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Rahman MM, Tikhomirova A, Modak JK, Hutton ML, Supuran CT, Roujeinikova A. Antibacterial activity of ethoxzolamide against Helicobacter pylori strains SS1 and 26695. Gut Pathog 2020; 12:20. [PMID: 32318117 PMCID: PMC7158114 DOI: 10.1186/s13099-020-00358-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/06/2020] [Indexed: 02/08/2023] Open
Abstract
With the rise of bacterial resistance to conventional antibiotics, re-purposing of Food and Drug Administration (FDA) approved drugs currently used to treat non-bacteria related diseases as new leads for antibacterial drug discovery has become an attractive alternative. Ethoxzolamide (EZA), an FDA-approved diuretic acting as a human carbonic anhydrase inhibitor, is known to kill the gastric pathogenic bacterium Helicobacter pylori in vitro via an, as yet, unknown mechanism. To date, EZA activity and resistance have been investigated for only one H. pylori strain, P12. We have now performed a susceptibility and resistance study with H. pylori strains SS1 and 26695. Mutants resistant to EZA were isolated, characterized and their genomes sequenced. Resistance-conferring mutations were confirmed by backcrossing the mutations into the parent strain. As with P12, resistance to EZA in strains SS1 and 26695 does not develop easily, since the rate of spontaneous resistance acquisition was less than 10−8. Acquisition of resistance was associated with mutations in 3 genes in strain SS1, and in 6 different genes in strain 26695, indicating that EZA targets multiple systems. All resistant isolates had mutations affecting cell wall synthesis and control of gene expression. EZA’s potential for treating duodenal ulcers has already been demonstrated. Our findings suggest that EZA may be developed into a novel anti-H. pylori drug.
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Affiliation(s)
- Mohammad M Rahman
- 1Department of Microbiology, Monash University, Clayton, VIC 3800 Australia.,2Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800 Australia
| | - Alexandra Tikhomirova
- 1Department of Microbiology, Monash University, Clayton, VIC 3800 Australia.,2Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800 Australia
| | - Joyanta K Modak
- 1Department of Microbiology, Monash University, Clayton, VIC 3800 Australia.,2Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800 Australia
| | - Melanie L Hutton
- 1Department of Microbiology, Monash University, Clayton, VIC 3800 Australia.,2Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800 Australia
| | - Claudiu T Supuran
- 3Neurofarba Department, Sezione di Scienze Farmaceutiche, Universita degli Studi di Firenze, Via U. Schiff 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Anna Roujeinikova
- 1Department of Microbiology, Monash University, Clayton, VIC 3800 Australia.,2Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800 Australia.,4Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC Australia
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Workman SD, Strynadka NCJ. A Slippery Scaffold: Synthesis and Recycling of the Bacterial Cell Wall Carrier Lipid. J Mol Biol 2020; 432:4964-4982. [PMID: 32234311 DOI: 10.1016/j.jmb.2020.03.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 01/20/2023]
Abstract
The biosynthesis of bacterial cell envelope polysaccharides such as peptidoglycan relies on the use of a dedicated carrier lipid both for the assembly of precursors at the cytoplasmic face of the plasma membrane and for the translocation of lipid linked oligosaccharides across the plasma membrane into the periplasmic space. This dedicated carrier lipid, undecaprenyl phosphate, results from the dephosphorylation of undecaprenyl pyrophosphate, which is generated de novo in the cytoplasm by undecaprenyl pyrophosphate synthase and released as a by-product when newly synthesized glycans are incorporated into the existing cell envelope. The de novo synthesis of undecaprenyl pyrophosphate has been thoroughly characterized from a structural and mechanistic standpoint; however, its dephosphorylation to the active carrier lipid form, both in the course of de novo synthesis and recycling, has only been begun to be studied in depth in recent years. This review provides an overview of bacterial carrier lipid synthesis and presents the current state of knowledge regarding bacterial carrier lipid recycling.
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Affiliation(s)
- Sean D Workman
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3.
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Chen L, Hou WT, Fan T, Liu B, Pan T, Li YH, Jiang YL, Wen W, Chen ZP, Sun L, Zhou CZ, Chen Y. Cryo-electron Microscopy Structure and Transport Mechanism of a Wall Teichoic Acid ABC Transporter. mBio 2020; 11:e02749-19. [PMID: 32184247 PMCID: PMC7078476 DOI: 10.1128/mbio.02749-19] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/21/2020] [Indexed: 01/24/2023] Open
Abstract
The wall teichoic acid (WTA) is a major cell wall component of Gram-positive bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA), a common cause of fatal clinical infections in humans. Thus, the indispensable ABC transporter TarGH, which flips WTA from cytoplasm to extracellular space, becomes a promising target of anti-MRSA drugs. Here, we report the 3.9-Å cryo-electron microscopy (cryo-EM) structure of a 50% sequence-identical homolog of TarGH from Alicyclobacillus herbarius at an ATP-free and inward-facing conformation. Structural analysis combined with activity assays enables us to clearly decode the binding site and inhibitory mechanism of the anti-MRSA inhibitor Targocil, which targets TarGH. Moreover, we propose a "crankshaft conrod" mechanism utilized by TarGH, which can be applied to similar ABC transporters that translocate a rather big substrate through relatively subtle conformational changes. These findings provide a structural basis for the rational design and optimization of antibiotics against MRSA.IMPORTANCE The wall teichoic acid (WTA) is a major component of cell wall and a pathogenic factor in methicillin-resistant Staphylococcus aureus (MRSA). The ABC transporter TarGH is indispensable for flipping WTA precursor from cytoplasm to the extracellular space, thus making it a promising drug target for anti-MRSA agents. The 3.9-Å cryo-EM structure of a TarGH homolog helps us to decode the binding site and inhibitory mechanism of a recently reported inhibitor, Targocil, and provides a structural platform for rational design and optimization of potential antibiotics. Moreover, we propose a "crankshaft conrod" mechanism to explain how a big substrate is translocated through subtle conformational changes of type II exporters. These findings advance our understanding of anti-MRSA drug design and ABC transporters.
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Affiliation(s)
- Li Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Wen-Tao Hou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Tao Fan
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, China
| | - Banghui Liu
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Ting Pan
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Yu-Hui Li
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, China
| | - Yong-Liang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Wen Wen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhi-Peng Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Linfeng Sun
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
- CAS Centre for Excellence in Molecular Cell Science, University of Science and Technology of China, Hefei, Anhui, China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
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Tan YH, Chen Y, Chu WHW, Sham LT, Gan YH. Cell envelope defects of different capsule-null mutants in K1 hypervirulent Klebsiella pneumoniae can affect bacterial pathogenesis. Mol Microbiol 2020; 113:889-905. [PMID: 31912541 PMCID: PMC7317392 DOI: 10.1111/mmi.14447] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 01/03/2020] [Accepted: 01/05/2020] [Indexed: 01/08/2023]
Abstract
Hypervirulent Klebsiella pneumoniae (hvKP) causes Klebsiella‐induced liver abscess. Capsule is important for the pathogenesis of Klebsiella in systemic infection, but its role in gut colonisation is not well understood. By generating ΔwcaJ, Δwza and Δwzy capsule‐null mutants in a prototypical K1 hypervirulent isolate, we show that inactivation of wza (capsule exportase) and wzy (capsule polymerase) confer cell envelope defects in addition to capsule loss, making them susceptible to bile salts and detergent stress. Bile salt resistance is restored when the initial glycosyltransferase wcaJ was inactivated together with wzy, indicating that build‐up of capsule intermediates contribute to cell envelope defects. Mouse gut colonisation competition assays show that the capsule and its regulator RmpA were not required for hvKP to persist in the gut, although initial colonisation was decreased in the mutants. Both ΔrmpA and ΔwcaJ mutants gradually outcompeted the wild type in the gut, whereas Δwza and Δwzy mutants were less fit than wild type. Together, our results advise caution in using the right capsule‐null mutant for determination of capsule's role in bacterial pathogenesis. With the use of ΔwcaJ mutant, we found that although the capsule is important for bacterial survival outside the gut environment, it imposes a fitness cost in the gut.
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Affiliation(s)
- Yi Han Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yahua Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Wilson H W Chu
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lok-To Sham
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yunn-Hwen Gan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Alexandraki V, Kazou M, Blom J, Pot B, Papadimitriou K, Tsakalidou E. Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species. Front Microbiol 2019; 10:2916. [PMID: 31956321 PMCID: PMC6951406 DOI: 10.3389/fmicb.2019.02916] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/03/2019] [Indexed: 12/24/2022] Open
Abstract
Streptococcus thermophilus is a major starter for the dairy industry with great economic importance. In this study we analyzed 23 fully sequenced genomes of S. thermophilus to highlight novel aspects of the evolution, biology and technological properties of this species. Pan/core genome analysis revealed that the species has an important number of conserved genes and that the pan genome is probably going to be closed soon. According to whole genome phylogeny and average nucleotide identity (ANI) analysis, most S. thermophilus strains were grouped in two major clusters (i.e., clusters A and B). More specifically, cluster A includes strains with chromosomes above 1.83 Mbp, while cluster B includes chromosomes below this threshold. This observation suggests that strains belonging to the two clusters may be differentiated by gene gain or gene loss events. Furthermore, certain strains of cluster A could be further subdivided in subgroups, i.e., subgroup I (ASCC 1275, DGCC 7710, KLDS SM, MN-BM-A02, and ND07), II (MN-BM-A01 and MN-ZLW-002), III (LMD-9 and SMQ-301), and IV (APC151 and ND03). In cluster B certain strains formed one distinct subgroup, i.e., subgroup I (CNRZ1066, CS8, EPS, and S9). Clusters and subgroups observed for S. thermophilus indicate the existence of lineages within the species, an observation which was further supported to a variable degree by the distribution and/or the architecture of several genomic traits. These would include exopolysaccharide (EPS) gene clusters, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)-CRISPR associated (Cas) systems, as well as restriction-modification (R-M) systems and genomic islands (GIs). Of note, the histidine biosynthetic cluster was found present in all cluster A strains (plus strain NCTC12958T) but was absent from all strains in cluster B. Other loci related to lactose/galactose catabolism and urea metabolism, aminopeptidases, the majority of amino acid and peptide transporters, as well as amino acid biosynthetic pathways were found to be conserved in all strains suggesting their central role for the species. Our study highlights the necessity of sequencing and analyzing more S. thermophilus complete genomes to further elucidate important aspects of strain diversity within this starter culture that may be related to its application in the dairy industry.
