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Rai AK, Sawasato K, Bennett HC, Kozlova A, Sparagna GC, Bogdanov M, Mitchell AM. Genetic evidence for functional diversification of gram-negative intermembrane phospholipid transporters. PLoS Genet 2024; 20:e1011335. [PMID: 38913742 PMCID: PMC11226057 DOI: 10.1371/journal.pgen.1011335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 07/05/2024] [Accepted: 06/07/2024] [Indexed: 06/26/2024] Open
Abstract
The outer membrane of gram-negative bacteria is a barrier to chemical and physical stress. Phospholipid transport between the inner and outer membranes has been an area of intense investigation and, in E. coli K-12, it has recently been shown to be mediated by YhdP, TamB, and YdbH, which are suggested to provide hydrophobic channels for phospholipid diffusion, with YhdP and TamB playing the major roles. However, YhdP and TamB have different phenotypes suggesting distinct functions. It remains unclear whether these functions are related to phospholipid metabolism. We investigated a synthetic cold sensitivity caused by deletion of fadR, a transcriptional regulator controlling fatty acid degradation and unsaturated fatty acid production, and yhdP, but not by ΔtamB ΔfadR or ΔydbH ΔfadR. Deletion of tamB recuses the ΔyhdP ΔfadR cold sensitivity further demonstrating the phenotype is related to functional diversification between these genes. The ΔyhdP ΔfadR strain shows a greater increase in cardiolipin upon transfer to the non-permissive temperature and genetically lowering cardiolipin levels can suppress cold sensitivity. These data also reveal a qualitative difference between cardiolipin synthases in E. coli, as deletion of clsA and clsC suppresses cold sensitivity but deletion of clsB does not. Moreover, increased fatty acid saturation is necessary for cold sensitivity and lowering this level genetically or through supplementation of oleic acid suppresses the cold sensitivity of the ΔyhdP ΔfadR strain. Together, our data clearly demonstrate that the diversification of function between YhdP and TamB is related to phospholipid metabolism. Although indirect regulatory effects are possible, we favor the parsimonious hypothesis that YhdP and TamB have differential phospholipid-substrate transport preferences. Thus, our data provide a potential mechanism for independent control of the phospholipid composition of the inner and outer membranes in response to changing conditions based on regulation of abundance or activity of YhdP and TamB.
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Affiliation(s)
- Ashutosh K. Rai
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - Katsuhiro Sawasato
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Haley C. Bennett
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - Anastasiia Kozlova
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Genevieve C. Sparagna
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Angela M. Mitchell
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
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Rai AK, Sawasato K, Bennett HC, Kozlova A, Sparagna GC, Bogdanov M, Mitchell AM. Genetic evidence for functional diversification of gram-negative intermembrane phospholipid transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.21.545913. [PMID: 37745482 PMCID: PMC10515749 DOI: 10.1101/2023.06.21.545913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The outer membrane of Gram-negative bacteria is a barrier to chemical and physical stress. Phospholipid transport between the inner and outer membranes has been an area of intense investigation and, in E. coli K-12, it has recently been shown to be mediated by YhdP, TamB, and YdbH, which are suggested to provide hydrophobic channels for phospholipid diffusion, with YhdP and TamB playing the major roles. However, YhdP and TamB have different phenotypes suggesting distinct functions. We investigated these functions using synthetic cold sensitivity (at 30 °C) caused by deletion of yhdP and fadR, a transcriptional regulator controlling fatty acid degradation and unsaturated fatty acid production, but not by ΔtamB ΔfadR or ΔydbH ΔfadR,. Deletion of tamB suppresses the ΔyhdP ΔfadR cold sensitivity suggesting this phenotype is related to phospholipid transport. The ΔyhdP ΔfadR strain shows a greater increase in cardiolipin upon transfer to the non-permissive temperature and genetically lowering cardiolipin levels can suppress cold sensitivity. These data also reveal a qualitative difference between cardiolipin synthases in E. coli, as deletion of clsA and clsC suppresses cold sensitivity but deletion of clsB does not despite lower cardiolipin levels. In addition to increased cardiolipin, increased fatty acid saturation is necessary for cold sensitivity and lowering this level genetically or through supplementation of oleic acid suppresses the cold sensitivity of the ΔyhdP ΔfadR strain. Although indirect effects are possible, we favor the parsimonious hypothesis that YhdP and TamB have differential substrate transport preferences, most likely with YhdP preferentially transporting more saturated phospholipids and TamB preferentially transporting more unsaturated phospholipids. We envision cardiolipin contributing to this transport preference by sterically clogging TamB-mediated transport of saturated phospholipids. Thus, our data provide a potential mechanism for independent control of the phospholipid composition of the inner and outer membranes in response to changing conditions.
