiliation(s)
- Brent W Simpson
- Department of Infectious Diseases, The University of Georgia, College of Veterinary Medicine, Athens, Georgia, USA
| | - Martin V Douglass
- Department of Infectious Diseases, The University of Georgia, College of Veterinary Medicine, Athens, Georgia, USA
| | - M Stephen Trent
- Department of Infectious Diseases, The University of Georgia, College of Veterinary Medicine, Athens, Georgia, USA
- Department of Microbiology, The University of Georgia, College of Veterinary Medicine, Athens, Georgia, USA
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Regulation of the First Committed Step in Lipopolysaccharide Biosynthesis Catalyzed by LpxC Requires the Essential Protein LapC (YejM) and HslVU Protease. Int J Mol Sci 2020; 21:ijms21239088. [PMID: 33260377 PMCID: PMC7730581 DOI: 10.3390/ijms21239088] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/29/2022] Open
Abstract
We previously showed that lipopolysaccharide (LPS) assembly requires the essential LapB protein to regulate FtsH-mediated proteolysis of LpxC protein that catalyzes the first committed step in the LPS synthesis. To further understand the essential function of LapB and its role in LpxC turnover, multicopy suppressors of ΔlapB revealed that overproduction of HslV protease subunit prevents its lethality by proteolytic degradation of LpxC, providing the first alternative pathway of LpxC degradation. Isolation and characterization of an extragenic suppressor mutation that prevents lethality of ΔlapB by restoration of normal LPS synthesis identified a frame-shift mutation after 377 aa in the essential gene designated lapC, suggesting LapB and LapC act antagonistically. The same lapC gene was identified during selection for mutations that induce transcription from LPS defects-responsive rpoEP3 promoter, confer sensitivity to LpxC inhibitor CHIR090 and a temperature-sensitive phenotype. Suppressors of lapC mutants that restored growth at elevated temperatures mapped to lapA/lapB, lpxC and ftsH genes. Such suppressor mutations restored normal levels of LPS and prevented proteolysis of LpxC in lapC mutants. Interestingly, a lapC deletion could be constructed in strains either overproducing LpxC or in the absence of LapB, revealing that FtsH, LapB and LapC together regulate LPS synthesis by controlling LpxC amounts.
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Gabale U, Peña Palomino PA, Kim H, Chen W, Ressl S. The essential inner membrane protein YejM is a metalloenzyme. Sci Rep 2020; 10:17794. [PMID: 33082366 PMCID: PMC7576196 DOI: 10.1038/s41598-020-73660-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 09/18/2020] [Indexed: 12/27/2022] Open
Abstract
Recent recurrent outbreaks of Gram-negative bacteria show the critical need to target essential bacterial mechanisms to fight the increase of antibiotic resistance. Pathogenic Gram-negative bacteria have developed several strategies to protect themselves against the host immune response and antibiotics. One such strategy is to remodel the outer membrane where several genes are involved. yejM was discovered as an essential gene in E. coli and S. typhimurium that plays a critical role in their virulence by changing the outer membrane permeability. How the inner membrane protein YejM with its periplasmic domain changes membrane properties remains unknown. Despite overwhelming structural similarity between the periplasmic domains of two YejM homologues with hydrolases like arylsulfatases, no enzymatic activity has been previously reported for YejM. Our studies reveal an intact active site with bound metal ions in the structure of YejM periplasmic domain. Furthermore, we show that YejM has a phosphatase activity that is dependent on the presence of magnesium ions and is linked to its function of regulating outer membrane properties. Understanding the molecular mechanism by which YejM is involved in outer membrane remodeling will help to identify a new drug target in the fight against the increased antibiotic resistance.
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Affiliation(s)
- Uma Gabale
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, 212 S Hawthrone Dr, Bloomington, IN, 47405, USA.
| | - Perla Arianna Peña Palomino
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, 212 S Hawthrone Dr, Bloomington, IN, 47405, USA
| | - HyunAh Kim
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, 212 S Hawthrone Dr, Bloomington, IN, 47405, USA
| | - Wenya Chen
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, 212 S Hawthrone Dr, Bloomington, IN, 47405, USA
| | - Susanne Ressl
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, 212 S Hawthrone Dr, Bloomington, IN, 47405, USA.
- Department of Neuroscience, The University of Texas At Austin, 100 E. 24th St., NHB 2.504, Austin, TX, 78712, USA.
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"Asymmetry Is the Rhythmic Expression of Functional Design," a Quotation from Jan Tschichold. J Bacteriol 2020; 202:JB.00370-20. [PMID: 32631947 DOI: 10.1128/jb.00370-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The outer membranes of Gram-negative bacteria provide a permeability barrier to antibiotics and other harmful chemicals. The integrity of this barrier relies on the maintenance of the lipid asymmetry of the outer membrane, and studies of suppressors of a decades-old mutant reveal that YejM plays a key regulatory role and provide a model for the maintenance of this asymmetry.
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