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Affiliation(s)
- Voula Alexandraki
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Maria Kazou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Bruno Pot
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium
| | - Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Effie Tsakalidou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
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56
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A Metabolic Dependency for Host Isoprenoids in the Obligate Intracellular Pathogen Rickettsia parkeri Underlies a Sensitivity to the Statin Class of Host-Targeted Therapeutics. mSphere 2019; 4:4/6/e00536-19. [PMID: 31722991 PMCID: PMC6854040 DOI: 10.1128/msphere.00536-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Obligate intracellular pathogens, which include viruses as well as certain bacteria and eukaryotes, are a subset of infectious microbes that are metabolically dependent on and unable to grow outside an infected host cell because they have lost or lack essential biosynthetic pathways. In this study, we describe a metabolic dependency of the bacterial pathogen Rickettsia parkeri on host isoprenoid molecules that are used in the biosynthesis of downstream products, including cholesterol, steroid hormones, and heme. Bacteria make products from isoprenoids, such as an essential lipid carrier for making the bacterial cell wall. We show that bacterial metabolic dependency can represent a potential Achilles’ heel and that inhibiting host isoprenoid biosynthesis with the FDA-approved statin class of drugs inhibits bacterial growth by interfering with the integrity of the cell wall. This work supports the potential to treat infections by obligate intracellular pathogens through inhibition of host biosynthetic pathways that are susceptible to parasitism. Gram-negative bacteria in the order Rickettsiales have an obligate intracellular growth requirement, and some species cause human diseases such as typhus and spotted fever. The bacteria have evolved a dependence on essential nutrients and metabolites from the host cell as a consequence of extensive genome reduction. However, it remains largely unknown which nutrients they acquire and whether their metabolic dependency can be exploited therapeutically. Here, we describe a genetic rewiring of bacterial isoprenoid biosynthetic pathways in the Rickettsiales that has resulted from reductive genome evolution. Furthermore, we investigated whether the spotted fever group Rickettsia species Rickettsia parkeri scavenges isoprenoid precursors directly from the host. Using targeted mass spectrometry, we found that infection caused decreases in host isoprenoid products and concomitant increases in bacterial isoprenoid metabolites. Additionally, we report that treatment of infected cells with statins, which inhibit host isoprenoid synthesis, prohibited bacterial growth. We show that growth inhibition correlates with changes in bacterial size and shape that mimic those caused by antibiotics that inhibit peptidoglycan biosynthesis, suggesting that statins lead to an inhibition of cell wall synthesis. Altogether, our results describe a potential Achilles’ heel of obligate intracellular pathogens that can potentially be exploited with host-targeted therapeutics that interfere with metabolic pathways required for bacterial growth. IMPORTANCE Obligate intracellular pathogens, which include viruses as well as certain bacteria and eukaryotes, are a subset of infectious microbes that are metabolically dependent on and unable to grow outside an infected host cell because they have lost or lack essential biosynthetic pathways. In this study, we describe a metabolic dependency of the bacterial pathogen Rickettsia parkeri on host isoprenoid molecules that are used in the biosynthesis of downstream products, including cholesterol, steroid hormones, and heme. Bacteria make products from isoprenoids, such as an essential lipid carrier for making the bacterial cell wall. We show that bacterial metabolic dependency can represent a potential Achilles’ heel and that inhibiting host isoprenoid biosynthesis with the FDA-approved statin class of drugs inhibits bacterial growth by interfering with the integrity of the cell wall. This work supports the potential to treat infections by obligate intracellular pathogens through inhibition of host biosynthetic pathways that are susceptible to parasitism.
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Salvador-Castell M, Tourte M, Oger PM. In Search for the Membrane Regulators of Archaea. Int J Mol Sci 2019; 20:E4434. [PMID: 31505830 PMCID: PMC6770870 DOI: 10.3390/ijms20184434] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 11/23/2022] Open
Abstract
Membrane regulators such as sterols and hopanoids play a major role in the physiological and physicochemical adaptation of the different plasmic membranes in Eukarya and Bacteria. They are key to the functionalization and the spatialization of the membrane, and therefore indispensable for the cell cycle. No archaeon has been found to be able to synthesize sterols or hopanoids to date. They also lack homologs of the genes responsible for the synthesis of these membrane regulators. Due to their divergent membrane lipid composition, the question whether archaea require membrane regulators, and if so, what is their nature, remains open. In this review, we review evidence for the existence of membrane regulators in Archaea, and propose tentative location and biological functions. It is likely that no membrane regulator is shared by all archaea, but that they may use different polyterpenes, such as carotenoids, polyprenols, quinones and apolar polyisoprenoids, in response to specific stressors or physiological needs.
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Affiliation(s)
- Marta Salvador-Castell
- Université de Lyon, CNRS, UMR 5240, F-69621 Villeurbanne, France.
- Université de Lyon, INSA de Lyon, UMR 5240, F-69621 Villeurbanne, France.
| | - Maxime Tourte
- Université de Lyon, CNRS, UMR 5240, F-69621 Villeurbanne, France.
- Université de Lyon, INSA de Lyon, UMR 5240, F-69621 Villeurbanne, France.
| | - Philippe M Oger
- Université de Lyon, CNRS, UMR 5240, F-69621 Villeurbanne, France.
- Université de Lyon, INSA de Lyon, UMR 5240, F-69621 Villeurbanne, France.
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58
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HupA, the main undecaprenyl pyrophosphate and phosphatidylglycerol phosphate phosphatase in Helicobacter pylori is essential for colonization of the stomach. PLoS Pathog 2019; 15:e1007972. [PMID: 31487328 PMCID: PMC6748449 DOI: 10.1371/journal.ppat.1007972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 09/17/2019] [Accepted: 07/09/2019] [Indexed: 12/24/2022] Open
Abstract
The biogenesis of bacterial cell-envelope polysaccharides requires the translocation, across the plasma membrane, of sugar sub-units that are produced inside the cytoplasm. To this end, the hydrophilic sugars are anchored to a lipid phosphate carrier (undecaprenyl phosphate (C55-P)), yielding membrane intermediates which are translocated to the outer face of the membrane. Finally, the glycan moiety is transferred to a nascent acceptor polymer, releasing the carrier in the “inactive” undecaprenyl pyrophosphate (C55-PP) form. Thus, C55-P is generated through the dephosphorylation of C55-PP, itself arising from either de novo synthesis or recycling. Two types of integral membrane C55-PP phosphatases were described: BacA enzymes and a sub-group of PAP2 enzymes (type 2 phosphatidic acid phosphatases). The human pathogen Helicobacter pylori does not contain BacA homologue but has four membrane PAP2 proteins: LpxE, LpxF, HP0350 and HP0851. Here, we report the physiological role of HP0851, renamed HupA, via multiple and complementary approaches ranging from a detailed biochemical characterization to the assessment of its effect on cell envelope metabolism and microbe-host interactions. HupA displays a dual function as being the main C55-PP pyrophosphatase (UppP) and phosphatidylglycerol phosphate phosphatase (PGPase). Although not essential in vitro, HupA was essential in vivo for stomach colonization. In vitro, the remaining UppP activity was carried out by LpxE in addition to its lipid A 1-phosphate phosphatase activity. Both HupA and LpxE have crucial roles in the biosynthesis of several cell wall polysaccharides and thus constitute potential targets for new therapeutic strategies. Helicobacter pylori colonizes the human’s gastric mucosa and infects around 50% of the world’s population. This pathogen is responsible for chronic gastritis, peptic ulcers and in worst cases leads to gastric cancer. It has been classified as a class I carcinogen by the World Health Organization in 1994. Here, we show that HP0851, renamed HupA, is the major undecaprenyl pyrophosphate (C55-PP) phosphatase (UppP) and the major phosphatidylglycerol phosphate phosphatase (PGPase). This enzyme is also involved in cationic antimicrobial peptide (CAMP) resistance to which H. pylori hupA mutant shows an increased sensitivity (4 fold). This mutant was unable to colonize the stomach in mouse model of infection showing that even if hupA was not essential in vitro, this gene was essential in vivo. Both HupA and LpxE have crucial roles in the biosynthesis of several cell wall polysaccharides and thus constitute potential targets for new therapeutic strategies.
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59
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Pal S, Verma J, Mallick S, Rastogi SK, Kumar A, Ghosh AS. Absence of the glycosyltransferase WcaJ in Klebsiella pneumoniae ATCC13883 affects biofilm formation, increases polymyxin resistance and reduces murine macrophage activation. Microbiology (Reading) 2019; 165:891-904. [PMID: 31246167 DOI: 10.1099/mic.0.000827] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Shilpa Pal
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal-721302, India
| | - Jyoti Verma
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, West Bengal-721302, India
| | - Sathi Mallick
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal-721302, India
| | - Sumit Kumar Rastogi
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal-721302, India
| | - Akash Kumar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal-721302, India
| | - Anindya S. Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal-721302, India
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60
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Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chem Rev 2019; 119:5775-5848. [PMID: 30758191 PMCID: PMC6509647 DOI: 10.1021/acs.chemrev.8b00451] [Citation(s) in RCA: 260] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 02/07/2023]
Abstract
Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable membrane environment for proteins to being embedded in to detailed roles in complicated and well-regulated protein functions. Experimental and computational advances are converging in a rapidly expanding research area of lipid-protein interactions. Experimentally, the database of high-resolution membrane protein structures is growing, as are capabilities to identify the complex lipid composition of different membranes, to probe the challenging time and length scales of lipid-protein interactions, and to link lipid-protein interactions to protein function in a variety of proteins. Computationally, more accurate membrane models and more powerful computers now enable a detailed look at lipid-protein interactions and increasing overlap with experimental observations for validation and joint interpretation of simulation and experiment. Here we review papers that use computational approaches to study detailed lipid-protein interactions, together with brief experimental and physiological contexts, aiming at comprehensive coverage of simulation papers in the last five years. Overall, a complex picture of lipid-protein interactions emerges, through a range of mechanisms including modulation of the physical properties of the lipid environment, detailed chemical interactions between lipids and proteins, and key functional roles of very specific lipids binding to well-defined binding sites on proteins. Computationally, despite important limitations, molecular dynamics simulations with current computer power and theoretical models are now in an excellent position to answer detailed questions about lipid-protein interactions.