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Affiliation(s)
- Ashutosh K. Rai
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Katsuhiro Sawasato
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Haley C. Bennett
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Anastasiia Kozlova
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Genevieve C. Sparagna
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Angela M. Mitchell
- Department of Biology, Texas A&M University, College Station, Texas, USA
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Dutta A, Kanaujia SP. The Structural Features of MlaD Illuminate its Unique Ligand-Transporting Mechanism and Ancestry. Protein J 2024; 43:298-315. [PMID: 38347327 DOI: 10.1007/s10930-023-10179-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2023] [Indexed: 05/01/2024]
Abstract
The membrane-associated solute-binding protein (SBP) MlaD of the maintenance of lipid asymmetry (Mla) system has been reported to help the transport of phospholipids (PLs) between the outer and inner membranes of Gram-negative bacteria. Despite the availability of structural information, the molecular mechanism underlying the transport of PLs and the ancestry of the protein MlaD remain unclear. In this study, we report the crystal structures of the periplasmic region of MlaD from Escherichia coli (EcMlaD) at a resolution range of 2.3-3.2 Å. The EcMlaD protomer consists of two distinct regions, viz. N-terminal β-barrel fold consisting of seven strands (referred to as MlaD domain) and C-terminal α-helical domain (HD). The protein EcMlaD oligomerizes to give rise to a homo-hexameric ring with a central channel that is hydrophobic and continuous with a variable diameter. Interestingly, the structural analysis revealed that the HD, instead of the MlaD domain, plays a critical role in determining the oligomeric state of the protein. Based on the analysis of available structural information, we propose a working mechanism of PL transport, viz. "asymmetric protomer movement (APM)". Wherein half of the EcMlaD hexamer would rise in the periplasmic side along with an outward movement of pore loops, resulting in the change of the central channel geometry. Furthermore, this study highlights that, unlike typical SBPs, EcMlaD possesses a fold similar to EF/AMT-type beta(6)-barrel and a unique ancestry. Altogether, the findings firmly establish EcMlaD to be a non-canonical SBP with a unique ligand-transport mechanism.
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Affiliation(s)
- Angshu Dutta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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Jiang YH, Liu T, Shi XC, Herrera-Balandrano DD, Xu MT, Wang SY, Laborda P. p-Aminobenzoic acid inhibits the growth of soybean pathogen Xanthomonas axonopodis pv. glycines by altering outer membrane integrity. PEST MANAGEMENT SCIENCE 2023; 79:4083-4093. [PMID: 37291956 DOI: 10.1002/ps.7608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND p-Aminobenzoic acid (pABA) is an environmentally friendly bioactive metabolite synthesized by Lysobacter antibioticus. This compound showed an unusual antifungal mode of action based on cytokinesis inhibition. However, the potential antibacterial properties of pABA remain unexplored. RESULTS In this study, pABA showed antibacterial activity against Gram-negative bacteria. This metabolite inhibited growth (EC50 = 4.02 mM), and reduced swimming motility, extracellular protease activity, and biofilm formation in the soybean pathogen Xanthomonas axonopodis pv. glycines (Xag). Although pABA was previously reported to inhibit fungal cell division, no apparent effect was observed on Xag cell division genes. Instead, pABA reduced the expression of various membrane integrity-related genes, such as cirA, czcA, czcB, emrE, and tolC. Consistently, scanning electron microscopy observations revealed that pABA caused major alternations in Xag morphology and blocked the formation of bacterial consortiums. In addition, pABA reduced the content and profile of outer membrane proteins and lipopolysaccharides in Xag, which may explain the observed effects. Preventive and curative applications of 10 mM pABA reduced Xag symptoms in soybean plants by 52.1% and 75.2%, respectively. CONCLUSIONS The antibacterial properties of pABA were studied for the first time, revealing new insights into its potential application for the management of bacterial pathogens. Although pABA was previously reported to show an antifungal mode of action based on cytokinesis inhibition, this compound inhibited Xag growth by altering the outer membrane's integrity. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yong-Hui Jiang
- School of Life Sciences, Nantong University, Nantong, China
| | - Ting Liu
- School of Life Sciences, Nantong University, Nantong, China
| | - Xin-Chi Shi
- School of Life Sciences, Nantong University, Nantong, China
| | | | - Mei-Ting Xu
- School of Life Sciences, Nantong University, Nantong, China
| | - Su-Yan Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Pedro Laborda
- School of Life Sciences, Nantong University, Nantong, China
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Dutta A, Prasad Kanaujia S. MlaC belongs to a unique class of non-canonical substrate-binding proteins and follows a novel phospholipid-binding mechanism. J Struct Biol 2022; 214:107896. [PMID: 36084896 DOI: 10.1016/j.jsb.2022.107896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 12/30/2022]
Abstract
The outer membrane (OM) of Gram-negative bacteria acts as a formidable barrier against a plethora of detrimental compounds owing to its asymmetric nature. This is because the OM possesses lipopolysaccharides (LPSs) in the outer leaflet and phospholipids (PLs) in the inner leaflet. The maintenance of lipid asymmetry (Mla) system is involved in preserving the distribution of PLs in OM. The periplasmic component of the system MlaC serves as the substrate-binding protein (SBP) that shuttles PLs between the inner and outer membranes. However, an in-depth report highlighting its mechanism of ligand binding is still lacking. This study reports the crystal structure of MlaC from Escherichia coli (EcMlaC) at a resolution of 2.5 Å in a quasi-open state, complexed with PL. The structural analysis reveals that EcMlaC and orthologs comprise two major domains, viz. nuclear transport factor 2-like (NTF2-like) and phospholipid-binding protein (PBP). Each domain can be further divided into two subdomains arranged in a discontinuous fashion. This study further reveals that EcMlaC is polyspecific in nature and follows a reverse mechanism of the opening of the substrate-binding site during the ligand binding. Furthermore, MlaC can bind two PLs by forming subsites in the binding pocket. These findings, altogether, have led to the proposition of the unique "segmented domain movement" mechanism of PL binding, not reported for any known SBP to date. Further, unlike typical SBPs, MlaC has originated from a cystatin-like fold. Overall, this study establishes MlaC to be a non-canonical SBP with a unique ligand-binding mechanism.