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Affiliation(s)
- Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Besian I. Sejdiu
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haydee Mesa-Galloso
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haleh Abdizadeh
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sergei Yu. Noskov
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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Herrou J, Willett JW, Fiebig A, Varesio LM, Czyż DM, Cheng JX, Ultee E, Briegel A, Bigelow L, Babnigg G, Kim Y, Crosson S. Periplasmic protein EipA determines envelope stress resistance and virulence in Brucella abortus. Mol Microbiol 2019; 111:637-661. [PMID: 30536925 DOI: 10.1111/mmi.14178] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2018] [Indexed: 12/17/2022]
Abstract
Molecular components of the Brucella abortus cell envelope play a major role in its ability to infect, colonize and survive inside mammalian host cells. In this study, we have defined a role for a conserved gene of unknown function in B. abortus envelope stress resistance and infection. Expression of this gene, which we name eipA, is directly activated by the essential cell cycle regulator, CtrA. eipA encodes a soluble periplasmic protein that adopts an unusual eight-stranded β-barrel fold. Deletion of eipA attenuates replication and survival in macrophage and mouse infection models, and results in sensitivity to treatments that compromise the cell envelope integrity. Transposon disruption of genes required for LPS O-polysaccharide biosynthesis is synthetically lethal with eipA deletion. This genetic connection between O-polysaccharide and eipA is corroborated by our discovery that eipA is essential in Brucella ovis, a naturally rough species that harbors mutations in several genes required for O-polysaccharide production. Conditional depletion of eipA expression in B. ovis results in a cell chaining phenotype, providing evidence that eipA directly or indirectly influences cell division in Brucella. We conclude that EipA is a molecular determinant of Brucella virulence that functions to maintain cell envelope integrity and influences cell division.
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Affiliation(s)
- Julien Herrou
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Jonathan W Willett
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Aretha Fiebig
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Lydia M Varesio
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Daniel M Czyż
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Jason X Cheng
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Eveline Ultee
- Department of Biology, Universiteit Leiden, Leiden, Netherlands
| | - Ariane Briegel
- Department of Biology, Universiteit Leiden, Leiden, Netherlands
| | - Lance Bigelow
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Gyorgy Babnigg
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Youngchang Kim
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Sean Crosson
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
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62
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Abstract
The peptidoglycan sacculus is a net-like polymer that surrounds the cytoplasmic membrane in most bacteria. It is essential to maintain the bacterial cell shape and protect from turgor. The peptidoglycan has a basic composition, common to all bacteria, with species-specific variations that can modify its biophysical properties or the pathogenicity of the bacteria. The synthesis of peptidoglycan starts in the cytoplasm and the precursor lipid II is flipped across the cytoplasmic membrane. The new peptidoglycan strands are synthesised and incorporated into the pre-existing sacculus by the coordinated activities of peptidoglycan synthases and hydrolases. In the model organism Escherichia coli there are two complexes required for the elongation and division. Each of them is regulated by different proteins from both the cytoplasmic and periplasmic sides that ensure the well-coordinated synthesis of new peptidoglycan.
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63
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Liu X, Meiresonne NY, Bouhss A, den Blaauwen T. FtsW activity and lipid II synthesis are required for recruitment of MurJ to midcell during cell division in Escherichia coli. Mol Microbiol 2018; 109:855-884. [PMID: 30112777 DOI: 10.1111/mmi.14104] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2018] [Indexed: 12/28/2022]
Abstract
Peptidoglycan (PG) is the unique cell shape-determining component of the bacterial envelope, and is a key target for antibiotics. PG synthesis requires the transmembrane movement of the precursor lipid II, and MurJ has been shown to provide this activity in Escherichia coli. However, how MurJ functions in vivo has not been reported. Here we show that MurJ localizes both in the lateral membrane and at midcell, and is recruited to midcell simultaneously with late-localizing divisome proteins and proteins MraY and MurG. MurJ septal localization is dependent on the presence of a complete and active divisome, lipid II synthesis and PBP3/FtsW activities. Inactivation of MurJ, either directly by mutation or through binding with MTSES, did not affect the midcell localization of MurJ. Our study visualizes MurJ localization in vivo and reveals a possible mechanism of MurJ recruitment during cell division.
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Affiliation(s)
- Xiaolong Liu
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Nils Y Meiresonne
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Ahmed Bouhss
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France.,Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - Tanneke den Blaauwen
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
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64
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A Defective Undecaprenyl Pyrophosphate Synthase Induces Growth and Morphological Defects That Are Suppressed by Mutations in the Isoprenoid Pathway of Escherichia coli. J Bacteriol 2018; 200:JB.00255-18. [PMID: 29986944 DOI: 10.1128/jb.00255-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/05/2018] [Indexed: 01/10/2023] Open
Abstract
The peptidoglycan exoskeleton shapes bacteria and protects them against osmotic forces, making its synthesis the target of many current antibiotics. Peptidoglycan precursors are attached to a lipid carrier and flipped from the cytoplasm into the periplasm to be incorporated into the cell wall. In Escherichia coli, this carrier is undecaprenyl phosphate (Und-P), which is synthesized as a diphosphate by the enzyme undecaprenyl pyrophosphate synthase (UppS). E. coli MG1655 exhibits wild-type morphology at all temperatures, but one of our laboratory strains (CS109) was highly aberrant when grown at 42°C. This strain contained mutations affecting the Und-P synthetic pathway genes uppS, ispH, and idi Normal morphology was restored by overexpressing uppS or by replacing the mutant (uppS31) with the wild-type allele. Importantly, moving uppS31 into MG1655 was lethal even at 30°C, indicating that the altered enzyme was highly deleterious, but growth was restored by adding the CS109 versions of ispH and idi Purified UppSW31R was enzymatically defective at all temperatures, suggesting that it could not supply enough Und-P during rapid growth unless suppressor mutations were present. We conclude that cell wall synthesis is profoundly sensitive to changes in the pool of polyisoprenoids and that isoprenoid homeostasis exerts a particularly strong evolutionary pressure.IMPORTANCE Bacterial morphology is determined primarily by the overall structure of the semirigid macromolecule peptidoglycan. Not only does peptidoglycan contribute to cell shape, but it also protects cells against lysis caused by excess osmotic pressure. Because it is critical for bacterial survival, it is no surprise that many antibiotics target peptidoglycan biosynthesis. However, important gaps remain in our understanding about how this process is affected by peptidoglycan precursor availability. Here, we report that a mutation altering the enzyme that synthesizes Und-P prevents cells from growing at high temperatures and that compensatory mutations in enzymes functioning upstream of uppS can reverse this phenotype. The results highlight the importance of Und-P metabolism for maintaining normal cell wall synthesis and shape.
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65
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Ma Z, Lasek-Nesselquist E, Lu J, Schneider R, Shah R, Oliva G, Pata J, McDonough K, Pai MP, Rose WE, Sakoulas G, Malik M. Characterization of genetic changes associated with daptomycin nonsusceptibility in Staphylococcus aureus. PLoS One 2018; 13:e0198366. [PMID: 29879195 PMCID: PMC5991675 DOI: 10.1371/journal.pone.0198366] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/17/2018] [Indexed: 11/25/2022] Open
Abstract
The extensive use of daptomycin (DAP) for treatment of methicillin-resistant Staphylococcus aureus (MRSA) infections in the last decade has led to the emergence of DAP non-susceptible (DNS) Staphylococcus aureus strains. A better understanding of the molecular changes underlying DAP-non-susceptibility is required for early diagnosis and intervention with alternate combination therapies. The phenotypic changes associated with DNS strains have been well established. However, the genotypic changes—especially the kinetics of expression of the genes responsible for DAP-non-susceptibility are not well understood. In this study, we used three clinically derived isogenic pairs of DAP-susceptible (DAP-S) and DNS S. aureus strains to study gene expression profiles with the objective of identifying the potential genotypic changes associated with DAP-nonsusceptibility. We determined the expression profiles of genes involved in cell membrane (CM) charge, autolysis, cell wall (CW) synthesis, and penicillin binding proteins in DAP-S and DNS isogenic pairs. Our results demonstrate characteristic expression profiles for mprF, dltABCD, vraS, femB, and pbp2a genes, which are common to all the DNS S. aureus strains tested. Whole genome sequencing of DAP-S and DNS clinical isolates of S. aureus showed non-synonymous mutations in all DNS strains in genes involved in CM charge, CM composition, CW thickness and CW composition. To conclude, this study unravels some of the complex molecular changes involved in the development of DAP-nonsusceptibility by demonstrating distinct differences in gene expression profiles and mutations in the DNS S. aureus strains. This knowledge will aid in rapid identification of DNS S. aureus in clinical settings.
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Affiliation(s)
- Zhuo Ma
- Albany College of Pharmacy and Health Sciences, Albany, New York, United States of America
| | - Erica Lasek-Nesselquist
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Jackson Lu
- Albany College of Pharmacy and Health Sciences, Albany, New York, United States of America
| | - Ryan Schneider
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Riddhi Shah
- Albany College of Pharmacy and Health Sciences, Albany, New York, United States of America
| | - George Oliva
- Albany College of Pharmacy and Health Sciences, Albany, New York, United States of America
| | - Janice Pata
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Kathleen McDonough
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Manjunath P. Pai
- Albany College of Pharmacy and Health Sciences, Albany, New York, United States of America
| | - Warren E. Rose
- Universtiy of Wisconsin-Madison, School of Pharmacy, Madison, Wisconsin, United States of America
| | - George Sakoulas
- Center for Immunity, Infection & Inflammation, UCSD School of Medicine, La Jolla, California, United States of America
| | - Meenakshi Malik
- Albany College of Pharmacy and Health Sciences, Albany, New York, United States of America
- * E-mail:
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66
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Caveney NA, Li FK, Strynadka NC. Enzyme structures of the bacterial peptidoglycan and wall teichoic acid biogenesis pathways. Curr Opin Struct Biol 2018; 53:45-58. [PMID: 29885610 DOI: 10.1016/j.sbi.2018.05.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/08/2018] [Accepted: 05/16/2018] [Indexed: 01/08/2023]
Abstract
The bacterial cell wall is a complex polymeric structure with essential roles in defence, survival and pathogenesis. Common to both Gram-positive and Gram-negative bacteria is the mesh-like peptidoglycan sacculus that surrounds the outer leaflet of the cytoplasmic membrane. Recent crystallographic studies of enzymes that comprise the peptidoglycan biosynthetic pathway have led to significant new understanding of all stages. These include initial multi-step cytosolic formation of sugar-pentapeptide precursors, transfer of the precursors to activated polyprenyl lipids at the membrane inner leaflet and flippase mediated relocalization of the resulting lipid II precursors to the outer leaflet where glycopolymerization and subsequent peptide crosslinking are finalized. Additional, species-specific enzymes allow customized peptidoglycan modifications and biosynthetic regulation that are important to bacterial virulence and survival. These studies have reinforced the unique and specific catalytic mechanisms at play in cell wall biogenesis and expanded the atomic foundation to develop novel, structure guided, antibacterial agents.