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Affiliation(s)
- Angshu Dutta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India.
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Li S, Ren R, Lyu L, Song J, Wang Y, Lin TW, Brun AL, Hsu HY, Shen HH. Solid and Liquid Surface-Supported Bacterial Membrane Mimetics as a Platform for the Functional and Structural Studies of Antimicrobials. MEMBRANES 2022; 12:membranes12100906. [PMID: 36295664 PMCID: PMC9609327 DOI: 10.3390/membranes12100906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/05/2022] [Accepted: 09/13/2022] [Indexed: 06/02/2023]
Abstract
Increasing antibiotic resistance has provoked the urgent need to investigate the interactions of antimicrobials with bacterial membranes. The reasons for emerging antibiotic resistance and innovations in novel therapeutic approaches are highly relevant to the mechanistic interactions between antibiotics and membranes. Due to the dynamic nature, complex compositions, and small sizes of native bacterial membranes, bacterial membrane mimetics have been developed to allow for the in vitro examination of structures, properties, dynamics, and interactions. In this review, three types of model membranes are discussed: monolayers, supported lipid bilayers, and supported asymmetric bilayers; this review highlights their advantages and constraints. From monolayers to asymmetric bilayers, biomimetic bacterial membranes replicate various properties of real bacterial membranes. The typical synthetic methods for fabricating each model membrane are introduced. Depending on the properties of lipids and their biological relevance, various lipid compositions have been used to mimic bacterial membranes. For example, mixtures of phosphatidylethanolamines (PE), phosphatidylglycerols (PG), and cardiolipins (CL) at various molar ratios have been used, approaching actual lipid compositions of Gram-positive bacterial membranes and inner membranes of Gram-negative bacteria. Asymmetric lipid bilayers can be fabricated on solid supports to emulate Gram-negative bacterial outer membranes. To probe the properties of the model bacterial membranes and interactions with antimicrobials, three common characterization techniques, including quartz crystal microbalance with dissipation (QCM-D), surface plasmon resonance (SPR), and neutron reflectometry (NR) are detailed in this review article. Finally, we provide examples showing that the combination of bacterial membrane models and characterization techniques is capable of providing crucial information in the design of new antimicrobials that combat bacterial resistance.
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Affiliation(s)
- Shiqi Li
- Department of Materials Science and Engineering, Faculty of Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Ruohua Ren
- Department of Materials Science and Engineering, Faculty of Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Letian Lyu
- Department of Materials Science and Engineering, Faculty of Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Jiangning Song
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Yajun Wang
- College of Chemistry & Materials Engineering, Wenzhou University, Wenzhou 325035, China
| | - Tsung-Wu Lin
- Department of Chemistry, Tunghai University, No. 1727, Sec. 4, Taiwan Boulevard, Xitun District, Taichung 40704, Taiwan
| | - Anton Le Brun
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Hsien-Yi Hsu
- Department of Materials Science and Engineering, School of Energy and Environment, City University of Hong Kong, Kowloon Tong, Hong Kong, China
| | - Hsin-Hui Shen
- Department of Materials Science and Engineering, Faculty of Engineering, Monash University, Clayton, VIC 3800, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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Valvano MA. Remodelling of the Gram-negative bacterial Kdo 2-lipid A and its functional implications. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35394417 DOI: 10.1099/mic.0.001159] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The lipopolysaccharide (LPS) is a characteristic molecule of the outer leaflet of the Gram-negative bacterial outer membrane, which consists of lipid A, core oligosaccharide, and O antigen. The lipid A is embedded in outer membrane and provides an efficient permeability barrier, which is particularly important to reduce the permeability of antibiotics, toxic cationic metals, and antimicrobial peptides. LPS, an important modulator of innate immune responses ranging from localized inflammation to disseminated sepsis, displays a high level of structural and functional heterogeneity, which arise due to regulated differences in the acylation of the lipid A and the incorporation of non-stoichiometric modifications in lipid A and the core oligosaccharide. This review focuses on the current mechanistic understanding of the synthesis and assembly of the lipid A molecule and its most salient non-stoichiometric modifications.