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Affiliation(s)
- Nathanael A Caveney
- University of British Columbia, Biochemistry and Molecular Biology and the Center for Blood Research, Rm 4350 Life Sciences Center, 2350 Health Sciences Mall, Vancouver V6T 1Z3 Canada
| | - Franco Kk Li
- University of British Columbia, Biochemistry and Molecular Biology and the Center for Blood Research, Rm 4350 Life Sciences Center, 2350 Health Sciences Mall, Vancouver V6T 1Z3 Canada
| | - Natalie Cj Strynadka
- University of British Columbia, Biochemistry and Molecular Biology and the Center for Blood Research, Rm 4350 Life Sciences Center, 2350 Health Sciences Mall, Vancouver V6T 1Z3 Canada.
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67
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Kawakami N, Fujisaki S. Undecaprenyl phosphate metabolism in Gram-negative and Gram-positive bacteria. Biosci Biotechnol Biochem 2018; 82:940-946. [DOI: 10.1080/09168451.2017.1401915] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Undecaprenyl phosphate (UP) is essential for the biosynthesis of bacterial extracellular polysaccharides. UP is produced by the dephosphorylation of undecaprenyl diphosphate (UPP) via de novo synthetic and recycling pathways. Gram-positive bacteria contain remarkable amounts of undecaprenol (UOH), which is phosphorylated to UP, although UOH has not been found in Gram-negative bacteria. Here, current knowledge about UPP phosphatase and UOH kinase is reviewed. Dephosphorylation of UPP is catalyzed by a BacA homologue and a type-2 phosphatidic acid phosphatase (PAP2) homologue. The presence of one of these UPP phosphatases is essential for bacterial growth. The catalytic center of both types of enzyme is located outside the cytoplasmic membrane. In Gram-positive bacteria, an enzyme homologous to DgkA, which is the diacylglycerol kinase of Escherichia coli, catalyzes UOH phosphorylation. The possible role of UOH and the significance of systematic construction of Staphylococcus aureus mutants to determine UP metabolism are discussed.
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Affiliation(s)
- Naoki Kawakami
- Faculty of Science, Department of Biomolecular Science, Toho University, Funabashi, Japan
| | - Shingo Fujisaki
- Faculty of Science, Department of Biomolecular Science, Toho University, Funabashi, Japan
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68
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Hernández-Rocamora VM, Otten CF, Radkov A, Simorre JP, Breukink E, VanNieuwenhze M, Vollmer W. Coupling of polymerase and carrier lipid phosphatase prevents product inhibition in peptidoglycan synthesis. ACTA ACUST UNITED AC 2018; 2:1-13. [PMID: 30046664 PMCID: PMC6053597 DOI: 10.1016/j.tcsw.2018.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 11/30/2022]
Abstract
Peptidoglycan (PG) is an essential component of the bacterial cell wall that maintains the shape and integrity of the cell. The PG precursor lipid II is assembled at the inner leaflet of the cytoplasmic membrane, translocated to the periplasmic side, and polymerized to glycan chains by membrane anchored PG synthases, such as the class A Penicillin-binding proteins (PBPs). Polymerization of PG releases the diphosphate form of the carrier lipid, undecaprenyl pyrophosphate (C55-PP), which is converted to the monophosphate form by membrane-embedded pyrophosphatases, generating C55-P for a new round of PG precursor synthesis. Here we report that deletion of the C55-PP pyrophosphatase gene pgpB in E. coli increases the susceptibility to cefsulodin, a β-lactam specific for PBP1A, indicating that the cellular function of PBP1B is impaired in the absence of PgpB. Purified PBP1B interacted with PgpB and another C55-PP pyrophosphatase, BacA and both, PgpB and BacA stimulated the glycosyltransferase activity of PBP1B. C55-PP was found to be a potent inhibitor of PBP1B. Our data suggest that the stimulation of PBP1B by PgpB is due to the faster removal and processing of C55-PP, and that PBP1B interacts with C55-PP phosphatases during PG synthesis to couple PG polymerization with the recycling of the carrier lipid and prevent product inhibition by C55-PP.
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Affiliation(s)
- Víctor M Hernández-Rocamora
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Christian F Otten
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Atanas Radkov
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405-7102, USA
| | - Jean-Pierre Simorre
- Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, France
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, University of Utrecht, Padualaan 8, 3584 Utrecht, The Netherlands
| | - Michael VanNieuwenhze
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405-7102, USA
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
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69
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Geisinger E, Mortman NJ, Vargas-Cuebas G, Tai AK, Isberg RR. A global regulatory system links virulence and antibiotic resistance to envelope homeostasis in Acinetobacter baumannii. PLoS Pathog 2018; 14:e1007030. [PMID: 29795704 PMCID: PMC5967708 DOI: 10.1371/journal.ppat.1007030] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/16/2018] [Indexed: 11/19/2022] Open
Abstract
The nosocomial pathogen Acinetobacter baumannii is a significant threat due to its ability to cause infections refractory to a broad range of antibiotic treatments. We show here that a highly conserved sensory-transduction system, BfmRS, mediates the coordinate development of both enhanced virulence and resistance in this microorganism. Hyperactive alleles of BfmRS conferred increased protection from serum complement killing and allowed lethal systemic disease in mice. BfmRS also augmented resistance and tolerance against an expansive set of antibiotics, including dramatic protection from β-lactam toxicity. Through transcriptome profiling, we showed that BfmRS governs these phenotypes through global transcriptional regulation of a post-exponential-phase-like program of gene expression, a key feature of which is modulation of envelope biogenesis and defense pathways. BfmRS activity defended against cell-wall lesions through both β-lactamase-dependent and -independent mechanisms, with the latter being connected to control of lytic transglycosylase production and proper coordination of morphogenesis and division. In addition, hypersensitivity of bfmRS knockouts could be suppressed by unlinked mutations restoring a short, rod cell morphology, indicating that regulation of drug resistance, pathogenicity, and envelope morphogenesis are intimately linked by this central regulatory system in A. baumannii. This work demonstrates that BfmRS controls a global regulatory network coupling cellular physiology to the ability to cause invasive, drug-resistant infections. Infections with the hospital-acquired bacterium Acinetobacter baumannii are highly difficult to treat. The pathogen has evolved multiple lines of defense against antimicrobial stress, including a barrier-forming cell envelope as well as control systems that respond to antimicrobial stresses by enhancing antibiotic resistance and virulence. Here, we uncovered the role of a key stress-response system, BfmRS, in controlling the transition of A. baumannii to a state of heightened resistance and virulence. We show that BfmRS enhances pathogenicity in mammalian hosts, and augments the ability to grow in the presence of diverse antibiotics and tolerate transient, high-level antibiotic exposures. Connected to these effects is the ability of BfmRS to globally reprogram gene expression and control multiple pathways that build, protect, and shape the cell envelope. Moreover, we determined that resistance-enhancing mutations bypassing the need for BfmRS also modulate envelope- and morphology-associated pathways, further linking control of physiology with resistance in A. baumannii. This work uncovers a global control circuit that shifts cellular physiology in ways that promote hospital-associated disease, and points to inhibition of this circuit as a potential strategy for disarming the pathogen.
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Affiliation(s)
- Edward Geisinger
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
| | - Nadav J. Mortman
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Germán Vargas-Cuebas
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Albert K. Tai
- Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Ralph R. Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
- * E-mail:
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70
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Hong X, Chen HD, Groisman EA. Gene expression kinetics governs stimulus-specific decoration of the Salmonella outer membrane. Sci Signal 2018; 11:11/529/eaar7921. [PMID: 29739882 DOI: 10.1126/scisignal.aar7921] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Lipid A is the innermost component of the lipopolysaccharide (LPS) molecules that occupy the outer leaflet of the outer membrane in Gram-negative bacteria. Lipid A is recognized by the host immune system and targeted by cationic antimicrobial compounds. In Salmonella enterica serovar Typhimurium, the phosphates of lipid A are chemically modified by enzymes encoded by targets of the transcriptional regulator PmrA. These modifications increase resistance to the cationic peptide antibiotic polymyxin B by reducing the negative charge of the LPS. We report the mechanism by which Salmonella produces different lipid A profiles when PmrA is activated by low Mg2+ versus a mildly acidic pH. Low Mg2+ favored modification of the lipid A phosphates with 4-amino-4-deoxy-l-aminoarabinose (l-Ara4N) by activating the regulatory protein PhoP, which initially increased the LPS negative charge by promoting transcription of lpxT, encoding an enzyme that adds an additional phosphate group to lipid A. Later, PhoP activated PmrA posttranslationally, resulting in expression of PmrA-activated genes, including those encoding the LpxT inhibitor PmrR and enzymes responsible for the incorporation of l-Ara4N. By contrast, a mildly acidic pH favored modification of the lipid A phosphates with a mixture of l-Ara4N and phosphoethanolamine (pEtN) by simultaneously inducing the PhoP-activated lpxT and PmrA-activated pmrR genes. Although l-Ara4N reduces the LPS negative charge more than does pEtN, modification of lipid A phosphates solely with l-Ara4N required a prior transient increase in lipid A negative charge. Our findings demonstrate how bacteria tailor their cell surface to different stresses, such as those faced inside phagocytes.
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Affiliation(s)
- Xinyu Hong
- Department of Cell Biology, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA.,Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA.,Yale Microbial Sciences Institute, P.O. Box 27389, West Haven, CT 06516, USA.,Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06536, USA
| | - H Deborah Chen
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA. .,Yale Microbial Sciences Institute, P.O. Box 27389, West Haven, CT 06516, USA
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71
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Membrane properties that shape the evolution of membrane enzymes. Curr Opin Struct Biol 2018; 51:80-91. [PMID: 29597094 DOI: 10.1016/j.sbi.2018.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/14/2018] [Accepted: 03/15/2018] [Indexed: 02/07/2023]
Abstract
Spectacular recent progress in structural biology has led to determination of the structures of many integral membrane enzymes that catalyze reactions in which at least one substrate also is membrane bound. A pattern of results seems to be emerging in which the active site chemistry of these enzymes is usually found to be analogous to what is observed for water soluble enzymes catalyzing the same reaction types. However, in light of the chemical, structural, and physical complexity of cellular membranes plus the presence of transmembrane gradients and potentials, these enzymes may be subject to membrane-specific regulatory mechanisms that are only now beginning to be uncovered. We review the membrane-specific environmental traits that shape the evolution of membrane-embedded biocatalysts.
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72
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Crystal structure of an intramembranal phosphatase central to bacterial cell-wall peptidoglycan biosynthesis and lipid recycling. Nat Commun 2018; 9:1159. [PMID: 29559664 PMCID: PMC5861054 DOI: 10.1038/s41467-018-03547-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/20/2018] [Indexed: 11/13/2022] Open
Abstract
Undecaprenyl pyrophosphate phosphatase (UppP) is an integral membrane protein that recycles the lipid carrier essential to the ongoing biosynthesis of the bacterial cell wall. Individual building blocks of peptidoglycan are assembled in the cytoplasm on undecaprenyl phosphate (C55-P) before being flipped to the periplasmic face, where they are polymerized and transferred to the existing cell wall sacculus, resulting in the side product undecaprenyl pyrophosphate (C55-PP). Interruption of UppP’s regeneration of C55-P from C55-PP leads to the buildup of cell wall intermediates and cell lysis. We present the crystal structure of UppP from Escherichia coli at 2.0 Å resolution, which reveals the mechanistic basis for intramembranal phosphatase action and substrate specificity using an inverted topology repeat. In addition, the observation of key structural motifs common to a variety of cross membrane transporters hints at a potential flippase function in the specific relocalization of the C55-P product back to the cytosolic space. Undecaprenyl pyrophosphate phosphatase (UppP) recycles the lipid carrier essential for bacterial cell wall synthesis. Here authors present the crystal structure of UppP from E. coli at 2.0 Å resolution, which sheds light on its phosphatase mechanism and indicates a potential flippase role for UppP.
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73
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Abstract
As a protective envelope surrounding the bacterial cell, the peptidoglycan sacculus is a site of vulnerability and an antibiotic target. Peptidoglycan components, assembled in the cytoplasm, are shuttled across the membrane in a cycle that uses undecaprenyl-phosphate. A product of peptidoglycan synthesis, undecaprenyl-pyrophosphate, is converted to undecaprenyl-phosphate for reuse in the cycle by the membrane integral pyrophosphatase, BacA. To understand how BacA functions, we determine its crystal structure at 2.6 Å resolution. The enzyme is open to the periplasm and to the periplasmic leaflet via a pocket that extends into the membrane. Conserved residues map to the pocket where pyrophosphorolysis occurs. BacA incorporates an interdigitated inverted topology repeat, a topology type thus far only reported in transporters and channels. This unique topology raises issues regarding the ancestry of BacA, the possibility that BacA has alternate active sites on either side of the membrane and its possible function as a flippase. Bacterial cell wall components are assembled in a transmembrane cycle that involves the membrane integral pyrophosphorylase, BacA. Here the authors solve the crystal structure of BacA which shows an interdigitated inverted topology repeat that hints towards a flippase function for BacA.
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74
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Otten C, Brilli M, Vollmer W, Viollier PH, Salje J. Peptidoglycan in obligate intracellular bacteria. Mol Microbiol 2018; 107:142-163. [PMID: 29178391 PMCID: PMC5814848 DOI: 10.1111/mmi.13880] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2017] [Indexed: 01/08/2023]
Abstract
Peptidoglycan is the predominant stress-bearing structure in the cell envelope of most bacteria, and also a potent stimulator of the eukaryotic immune system. Obligate intracellular bacteria replicate exclusively within the interior of living cells, an osmotically protected niche. Under these conditions peptidoglycan is not necessarily needed to maintain the integrity of the bacterial cell. Moreover, the presence of peptidoglycan puts bacteria at risk of detection and destruction by host peptidoglycan recognition factors and downstream effectors. This has resulted in a selective pressure and opportunity to reduce the levels of peptidoglycan. In this review we have analysed the occurrence of genes involved in peptidoglycan metabolism across the major obligate intracellular bacterial species. From this comparative analysis, we have identified a group of predicted 'peptidoglycan-intermediate' organisms that includes the Chlamydiae, Orientia tsutsugamushi, Wolbachia and Anaplasma marginale. This grouping is likely to reflect biological differences in their infection cycle compared with peptidoglycan-negative obligate intracellular bacteria such as Ehrlichia and Anaplasma phagocytophilum, as well as obligate intracellular bacteria with classical peptidoglycan such as Coxiella, Buchnera and members of the Rickettsia genus. The signature gene set of the peptidoglycan-intermediate group reveals insights into minimal enzymatic requirements for building a peptidoglycan-like sacculus and/or division septum.
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Affiliation(s)
- Christian Otten
- The Centre for Bacterial Cell BiologyInstitute for Cell and Molecular Biosciences, Newcastle UniversityNewcastle upon TyneNE2 4AXUK
| | - Matteo Brilli
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE)University of Padova. Agripolis ‐ V.le dell'Università, 16 | 35020 Legnaro PadovaItaly
- Present address:
Department of BiosciencesUniversity of Milan, via Celoria 26(MI)Italy
| | - Waldemar Vollmer
- The Centre for Bacterial Cell BiologyInstitute for Cell and Molecular Biosciences, Newcastle UniversityNewcastle upon TyneNE2 4AXUK
| | - Patrick H. Viollier
- Department of Microbiology and Molecular MedicineInstitute of Genetics & Genomics in Geneva (iGE3), University of GenevaGenevaSwitzerland
| | - Jeanne Salje
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global HealthUniversity of OxfordOxfordUK
- Mahidol‐Oxford Tropical Medicine Research UnitMahidol UniversityBangkokThailand
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75
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Pazos M, Otten C, Vollmer W. Bacterial Cell Wall Precursor Phosphatase Assays Using Thin-layer Chromatography (TLC) and High Pressure Liquid Chromatography (HPLC). Bio Protoc 2018; 8:e2761. [PMID: 29651453 DOI: 10.21769/bioprotoc.2761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Peptidoglycan encases the bacterial cytoplasmic membrane to protect the cell from lysis due to the turgor. The final steps of peptidoglycan synthesis require a membrane-anchored substrate called lipid II, in which the peptidoglycan subunit is linked to the carrier lipid undecaprenol via a pyrophosphate moiety. Lipid II is the target of glycopeptide antibiotics and several antimicrobial peptides, and is degraded by 'attacking' enzymes involved in bacterial competition to induce lysis. Here we describe two protocols using thin-layer chromatography (TLC) and high pressure liquid chromatography (HPLC), respectively, to assay the digestion of lipid II by phosphatases such as Colicin M or the LXG toxin protein TelC from Streptococcus intermedius. The TLC method can also monitor the digestion of undecaprenyl (pyro)phosphate, whereas the HPLC method allows to separate the di-, mono- or unphosphorylated disaccharide pentapeptide products of lipid II.
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Affiliation(s)
- Manuel Pazos
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Christian Otten
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
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76
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Radeck J, Lautenschläger N, Mascher T. The Essential UPP Phosphatase Pair BcrC and UppP Connects Cell Wall Homeostasis during Growth and Sporulation with Cell Envelope Stress Response in Bacillus subtilis. Front Microbiol 2017; 8:2403. [PMID: 29259598 PMCID: PMC5723303 DOI: 10.3389/fmicb.2017.02403] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/20/2017] [Indexed: 12/03/2022] Open
Abstract
The bacterial cell wall separates the cell from its surrounding and protects it from environmental stressors. Its integrity is maintained by a highly regulated process of cell wall biosynthesis. The membrane-located lipid II cycle provides cell wall building blocks that are assembled inside the cytoplasm to the outside for incorporation. Its carrier molecule, undecaprenyl phosphate (UP), is then recycled by dephosphorylation from undecaprenyl pyrophosphate (UPP). In Bacillus subtilis, this indispensable reaction is catalyzed by the UPP phosphatases BcrC and UppP. Here, we study the physiological function of both phosphatases with respect to morphology, cell wall homeostasis and the resulting cell envelope stress response (CESR). We demonstrate that uppP and bcrC represent a synthetic lethal gene pair, which encodes an essential physiological function. Accordingly, cell growth and morphology were severely impaired during exponential growth if the overall UPP phosphatase level was limiting. UppP, but not BcrC, was crucial for normal sporulation. Expression of bcrC, but not uppP, was upregulated in the presence of cell envelope stress conditions caused by bacitracin if UPP phosphatase levels were limited. This homeostatic feedback renders BcrC more important during growth than UppP, particularly in defense against cell envelope stress.
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Affiliation(s)
- Jara Radeck
- Institute of Microbiology, Technische Universität Dresden, Dresden, Germany
| | | | - Thorsten Mascher
- Institute of Microbiology, Technische Universität Dresden, Dresden, Germany
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77
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Yurchenko T, Ševčíková T, Strnad H, Butenko A, Eliáš M. The plastid genome of some eustigmatophyte algae harbours a bacteria-derived six-gene cluster for biosynthesis of a novel secondary metabolite. Open Biol 2017; 6:rsob.160249. [PMID: 27906133 PMCID: PMC5133447 DOI: 10.1098/rsob.160249] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/31/2016] [Indexed: 01/26/2023] Open
Abstract
Acquisition of genes by plastid genomes (plastomes) via horizontal gene transfer (HGT) seems to be a rare phenomenon. Here, we report an interesting case of HGT revealed by sequencing the plastomes of the eustigmatophyte algae Monodopsis sp. MarTras21 and Vischeria sp. CAUP Q 202. These plastomes proved to harbour a unique cluster of six genes, most probably acquired from a bacterium of the phylum Bacteroidetes, with homologues in various bacteria, typically organized in a conserved uncharacterized putative operon. Sequence analyses of the six proteins encoded by the operon yielded the following annotation for them: (i) a novel family without discernible homologues; (ii) a new family within the superfamily of metallo-dependent hydrolases; (iii) a novel subgroup of the UbiA superfamily of prenyl transferases; (iv) a new clade within the sugar phosphate cyclase superfamily; (v) a new family within the xylose isomerase-like superfamily; and (vi) a hydrolase for a phosphate moiety-containing substrate. We suggest that the operon encodes enzymes of a pathway synthesizing an isoprenoid–cyclitol-derived compound, possibly an antimicrobial or other protective substance. To the best of our knowledge, this is the first report of an expansion of the metabolic capacity of a plastid mediated by HGT into the plastid genome.