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Affiliation(s)
- Miguel A Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, UK
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Park S, Park K, Cho H, Kwon J, Kim KS, Yang H. Wash-Free Amperometric Escherichia coli Detection via Rapid and Specific Proteolytic Cleavage by Its Outer Membrane OmpT. Anal Chem 2022; 94:4756-4762. [PMID: 35143182 DOI: 10.1021/acs.analchem.1c05299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Various methods have been developed for the detection of Escherichia coli (E. coli); however, they are complex and time-consuming. OmpT─a cell membrane endopeptidase of E. coli─strongly embedded in the outer membrane of only E. coli, exposed to external solutions, with high proteolytic activity, could be a suitable target molecule for the rapid and straightforward detection of E. coli. Herein, a wash-free, sensitive, and selective amperometric method for E. coli detection, based on rapid and specific proteolytic cleavage by OmpT, has been reported. The method involved (i) rapid proteolytic cleavage of consecutive amino acids, after cleavage by OmpT, linked to an electrochemical species (4-aminophenol, AP), by leucine aminopeptidase (LAP, an exopeptidase), (ii) affinity binding of E. coli on an electrode, and (iii) electrochemical-enzymatic (EN) redox cycling. OmpT cleaved the intermediate peptide bond of a peptide substrate containing alanine-arginine-arginine-leucine-AP (-A-R-R-L-AP), forming R-L-AP, followed by the cleavage of two peptide bonds of R-L-AP sequentially by LAP, to liberate an electroactive AP. Affinity binding and EN redox cycling, in addition to rapid proteolytic cleavage by OmpT and LAP, enabled high electrochemical signal amplification. Two-sequential-cleavage was employed for the first time in protease-based detection. The calculated detection limit for E. coli cells in tap water (approximately 103 CFU/mL after 1 h incubation) was lower than those obtained without affinity binding and EN redox cycling. The detection method was highly selective to E. coli as OmpT is present in only E. coli. High sensitivity, selectivity, and the absence of wash steps make the developed detection method practically promising.
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Affiliation(s)
- Seonhwa Park
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea
| | - Kiryeon Park
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea
| | - Hyejin Cho
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea
| | - Jungwook Kwon
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea
| | - Kwang-Sun Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea
| | - Haesik Yang
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea
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Sulatskaya AI, Kosolapova AO, Bobylev AG, Belousov MV, Antonets KS, Sulatsky MI, Kuznetsova IM, Turoverov KK, Stepanenko OV, Nizhnikov AA. β-Barrels and Amyloids: Structural Transitions, Biological Functions, and Pathogenesis. Int J Mol Sci 2021; 22:11316. [PMID: 34768745 PMCID: PMC8582884 DOI: 10.3390/ijms222111316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 01/17/2023] Open
Abstract
Insoluble protein aggregates with fibrillar morphology called amyloids and β-barrel proteins both share a β-sheet-rich structure. Correctly folded β-barrel proteins can not only function in monomeric (dimeric) form, but also tend to interact with one another-followed, in several cases, by formation of higher order oligomers or even aggregates. In recent years, findings proving that β-barrel proteins can adopt cross-β amyloid folds have emerged. Different β-barrel proteins were shown to form amyloid fibrils in vitro. The formation of functional amyloids in vivo by β-barrel proteins for which the amyloid state is native was also discovered. In particular, several prokaryotic and eukaryotic proteins with β-barrel domains were demonstrated to form amyloids in vivo, where they participate in interspecies interactions and nutrient storage, respectively. According to recent observations, despite the variety of primary structures of amyloid-forming proteins, most of them can adopt a conformational state with the β-barrel topology. This state can be intermediate on the pathway of fibrillogenesis ("on-pathway state"), or can be formed as a result of an alternative assembly of partially unfolded monomers ("off-pathway state"). The β-barrel oligomers formed by amyloid proteins possess toxicity, and are likely to be involved in the development of amyloidoses, thus representing promising targets for potential therapy of these incurable diseases. Considering rapidly growing discoveries of the amyloid-forming β-barrels, we may suggest that their real number and diversity of functions are significantly higher than identified to date, and represent only "the tip of the iceberg". Here, we summarize the data on the amyloid-forming β-barrel proteins, their physicochemical properties, and their biological functions, and discuss probable means and consequences of the amyloidogenesis of these proteins, along with structural relationships between these two widespread types of β-folds.
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Affiliation(s)
- Anna I. Sulatskaya
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Anastasiia O. Kosolapova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Alexander G. Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 3 Institutskaya St., 142290 Moscow, Russia;
| | - Mikhail V. Belousov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Maksim I. Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia;
| | - Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Olesya V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Av., 194064 St. Petersburg, Russia; (I.M.K.); (K.K.T.); (O.V.S.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelskogo Sh., Pushkin, 196608 St. Petersburg, Russia; (A.I.S.); (A.O.K.); (M.V.B.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya Emb., 199034 St. Petersburg, Russia
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10
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Chen Q, Li Z, Liu S, Chi Y, Jia D, Wei T. Infection and distribution of Candidatus Liberibacter asiaticus in citrus plants and psyllid vectors at the cellular level. Microb Biotechnol 2021; 15:1221-1234. [PMID: 34469634 PMCID: PMC8966020 DOI: 10.1111/1751-7915.13914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/19/2021] [Indexed: 12/01/2022] Open
Abstract
Huanglongbing (HLB) is currently considered the most destructive disease of citrus worldwide. In the major citrus‐growing areas in Asia and the US, the major causal agent of HLB is the bacterial pathogen Candidatus Liberibacter asiaticus (CLas). CLas is vectored by the Asian citrus psyllid, Diaphorina citri, in a persistent propagative manner. CLas cannot be cultured in vitro because of its unclear growth factors, leading to uncertainty in the infection mechanism of CLas at the cellular level in citrus and in D. citri. To characterize the detailed infection of CLas in the host and vector, the incidence of HLB was first investigated in citrus‐growing fields in Fujian Province, China. It was found that the positive association of the level of CLas infection in the leaves correlated with the symptoms. Then antibodies against peptides of the outer membrane protein (OMP) of CLas were prepared and tested. The antibodies OMP‐225, OMP‐333 and OMP724 showed specificity to citrus plants in western blot analyses, whereas the antibodies OMP‐47 and OMP‐225 displayed specificity to the D. citri vector. The application of OMP‐225 in the immunofluorescence assay indicated that CLas was located in and distributed throughout the phloem sieve cells of the leaf midribs and axile placenta of the fruit. CLas also infected the epithelial cells and visceral muscles of the alimentary canal of D. citri. The application of OMP‐333 in immunoelectron microscopy indicated the round or oval CLas in the sieve cells of leaf midribs and axile placenta of fruit as well as in the epithelial cells and reticular tissue of D. citri alimentary canal. These results provide a reliable means for HLB detection, and enlighten a strategy via neutralizing OMP to control HLB. These findings also provide insight for the further investigation on CLas infection and pathogenesis, as well as CLas–vector interaction.