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Affiliation(s)
- Tatiana Yurchenko
- Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic.,Faculty of Science, Institute of Environmental Technologies, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Tereza Ševčíková
- Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Hynek Strnad
- Institute of Molecular Genetics of the ASCR, v. v. i., Prague, Czech Republic
| | - Anzhelika Butenko
- Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Marek Eliáš
- Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic .,Faculty of Science, Institute of Environmental Technologies, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
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78
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López-Lara IM, Geiger O. Bacterial lipid diversity. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:1287-1299. [DOI: 10.1016/j.bbalip.2016.10.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 10/10/2016] [Accepted: 10/11/2016] [Indexed: 11/25/2022]
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79
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Huang LY, Wang SC, Cheng TJR, Wong CH. Undecaprenyl Phosphate Phosphatase Activity of Undecaprenol Kinase Regulates the Lipid Pool in Gram-Positive Bacteria. Biochemistry 2017; 56:5417-5427. [PMID: 28872301 DOI: 10.1021/acs.biochem.7b00603] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacteria cell walls contain many repeating glycan structures, such as peptidoglycans, lipopolysaccharides, teichoic acids, and capsular polysaccharides. Their synthesis starts in the cytosol, and they are constructed from a glycan lipid carrier, undecaprenyl phosphate (C55P), which is essential for cell growth and survival. The lipid derivative undecaprenol (C55OH) is predominant in many Gram-positive bacteria but has not been detected in Gram-negative bacteria; its origin and role have thus remained unknown. Recently, a homologue of diacylglycerol kinase (DgkA) in Escherichia coli (E. coli) was demonstrated to be an undecaprenol kinase (UK) in the Gram-positive bacterium Streptococcus mutans (S. mutans). In this study, we found that S. mutans UK was not only an undecaprenol kinase but also a Mg-ADP-dependent undecaprenyl phosphate phosphatase (UpP), catalyzing the hydrolysis of C55P to C55OH and a free inorganic phosphate. Furthermore, the naturally undetectable C55OH was observed in E. coli cells expressing S. mutans dgkA, supporting the phosphatase activity of UK/UpP in vivo. These two activities were indispensable to each other and utilized identical essential residues binding to their substrates, suggesting that both activities share the same active site and might involve a direct phosphoryl transfer mechanism. This study revealed a unique membrane enzyme displaying bifunctional activities determined by substrate binding and C55OH production. The reciprocal conversion of C55P and the undecaprenol pool efficiently regulate cell wall synthesis, especially in Gram-positive bacteria.
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Affiliation(s)
- Lin-Ya Huang
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan
| | - Shih-Chi Wang
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University , Taipei 112, Taiwan
| | | | - Chi-Huey Wong
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University , Taipei 112, Taiwan
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80
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van Teeseling MCF, de Pedro MA, Cava F. Determinants of Bacterial Morphology: From Fundamentals to Possibilities for Antimicrobial Targeting. Front Microbiol 2017; 8:1264. [PMID: 28740487 PMCID: PMC5502672 DOI: 10.3389/fmicb.2017.01264] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 06/23/2017] [Indexed: 12/11/2022] Open
Abstract
Bacterial morphology is extremely diverse. Specific shapes are the consequence of adaptive pressures optimizing bacterial fitness. Shape affects critical biological functions, including nutrient acquisition, motility, dispersion, stress resistance and interactions with other organisms. Although the characteristic shape of a bacterial species remains unchanged for vast numbers of generations, periodical variations occur throughout the cell (division) and life cycles, and these variations can be influenced by environmental conditions. Bacterial morphology is ultimately dictated by the net-like peptidoglycan (PG) sacculus. The species-specific shape of the PG sacculus at any time in the cell cycle is the product of multiple determinants. Some morphological determinants act as a cytoskeleton to guide biosynthetic complexes spatiotemporally, whereas others modify the PG sacculus after biosynthesis. Accumulating evidence supports critical roles of morphogenetic processes in bacteria-host interactions, including pathogenesis. Here, we review the molecular determinants underlying morphology, discuss the evidence linking bacterial morphology to niche adaptation and pathogenesis, and examine the potential of morphological determinants as antimicrobial targets.
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Affiliation(s)
- Muriel C F van Teeseling
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden
| | - Miguel A de Pedro
- Centro de Biología Molecular "Severo Ochoa" - Consejo Superior de Investigaciones Científicas, Universidad Autónoma de MadridMadrid, Spain
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden
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81
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Ghachi ME, Howe N, Auger R, Lambion A, Guiseppi A, Delbrassine F, Manat G, Roure S, Peslier S, Sauvage E, Vogeley L, Rengifo-Gonzalez JC, Charlier P, Mengin-Lecreulx D, Foglino M, Touzé T, Caffrey M, Kerff F. Crystal structure and biochemical characterization of the transmembrane PAP2 type phosphatidylglycerol phosphate phosphatase from Bacillus subtilis. Cell Mol Life Sci 2017; 74:2319-2332. [PMID: 28168443 PMCID: PMC11107685 DOI: 10.1007/s00018-017-2464-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/14/2016] [Accepted: 01/11/2017] [Indexed: 10/20/2022]
Abstract
Type 2 phosphatidic acid phosphatases (PAP2s) can be either soluble or integral membrane enzymes. In bacteria, integral membrane PAP2s play major roles in the metabolisms of glycerophospholipids, undecaprenyl-phosphate (C55-P) lipid carrier and lipopolysaccharides. By in vivo functional experiments and biochemical characterization we show that the membrane PAP2 coded by the Bacillus subtilis yodM gene is the principal phosphatidylglycerol phosphate (PGP) phosphatase of B. subtilis. We also confirm that this enzyme, renamed bsPgpB, has a weaker activity on C55-PP. Moreover, we solved the crystal structure of bsPgpB at 2.25 Å resolution, with tungstate (a phosphate analog) in the active site. The structure reveals two lipid chains in the active site vicinity, allowing for PGP substrate modeling and molecular dynamic simulation. Site-directed mutagenesis confirmed the residues important for substrate specificity, providing a basis for predicting the lipids preferentially dephosphorylated by membrane PAP2s.
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Affiliation(s)
- Meriem El Ghachi
- Centre d'Ingénierie des Protéines, InBioS, Université de Liège, allée du 6 Août 19, Bât B5a, 4000, Liège, Belgium
| | - Nicole Howe
- Membrane Structural and Functional Biology Group, Schools of Medicine and Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Rodolphe Auger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Alexandre Lambion
- Centre d'Ingénierie des Protéines, InBioS, Université de Liège, allée du 6 Août 19, Bât B5a, 4000, Liège, Belgium
| | - Annick Guiseppi
- Laboratoire de Chimie Bactérienne UMR 7283, Aix-Marseille Université, Marseille, France
| | - François Delbrassine
- Centre d'Ingénierie des Protéines, InBioS, Université de Liège, allée du 6 Août 19, Bât B5a, 4000, Liège, Belgium
| | - Guillaume Manat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Sophie Roure
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Sabine Peslier
- Laboratoire de Chimie Bactérienne UMR 7283, Aix-Marseille Université, Marseille, France
| | - Eric Sauvage
- Centre d'Ingénierie des Protéines, InBioS, Université de Liège, allée du 6 Août 19, Bât B5a, 4000, Liège, Belgium
| | - Lutz Vogeley
- Membrane Structural and Functional Biology Group, Schools of Medicine and Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Juan-Carlos Rengifo-Gonzalez
- Centre d'Ingénierie des Protéines, InBioS, Université de Liège, allée du 6 Août 19, Bât B5a, 4000, Liège, Belgium
| | - Paulette Charlier
- Centre d'Ingénierie des Protéines, InBioS, Université de Liège, allée du 6 Août 19, Bât B5a, 4000, Liège, Belgium
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Maryline Foglino
- Laboratoire de Chimie Bactérienne UMR 7283, Aix-Marseille Université, Marseille, France
| | - Thierry Touzé
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
| | - Martin Caffrey
- Membrane Structural and Functional Biology Group, Schools of Medicine and Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.
| | - Frédéric Kerff
- Centre d'Ingénierie des Protéines, InBioS, Université de Liège, allée du 6 Août 19, Bât B5a, 4000, Liège, Belgium.
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82
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Abstract
More than 5 decades of work support the idea that cell envelope synthesis, including the inward growth of cell division, is tightly coordinated with DNA replication and protein synthesis through central metabolism. Remarkably, no unifying model exists to account for how these fundamentally disparate processes are functionally coupled. Recent studies demonstrate that proteins involved in carbohydrate and nitrogen metabolism can moonlight as direct regulators of cell division, coordinate cell division and DNA replication, and even suppress defects in DNA replication. In this minireview, we focus on studies illustrating the intimate link between metabolism and regulation of peptidoglycan (PG) synthesis during growth and division, and we identify the following three recurring themes. (i) Nutrient availability, not growth rate, is the primary determinant of cell size. (ii) The degree of gluconeogenic flux is likely to have a profound impact on the metabolites available for cell envelope synthesis, so growth medium selection is a critical consideration when designing and interpreting experiments related to morphogenesis. (iii) Perturbations in pathways relying on commonly shared and limiting metabolites, like undecaprenyl phosphate (Und-P), can lead to pleotropic phenotypes in unrelated pathways.
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83
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Ibáñez MI, Cabello P, Luque-Almagro VM, Sáez LP, Olaya A, Sánchez de Medina V, Luque de Castro MD, Moreno-Vivián C, Roldán MD. Quantitative proteomic analysis of Pseudomonas pseudoalcaligenes CECT5344 in response to industrial cyanide-containing wastewaters using Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS). PLoS One 2017; 12:e0172908. [PMID: 28253357 PMCID: PMC5333837 DOI: 10.1371/journal.pone.0172908] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/31/2017] [Indexed: 11/20/2022] Open
Abstract
Biological treatments to degrade cyanide are a powerful technology for cyanide removal from industrial wastewaters. It has been previously demonstrated that the alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 is able to use free cyanide and several metal−cyanide complexes as the sole nitrogen source. In this work, the strain CECT5344 has been used for detoxification of the different chemical forms of cyanide that are present in alkaline wastewaters from the jewelry industry. This liquid residue also contains large concentrations of metals like iron, copper and zinc, making this wastewater even more toxic. To elucidate the molecular mechanisms involved in the bioremediation process, a quantitative proteomic analysis by LC-MS/MS has been carried out in P. pseudoalcaligenes CECT5344 cells grown with the jewelry residue as sole nitrogen source. Different proteins related to cyanide and cyanate assimilation, as well as other proteins involved in transport and resistance to metals were induced by the cyanide-containing jewelry residue. GntR-like regulatory proteins were also induced by this industrial residue and mutational analysis revealed that GntR-like regulatory proteins may play a role in the regulation of cyanide assimilation in P. pseudoalcaligenes CECT5344. The strain CECT5344 has been used in a batch reactor to remove at pH 9 the different forms of cyanide present in industrial wastewaters from the jewelry industry (0.3 g/L, ca. 12 mM total cyanide, including both free cyanide and metal−cyanide complexes). This is the first report describing the biological removal at alkaline pH of such as elevated concentration of cyanide present in a heterogeneous mixture from an industrial source.
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Affiliation(s)
- María Isabel Ibáñez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Purificación Cabello
- Departamento de Botánica, Ecología y Fisiología Vegetal, Edificio Celestino Mutis, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Víctor Manuel Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Lara P. Sáez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Alfonso Olaya
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Verónica Sánchez de Medina
- Departamento de Química Analítica, Edificio Marie Curie, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - María Dolores Luque de Castro
- Departamento de Química Analítica, Edificio Marie Curie, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
- * E-mail:
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84
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Lombard J. Early evolution of polyisoprenol biosynthesis and the origin of cell walls. PeerJ 2016; 4:e2626. [PMID: 27812422 PMCID: PMC5088576 DOI: 10.7717/peerj.2626] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/27/2016] [Indexed: 11/30/2022] Open
Abstract
After being a matter of hot debate for years, the presence of lipid membranes in the last common ancestor of extant organisms (i.e., the cenancestor) now begins to be generally accepted. By contrast, cenancestral cell walls have attracted less attention, probably owing to the large diversity of cell walls that exist in the three domains of life. Many prokaryotic cell walls, however, are synthesized using glycosylation pathways with similar polyisoprenol lipid carriers and topology (i.e., orientation across the cell membranes). Here, we provide the first systematic phylogenomic report on the polyisoprenol biosynthesis pathways in the three domains of life. This study shows that, whereas the last steps of the polyisoprenol biosynthesis are unique to the respective domain of life of which they are characteristic, the enzymes required for basic unsaturated polyisoprenol synthesis can be traced back to the respective last common ancestor of each of the three domains of life. As a result, regardless of the topology of the tree of life that may be considered, the most parsimonious hypothesis is that these enzymes were inherited in modern lineages from the cenancestor. This observation supports the presence of an enzymatic mechanism to synthesize unsaturated polyisoprenols in the cenancestor and, since these molecules are notorious lipid carriers in glycosylation pathways involved in the synthesis of a wide diversity of prokaryotic cell walls, it provides the first indirect evidence of the existence of a hypothetical unknown cell wall synthesis mechanism in the cenancestor.
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Affiliation(s)
- Jonathan Lombard
- Biosciences, University of Exeter, Exeter, United Kingdom; National Evolutionary Synthesis Center, Durham, NC, United States of America
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85
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Depletion of Undecaprenyl Pyrophosphate Phosphatases Disrupts Cell Envelope Biogenesis in Bacillus subtilis. J Bacteriol 2016; 198:2925-2935. [PMID: 27528508 DOI: 10.1128/jb.00507-16] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/02/2016] [Indexed: 11/20/2022] Open
Abstract
The integrity of the bacterial cell envelope is essential to sustain life by countering the high turgor pressure of the cell and providing a barrier against chemical insults. In Bacillus subtilis, synthesis of both peptidoglycan and wall teichoic acids requires a common C55 lipid carrier, undecaprenyl-pyrophosphate (UPP), to ferry precursors across the cytoplasmic membrane. The synthesis and recycling of UPP requires a phosphatase to generate the monophosphate form Und-P, which is the substrate for peptidoglycan and wall teichoic acid synthases. Using an optimized clustered regularly interspaced short palindromic repeat (CRISPR) system with catalytically inactive ("dead") CRISPR-associated protein 9 (dCas9)-based transcriptional repression system (CRISPR interference [CRISPRi]), we demonstrate that B. subtilis requires either of two UPP phosphatases, UppP or BcrC, for viability. We show that a third predicted lipid phosphatase (YodM), with homology to diacylglycerol pyrophosphatases, can also support growth when overexpressed. Depletion of UPP phosphatase activity leads to morphological defects consistent with a failure of cell envelope synthesis and strongly activates the σM-dependent cell envelope stress response, including bcrC, which encodes one of the two UPP phosphatases. These results highlight the utility of an optimized CRISPRi system for the investigation of synthetic lethal gene pairs, clarify the nature of the B. subtilis UPP-Pase enzymes, and provide further evidence linking the σM regulon to cell envelope homeostasis pathways. IMPORTANCE The emergence of antibiotic resistance among bacterial pathogens is of critical concern and motivates efforts to develop new therapeutics and increase the utility of those already in use. The lipid II cycle is one of the most frequently targeted processes for antibiotics and has been intensively studied. Despite these efforts, some steps have remained poorly defined, partly due to genetic redundancy. CRISPRi provides a powerful tool to investigate the functions of essential genes and sets of genes. Here, we used an optimized CRISPRi system to demonstrate functional redundancy of two UPP phosphatases that are required for the conversion of the initially synthesized UPP lipid carrier to Und-P, the substrate for the synthesis of the initial lipid-linked precursors in peptidoglycan and wall teichoic acid synthesis.
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86
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Kohler S, Voß F, Gómez Mejia A, Brown JS, Hammerschmidt S. Pneumococcal lipoproteins involved in bacterial fitness, virulence, and immune evasion. FEBS Lett 2016; 590:3820-3839. [DOI: 10.1002/1873-3468.12352] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 08/01/2016] [Accepted: 08/05/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Sylvia Kohler
- Department Genetics of Microorganisms; Interfaculty Institute for Genetics and Functional Genomics; University of Greifswald; Germany
| | - Franziska Voß
- Department Genetics of Microorganisms; Interfaculty Institute for Genetics and Functional Genomics; University of Greifswald; Germany
| | - Alejandro Gómez Mejia
- Department Genetics of Microorganisms; Interfaculty Institute for Genetics and Functional Genomics; University of Greifswald; Germany
| | - Jeremy S. Brown
- Department of Medicine; Centre for Inflammation and Tissue Repair; University College Medical School; London UK
| | - Sven Hammerschmidt
- Department Genetics of Microorganisms; Interfaculty Institute for Genetics and Functional Genomics; University of Greifswald; Germany
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87
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Kay EJ, Yates LE, Terra VS, Cuccui J, Wren BW. Recombinant expression of Streptococcus pneumoniae capsular polysaccharides in Escherichia coli. Open Biol 2016; 6:150243. [PMID: 27110302 PMCID: PMC4838161 DOI: 10.1098/rsob.150243] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/15/2016] [Indexed: 12/13/2022] Open
Abstract
Currently, Streptococcus pneumoniae is responsible for over 14 million cases of pneumonia worldwide annually, and over 1 million deaths, the majority of them children. The major determinant for pathogenesis is a polysaccharide capsule that is variable and is used to distinguish strains based on their serotype. The capsule forms the basis of the pneumococcal polysaccharide vaccine (PPV23) that contains purified capsular polysaccharide from 23 serotypes, and the pneumococcal conjugate vaccine (PCV13), containing 13 common serotypes conjugated to CRM197 (mutant diphtheria toxin). Purified capsule from S. pneumoniae is required for pneumococcal conjugate vaccine production, and costs can be prohibitively high, limiting accessibility of the vaccine in low-income countries. In this study, we demonstrate the recombinant expression of the capsule-encoding locus from four different serotypes of S. pneumoniae within Escherichia coli. Furthermore, we attempt to identify the minimum set of genes necessary to reliably and efficiently express these capsules heterologously. These E. coli strains could be used to produce a supply of S. pneumoniae serotype-specific capsules without the need to culture pathogenic bacteria. Additionally, these strains could be applied to synthetic glycobiological applications: recombinant vaccine production using E. coli outer membrane vesicles or coupling to proteins using protein glycan coupling technology.
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Affiliation(s)
- Emily J Kay
- Department of Pathogen Molecular Biology , London School of Hygiene and Tropical Medicine , Keppel Street, London WC1E 7HT , UK
| | - Laura E Yates
- Department of Pathogen Molecular Biology , London School of Hygiene and Tropical Medicine , Keppel Street, London WC1E 7HT , UK
| | - Vanessa S Terra
- Department of Pathogen Molecular Biology , London School of Hygiene and Tropical Medicine , Keppel Street, London WC1E 7HT , UK
| | - Jon Cuccui
- Department of Pathogen Molecular Biology , London School of Hygiene and Tropical Medicine , Keppel Street, London WC1E 7HT , UK
| | - Brendan W Wren
- Department of Pathogen Molecular Biology , London School of Hygiene and Tropical Medicine , Keppel Street, London WC1E 7HT , UK
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88
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Abstract
The practice of medicine was profoundly transformed by the introduction of the antibiotics (compounds isolated from Nature) and the antibacterials (compounds prepared by synthesis) for the control of bacterial infection. As a result of the extraordinary success of these compounds over decades of time, a timeless biological activity for these compounds has been presumed. This presumption is no longer. The inexorable acquisition of resistance mechanisms by bacteria is retransforming medical practice. Credible answers to this dilemma are far better recognized than they are being implemented. In this perspective we examine (and in key respects, reiterate) the chemical and biological strategies being used to address the challenge of bacterial resistance.