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Affiliation(s)
- Qian Chen
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Zhiqiang Li
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Shulin Liu
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Yunhua Chi
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Dongsheng Jia
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Taiyun Wei
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
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11
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Deletion of Yersinia pestis ail causes temperature sensitive pleiotropic effects including cell lysis that are suppressed by carbon source, cations, or loss of phospholipase A activity. J Bacteriol 2021; 203:e0036121. [PMID: 34398663 PMCID: PMC8508112 DOI: 10.1128/jb.00361-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Maintenance of phospholipid (PL) and lipopoly- or lipooligo-saccharide (LPS or LOS) asymmetry in the outer membrane (OM) of Gram-negative bacteria is essential but poorly understood. The Yersinia pestis OM Ail protein was required to maintain lipid homeostasis and cell integrity at elevated temperature (37° C). Loss of this protein had pleiotropic effects. A Y. pestis Δail mutant and KIM6+ wild- type were systematically compared for (i) growth requirements at 37° C, (ii) cell structure, (iii) antibiotic and detergent sensitivity, (iv) proteins released into supernates, (v) induction of the heat shock response, and (vi) physiological and genetic suppressors that restored the wild- type phenotype. The Δail mutant grew normally at 28° C but lysed at 37° C when it entered stationary phase as shown by cell count, SDS-PAGE of cell supernatants, and electron microscopy. Immuno-fluorescent microscopy showed that the Δail mutant did not assemble Caf1 capsule. Expression of heat shock promoters rpoE or rpoH fused to a lux operon reporter were not induced when the Δail mutant was shifted from the 28° C to 37° C (p<0.001 and p<0.01 respectively). Mutant lysis was suppressed by addition of 11 mM glucose, 22 or 44 mM glycerol, 2.5 mM Ca2+, or 2.5 mM Mg2+ to the growth medium, or by a mutation in the phospholipase A gene (pldA::miniTn5, ΔpldA, or PldAS164A). A model, accounting for the temperature-sensitive lysis of the Δail mutant and the Ail-dependent stabilization of the OM tetraacylated LOS at 37°C is presented. IMPORTANCE The Gram-negative pathogen, Yersinia pestis, transitions between a flea vector (ambient temperature) and a mammalian host (37° C). In response to 37° C, Y. pestis modifies its outer membrane (OM) by reducing the fatty acid content in lipid A, changing the outer leaflet from being predominantly hexaacylated to being predominantly tetraacylated. It also increases the Ail concentration, so it becomes the most prominent OM protein. Both measures are needed for Y. pestis to evade the host innate immune response. Deletion of ail destabilizes the OM at 37° C causing the cells to lyse. These results show that a protein is essential for maintaining lipid asymmetry and lipid homeostasis in the bacterial OM.
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12
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Dutta A, Chandravanshi M, Kanaujia SP. Conserved features of the MlaD domain aid the trafficking of hydrophobic molecules. Proteins 2021; 89:1473-1488. [PMID: 34196044 DOI: 10.1002/prot.26168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/18/2021] [Accepted: 06/25/2021] [Indexed: 11/09/2022]
Abstract
In Gram-negative bacteria, the maintenance of lipid asymmetry (Mla) system is involved in the transport of phospholipids between the inner (IM) and outer membrane. The Mla system utilizes a unique IM-associated periplasmic solute-binding protein, MlaD, which possesses a conserved domain, MlaD domain. While proteins carrying the MlaD domain are known to be primarily involved in the trafficking of hydrophobic molecules, not much is known about this domain itself. Thus, in this study, the characterization of the MlaD domain employing bioinformatics analysis is reported. The profiling of the MlaD domain of different architectures reveals the abundance of glycine and hydrophobic residues and the lack of cysteine residues. The domain possesses a conserved N-terminal region and a well-preserved glycine residue that constitutes a consensus motif across different architectures. Phylogenetic analysis shows that the MlaD domain archetypes are evolutionarily closer and marked by the conservation of a functionally crucial pore loop located at the C-terminal region. The study also establishes the critical role of the domain-associated permeases and the driving forces governing the transport of hydrophobic molecules. This sheds sufficient light on the structure-function-evolutionary relationship of MlaD domain. The hexameric interface analysis reveals that the MlaD domain itself is not a sole player in the oligomerization of the proteins. Further, an operonic and interactome map analysis reveals that the Mla and the Mce systems are dependent on the structural homologs of the nuclear transport factor 2 superfamily.