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Affiliation(s)
- Jed F. Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame IN 46556–5670, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame IN 46556–5670, USA
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89
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Manat G, El Ghachi M, Auger R, Baouche K, Olatunji S, Kerff F, Touzé T, Mengin-Lecreulx D, Bouhss A. Membrane Topology and Biochemical Characterization of the Escherichia coli BacA Undecaprenyl-Pyrophosphate Phosphatase. PLoS One 2015; 10:e0142870. [PMID: 26560897 PMCID: PMC4641660 DOI: 10.1371/journal.pone.0142870] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 10/27/2015] [Indexed: 11/18/2022] Open
Abstract
Several integral membrane proteins exhibiting undecaprenyl-pyrophosphate (C55-PP) phosphatase activity were previously identified in Escherichia coli that belonged to two distinct protein families: the BacA protein, which accounts for 75% of the C55-PP phosphatase activity detected in E. coli cell membranes, and three members of the PAP2 phosphatidic acid phosphatase family, namely PgpB, YbjG and LpxT. This dephosphorylation step is required to provide the C55-P carrier lipid which plays a central role in the biosynthesis of various cell wall polymers. We here report detailed investigations of the biochemical properties and membrane topology of the BacA protein. Optimal activity conditions were determined and a narrow-range substrate specificity with a clear preference for C55-PP was observed for this enzyme. Alignments of BacA protein sequences revealed two particularly well-conserved regions and several invariant residues whose role in enzyme activity was questioned by using a site-directed mutagenesis approach and complementary in vitro and in vivo activity assays. Three essential residues Glu21, Ser27, and Arg174 were identified, allowing us to propose a catalytic mechanism for this enzyme. The membrane topology of the BacA protein determined here experimentally did not validate previous program-based predicted models. It comprises seven transmembrane segments and contains in particular two large periplasmic loops carrying the highly-conserved active site residues. Our data thus provide evidence that all the different E. coli C55-PP phosphatases identified to date (BacA and PAP2) catalyze the dephosphorylation of C55-PP molecules on the same (outer) side of the plasma membrane.
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Affiliation(s)
- Guillaume Manat
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198, CEA, CNRS, Université Paris Sud, Bâtiment 430, F-91400, Orsay, France
| | - Meriem El Ghachi
- Centre d'Ingénierie des Protéines, Université de Liège, Institut de Physique B5a et Institut de Chimie B6a, Sart-Tilman, B-4000, Liège, Belgium
| | - Rodolphe Auger
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198, CEA, CNRS, Université Paris Sud, Bâtiment 430, F-91400, Orsay, France
| | - Karima Baouche
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198, CEA, CNRS, Université Paris Sud, Bâtiment 430, F-91400, Orsay, France
| | - Samir Olatunji
- Centre d'Ingénierie des Protéines, Université de Liège, Institut de Physique B5a et Institut de Chimie B6a, Sart-Tilman, B-4000, Liège, Belgium
| | - Frédéric Kerff
- Centre d'Ingénierie des Protéines, Université de Liège, Institut de Physique B5a et Institut de Chimie B6a, Sart-Tilman, B-4000, Liège, Belgium
| | - Thierry Touzé
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198, CEA, CNRS, Université Paris Sud, Bâtiment 430, F-91400, Orsay, France
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198, CEA, CNRS, Université Paris Sud, Bâtiment 430, F-91400, Orsay, France
| | - Ahmed Bouhss
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198, CEA, CNRS, Université Paris Sud, Bâtiment 430, F-91400, Orsay, France
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90
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Teo ACK, Roper DI. Core Steps of Membrane-Bound Peptidoglycan Biosynthesis: Recent Advances, Insight and Opportunities. Antibiotics (Basel) 2015; 4:495-520. [PMID: 27025638 PMCID: PMC4790310 DOI: 10.3390/antibiotics4040495] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/03/2015] [Accepted: 10/26/2015] [Indexed: 11/16/2022] Open
Abstract
We are entering an era where the efficacy of current antibiotics is declining, due to the development and widespread dispersion of antibiotic resistance mechanisms. These factors highlight the need for novel antimicrobial discovery. A large number of antimicrobial natural products elicit their effect by directly targeting discrete areas of peptidoglycan metabolism. Many such natural products bind directly to the essential cell wall precursor Lipid II and its metabolites, i.e., preventing the utlisation of vital substrates by direct binding rather than inhibiting the metabolising enzymes themselves. Concurrently, there has been an increase in the knowledge surrounding the proteins essential to the metabolism of Lipid II at and across the cytoplasmic membrane. In this review, we draw these elements together and look to future antimicrobial opportunities in this area.
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Affiliation(s)
- Alvin C K Teo
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| | - David I Roper
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
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91
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Schrempf H, Merling P. Extracellular Streptomyces lividans vesicles: composition, biogenesis and antimicrobial activity. Microb Biotechnol 2015; 8:644-58. [PMID: 25851532 PMCID: PMC4476819 DOI: 10.1111/1751-7915.12274] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 02/09/2015] [Accepted: 02/09/2015] [Indexed: 11/27/2022] Open
Abstract
We selected Streptomyces lividans to elucidate firstly the biogenesis and antimicrobial activities of extracellular vesicles that a filamentous and highly differentiated Gram-positive bacterium produces. Vesicle types range in diameter from 110 to 230 nm and 20 to 60 nm, respectively; they assemble to clusters, and contain lipids and phospholipids allowing their in situ imaging by specific fluorescent dyes. The presence of the identified secondary metabolite undecylprodigiosin provokes red fluorescence of a portion of the heterogeneous vesicle populations facilitating in vivo monitoring. Protuberances containing vesicles generate at tips, and alongside of substrate hyphae, and enumerate during late vegetative growth to droplet-like exudates. Owing to in situ imaging in the presence and absence of a green fluorescent vancomycin derivative, we conclude that protuberances comprising vesicles arise at sites with enhanced levels of peptidoglycan subunits [pentapeptide of lipid II (C55)-linked disaccharides], and reduced levels of polymerized and cross-linked peptidoglycan within hyphae. These sites correlate with enhanced levels of anionic phospholipids and lipids. Vesicles provoke pronounced damages of Aspergillus proliferans, Verticillium dahliae and induced clumping and distortion of Escherichia coli. These harmful effects are likely attributable to the action of the identified vesicular compounds including different enzyme types, components of signal transduction cascades and undecylprodigiosin. Based on our pioneering findings, we highlight novel clues with environmental implications and application potential.
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Affiliation(s)
- Hildgund Schrempf
- FB Biology/Chemistry, Applied Genetics of Microorganisms, University Osnabrück, Barbarastr. 13, D-49069, Osnabrück, Germany
| | - Philipp Merling
- FB Biology/Chemistry, Applied Genetics of Microorganisms, University Osnabrück, Barbarastr. 13, D-49069, Osnabrück, Germany
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92
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Taylor VL, Huszczynski SM, Lam JS. Membrane Translocation and Assembly of Sugar Polymer Precursors. Curr Top Microbiol Immunol 2015; 404:95-128. [PMID: 26853690 DOI: 10.1007/82_2015_5014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bacterial polysaccharides play an essential role in cell viability, virulence, and evasion of host defenses. Although the polysaccharides themselves are highly diverse, the pathways by which bacteria synthesize these essential polymers are conserved in both Gram-negative and Gram-positive organisms. By utilizing a lipid linker, a series of glycosyltransferases and integral membrane proteins act in concert to synthesize capsular polysaccharide, teichoic acid, and teichuronic acid. The pathways used to produce these molecules are the Wzx/Wzy-dependent, the ABC-transporter-dependent, and the synthase-dependent pathways. This chapter will cover the initiation, synthesis of the various polysaccharides on the cytoplasmic face of the membrane using nucleotide sugar precursors, and export of the nascent chain from the cytoplasm to the extracellular milieu. As microbial glycobiology is an emerging field in Gram-positive bacteria research, parallels will be drawn to the more widely studied polysaccharide biosynthesis systems in Gram-negative species in order to provide greater understanding of these biologically significant molecules.
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Affiliation(s)
- Véronique L Taylor
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Steven M Huszczynski
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Joseph S Lam
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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93
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Biology and Assembly of the Bacterial Envelope. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 883:41-76. [PMID: 26621461 DOI: 10.1007/978-3-319-23603-2_3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
All free-living bacterial cells are delimited and protected by an envelope of high complexity. This physiological barrier is essential for bacterial survival and assures multiple functions. The molecular assembly of the different envelope components into a functional structure represents a tremendous biological challenge and is of high interest for fundamental sciences. The study of bacterial envelope assembly has also been fostered by the need for novel classes of antibacterial agents to fight the problematic of bacterial resistance to antibiotics. This chapter focuses on the two most intensively studied classes of bacterial envelopes that belong to the phyla Firmicutes and Proteobacteria. The envelope of Firmicutes typically has one membrane and is defined as being monoderm whereas the envelope of Proteobacteria contains two distinct membranes and is referred to as being diderm. In this chapter, we will first discuss the multiple roles of the bacterial envelope and clarify the nomenclature used to describe the different types of envelopes. We will then define the architecture and composition of the envelopes of Firmicutes and Proteobacteria while outlining their similarities and differences. We will further cover the extensive progress made in the field of bacterial envelope assembly over the last decades, using Bacillus subtilis and Escherichia coli as model systems for the study of the monoderm and diderm bacterial envelopes, respectively. We will detail our current understanding of how molecular machines assure the secretion, insertion and folding of the envelope proteins as well as the assembly of the glycosidic components of the envelope. Finally, we will highlight the topics that are still under investigation, and that will surely lead to important discoveries in the near future.
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94
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The sentinel role of peptidoglycan recycling in the β-lactam resistance of the Gram-negative Enterobacteriaceae and Pseudomonas aeruginosa. Bioorg Chem 2014; 56:41-8. [PMID: 24955547 DOI: 10.1016/j.bioorg.2014.05.011] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 01/16/2023]
Abstract
The peptidoglycan is the structural polymer of the bacterial cell envelope. In contrast to an expectation of a structural stasis for this polymer, during the growth of the Gram-negative bacterium this polymer is in a constant state of remodeling and extension. Our current understanding of this peptidoglycan "turnover" intertwines with the deeply related phenomena of the liberation of small peptidoglycan segments (muropeptides) during turnover, the presence of dedicated recycling pathways for reuse of these muropeptides, β-lactam inactivation of specific penicillin-binding proteins as a mechanism for the perturbation of the muropeptide pool, and this perturbation as a controlling mechanism for signal transduction leading to the expression of β-lactamase(s) as a key resistance mechanism against the β-lactam antibiotics. The nexus for many of these events is the control of the AmpR transcription factor by the composition of the muropeptide pool generated during peptidoglycan recycling. In this review we connect the seminal observations of the past decades to new observations that resolve some, but certainly not all, of the key structures and mechanisms that connect to AmpR.
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