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Affiliation(s)
- Angshu Dutta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Monika Chandravanshi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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13
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NAD(H)-mediated tetramerization controls the activity of Legionella pneumophila phospholipase PlaB. Proc Natl Acad Sci U S A 2021; 118:2017046118. [PMID: 34074754 DOI: 10.1073/pnas.2017046118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The virulence factor PlaB promotes lung colonization, tissue destruction, and intracellular replication of Legionella pneumophila, the causative agent of Legionnaires' disease. It is a highly active phospholipase exposed at the bacterial surface and shows an extraordinary activation mechanism by tetramer deoligomerization. To unravel the molecular basis for enzyme activation and localization, we determined the crystal structure of PlaB in its tetrameric form. We found that the tetramer is a dimer of identical dimers, and a monomer consists of an N-terminal α/β-hydrolase domain expanded by two noncanonical two-stranded β-sheets, β-6/β-7 and β-9/β-10. The C-terminal domain reveals a fold displaying a bilobed β-sandwich with a hook structure required for dimer formation and structural complementation of the enzymatic domain in the neighboring monomer. This highlights the dimer as the active form. Δβ-9/β-10 mutants showed a decrease in the tetrameric fraction and altered activity profiles. The variant also revealed restricted binding to membranes resulting in mislocalization and bacterial lysis. Unexpectedly, we observed eight NAD(H) molecules at the dimer/dimer interface, suggesting that these molecules stabilize the tetramer and hence lead to enzyme inactivation. Indeed, addition of NAD(H) increased the fraction of the tetramer and concomitantly reduced activity. Together, these data reveal structural elements and an unprecedented NAD(H)-mediated tetramerization mechanism required for spatial and enzymatic control of a phospholipase virulence factor. The allosteric regulatory process identified here is suited to fine tune PlaB in a way that protects Legionella pneumophila from self-inflicted lysis while ensuring its activity at the pathogen-host interface.
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14
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Wang B, Wu G, Li K, Ling J, Zhao Y, Liu F. A Glycoside Hydrolase Family 99-Like Domain-Containing Protein Modifies Outer Membrane Proteins to Maintain Xanthomonas Pathogenicity and Viability in Stressful Environments. PHYTOPATHOLOGY 2021; 111:929-939. [PMID: 33174820 DOI: 10.1094/phyto-08-20-0327-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Protein glycosylation is an essential process that plays an important role in proteome stability, protein structure, and protein function modulation in eukaryotes. However, in bacteria, especially plant pathogenic bacteria, similar studies are lacking. Here, we investigated the relationship between protein glycosylation and pathogenicity by using Xanthomonas oryzae pv. oryzae, the causal agent of bacterial leaf blight in rice, as a well-defined example. In our previous work, we identified a virulence-related hypothetical protein, PXO_03177, but how this protein regulates X. oryzae pv. oryzae virulence has remained unclear. BLAST analysis showed that most homologous proteins of PXO_03177 are glycoside hydrolase family 99-like domain-containing proteins. In the current study, we found that the outer membrane integrity of ΔPXO_03177 appeared to be disrupted. Extracting the outer membrane proteins (OMPs) and performing comparative proteomics and sodium dodecyl sulphate-polyacrylamide gel electrophoresis gel staining analyses revealed that PXO_03177 deletion altered the protein levels of 13 OMPs. Western blot analyses showed that the protein level and glycosylation modification of PXO_02523, a related OmpA family-like protein, was changed in the ΔPXO_03177 mutant background strain. Additionally, the interaction between PXO_03177 and PXO_02523 was confirmed by coimmunoprecipitation. Both PXO_03177 and PXO_02523 play important roles in regulating pathogen virulence and viability in stressful environments. This work provides the first evidence that protein glycosylation is necessary for the virulence of plant pathogenic bacteria.
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Affiliation(s)
- Bo Wang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P.R. China
| | - Guichun Wu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P.R. China
| | - Kaihuai Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P.R. China
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Ling
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P.R. China
| | - Yancun Zhao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P.R. China
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, P.R. China
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15
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Jiang V, Khare SD, Banta S. Computational structure prediction provides a plausible mechanism for electron transfer by the outer membrane protein Cyc2 from Acidithiobacillus ferrooxidans. Protein Sci 2021; 30:1640-1652. [PMID: 33969560 DOI: 10.1002/pro.4106] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 12/14/2022]
Abstract
Cyc2 is the key protein in the outer membrane of Acidithiobacillus ferrooxidans that mediates electron transfer between extracellular inorganic iron and the intracellular central metabolism. This cytochrome c is specific for iron and interacts with periplasmic proteins to complete a reversible electron transport chain. A structure of Cyc2 has not yet been characterized experimentally. Here we describe a structural model of Cyc2, and associated proteins, to highlight a plausible mechanism for the ferrous iron electron transfer chain. A comparative modeling protocol specific for trans membrane beta barrel (TMBB) proteins in acidophilic conditions (pH ~ 2) was applied to the primary sequence of Cyc2. The proposed structure has three main regimes: Extracellular loops exposed to low-pH conditions, a TMBB, and an N-terminal cytochrome-like region within the periplasmic space. The Cyc2 model was further refined by identifying likely iron and heme docking sites. This represents the first computational model of Cyc2 that accounts for the membrane microenvironment and the acidity in the extracellular matrix. This approach can be used to model other TMBBs which can be critical for chemolithotrophic microbial growth.
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Affiliation(s)
- Virginia Jiang
- Department of Chemical Engineering, Columbia University in the City of New York, New York, New York, USA
| | - Sagar D Khare
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University in the City of New York, New York, New York, USA
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16
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Mondal A, Bhat IA, Karunakaran S, De M. Supramolecular Interaction of Molecular Cage and β-Galactosidase: Application in Enzymatic Inhibition, Drug Delivery and Antimicrobial Activity. Chembiochem 2021; 22:1955-1960. [PMID: 33817948 DOI: 10.1002/cbic.202100008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/31/2021] [Indexed: 12/20/2022]
Abstract
Enzyme inhibitors play a crucial role in diagnosis of a wide spectrum of diseases related to bacterial infections. We report here the effect of a water-soluble self-assembled PdII 8 molecular cage towards β-galactosidase enzyme activity. The molecular cage is composed of a tetrapyridyl donor (L) and cis-[(en)Pd(NO3 )2 ] (en=ethane-1,2-diamine) acceptor and it has a hydrophobic internal cavity. We have observed that the acceptor moiety mainly possesses the ability to inactivate the β-galactosidase enzyme activity. Kinetic investigation revealed the mixed mode of inhibition. This inhibition strategy was extended to control the growth of methicillin-resistant Staphylococcus aureus. The internalization of the Pd(II) cage inside the bacteria was confirmed when bacterial solutions were incubated with curcumin loaded cage. The intrinsic green fluorescence of curcumin made the bacteria glow when put under an optical microscope. Furthermore, this curcumin loaded molecular cage shows an enhanced antibacterial activity. Thus, PdII 8 molecular cage is quite attractive due to its dual role as enzyme inhibitor and drug carrier.
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Affiliation(s)
- Avijit Mondal
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Imtiyaz Ahmad Bhat
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Subbaraj Karunakaran
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Mrinmoy De
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
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17
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Saha S, Lach SR, Konovalova A. Homeostasis of the Gram-negative cell envelope. Curr Opin Microbiol 2021; 61:99-106. [PMID: 33901778 DOI: 10.1016/j.mib.2021.03.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 01/08/2023]
Abstract
The Gram-negative bacterial cell envelope is a complex structure and its homeostasis is essential for bacterial survival. Envelope stress responses (ESRs) are signal transduction pathways that monitor the fidelity of envelope assembly during normal growth and also detect and repair envelope damage caused by external assaults, including immune factors, protein toxins, and antibiotics. In this review, we focus on three best-studied ESRs and discuss the mechanisms by which ESRs detect various perturbations of envelope assembly and integrity and regulate envelope remodeling to promote bacterial survival. We will highlight the complex relationship of ESRs with envelope biogenesis pathways and discuss some of the challenges in this field on the road to mapping the global regulatory network of envelope homeostasis.
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Affiliation(s)
- Shreya Saha
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), 6431 Fannin Street, Houston, TX, 77030, USA
| | - Sarah R Lach
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), 6431 Fannin Street, Houston, TX, 77030, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 6767 Bertner Avenue, Houston, TX, 77030, USA
| | - Anna Konovalova
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), 6431 Fannin Street, Houston, TX, 77030, USA.
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18
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Roumia AF, Tsirigos KD, Theodoropoulou MC, Tamposis IA, Hamodrakas SJ, Bagos PG. OMPdb: A Global Hub of Beta-Barrel Outer Membrane Proteins. FRONTIERS IN BIOINFORMATICS 2021; 1:646581. [PMID: 36303794 PMCID: PMC9581022 DOI: 10.3389/fbinf.2021.646581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/18/2021] [Indexed: 11/14/2022] Open
Abstract
OMPdb (www.ompdb.org) was introduced as a database for β-barrel outer membrane proteins from Gram-negative bacteria in 2011 and then included 69,354 entries classified into 85 families. The database has been updated continuously using a collection of characteristic profile Hidden Markov Models able to discriminate between the different families of prokaryotic transmembrane β-barrels. The number of families has increased ultimately to a total of 129 families in the current, second major version of OMPdb. New additions have been made in parallel with efforts to update existing families and add novel families. Here, we present the upgrade of OMPdb, which from now on aims to become a global repository for all transmembrane β-barrel proteins, both eukaryotic and bacterial.
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Affiliation(s)
- Ahmed F. Roumia
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | | | | | - Ioannis A. Tamposis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Stavros J. Hamodrakas
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Pantelis G. Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- *Correspondence: Pantelis G. Bagos
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19
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Guest RL, Rutherford ST, Silhavy TJ. Border Control: Regulating LPS Biogenesis. Trends Microbiol 2021; 29:334-345. [PMID: 33036869 PMCID: PMC7969359 DOI: 10.1016/j.tim.2020.09.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/20/2022]
Abstract
The outer membrane (OM) is a defining feature of Gram-negative bacteria that serves as a permeability barrier and provides rigidity to the cell. Critical to OM function is establishing and maintaining an asymmetrical bilayer structure with phospholipids in the inner leaflet and the complex glycolipid lipopolysaccharide (LPS) in the outer leaflet. Cells ensure this asymmetry by regulating the biogenesis of lipid A, the conserved and essential anchor of LPS. Here we review the consequences of disrupting the regulatory components that control lipid A biogenesis, focusing on the rate-limiting step performed by LpxC. Dissection of these processes provides critical insights into bacterial physiology and potential new targets for antibiotics able to overcome rapidly spreading resistance mechanisms.
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Affiliation(s)
- Randi L Guest
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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20
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Marx DC, Leblanc MJ, Plummer AM, Krueger S, Fleming KG. Domain interactions determine the conformational ensemble of the periplasmic chaperone SurA. Protein Sci 2020; 29:2043-2053. [PMID: 32748422 PMCID: PMC7513704 DOI: 10.1002/pro.3924] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 12/17/2022]
Abstract
SurA is thought to be the most important periplasmic chaperone for outer membrane protein (OMP) biogenesis. Its structure is composed of a core region and two peptidylprolyl isomerase domains, termed P1 and P2, connected by flexible linkers. As such these three independent folding units are able to adopt a number of distinct spatial positions with respect to each other. The conformational dynamics of these domains are thought to be functionally important yet are largely unresolved. Here we address this question of the conformational ensemble using sedimentation equilibrium, small-angle neutron scattering, and folding titrations. This combination of orthogonal methods converges on a SurA population that is monomeric at physiological concentrations. The conformation that dominates this population has the P1 and core domains docked to one another, for example, "P1-closed" and the P2 domain extended in solution. We discovered that the distribution of domain orientations is defined by modest and favorable interactions between the core domain and either the P1 or the P2 domains. These two peptidylprolyl domains compete with each other for core-binding but are thermodynamically uncoupled. This arrangement implies two novel insights. Firstly, an open conformation must exist to facilitate P1 and P2 exchange on the core, indicating that the open client-binding conformation is populated at low levels even in the absence of client unfolded OMPs. Secondly, competition between P1 and P2 binding paradoxically occludes the client binding site on the core, which may serve to preserve the reservoir of binding-competent apo-SurA in the periplasm.
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Affiliation(s)
- Dagan C. Marx
- Thomas C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Mathis J. Leblanc
- Thomas C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Ashlee M. Plummer
- Thomas C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
- Department of Cell BiologyHarvard Medical SchoolBostonMassachusettsUSA
| | - Susan Krueger
- National Institute of Standards and TechnologyGaithersburgMarylandUSA
| | - Karen G. Fleming
- Thomas C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
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21
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Early evolutionary loss of the lipid A modifying enzyme PagP resulting in innate immune evasion in Yersinia pestis. Proc Natl Acad Sci U S A 2020; 117:22984-22991. [PMID: 32868431 DOI: 10.1073/pnas.1917504117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Immune evasion through membrane remodeling is a hallmark of Yersinia pestis pathogenesis. Yersinia remodels its membrane during its life cycle as it alternates between mammalian hosts (37 °C) and ambient (21 °C to 26 °C) temperatures of the arthropod transmission vector or external environment. This shift in growth temperature induces changes in number and length of acyl groups on the lipid A portion of lipopolysaccharide (LPS) for the enteric pathogens Yersinia pseudotuberculosis (Ypt) and Yersinia enterocolitica (Ye), as well as the causative agent of plague, Yersinia pestis (Yp). Addition of a C16 fatty acid (palmitate) to lipid A by the outer membrane acyltransferase enzyme PagP occurs in immunostimulatory Ypt and Ye strains, but not in immune-evasive Yp Analysis of Yp pagP gene sequences identified a single-nucleotide polymorphism that results in a premature stop in translation, yielding a truncated, nonfunctional enzyme. Upon repair of this polymorphism to the sequence present in Ypt and Ye, lipid A isolated from a Yp pagP+ strain synthesized two structures with the C16 fatty acids located in acyloxyacyl linkage at the 2' and 3' positions of the diglucosamine backbone. Structural modifications were confirmed by mass spectrometry and gas chromatography. With the genotypic restoration of PagP enzymatic activity in Yp, a significant increase in lipid A endotoxicity mediated through the MyD88 and TRIF/TRAM arms of the TLR4-signaling pathway was observed. Discovery and repair of an evolutionarily lost lipid A modifying enzyme provides evidence of lipid A as a crucial determinant in Yp infectivity, pathogenesis, and host innate immune evasion.
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22
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Ribosome Display Technology: Applications in Disease Diagnosis and Control. Antibodies (Basel) 2020; 9:antib9030028. [PMID: 32605027 PMCID: PMC7551589 DOI: 10.3390/antib9030028] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 12/28/2022] Open
Abstract
Antibody ribosome display remains one of the most successful in vitro selection technologies for antibodies fifteen years after it was developed. The unique possibility of direct generation of whole proteins, particularly single-chain antibody fragments (scFvs), has facilitated the establishment of this technology as one of the foremost antibody production methods. Ribosome display has become a vital tool for efficient and low-cost production of antibodies for diagnostics due to its advantageous ability to screen large libraries and generate binders of high affinity. The remarkable flexibility of this method enables its applicability to various platforms. This review focuses on the applications of ribosome display technology in biomedical and agricultural fields in the generation of recombinant scFvs for disease diagnostics and control.
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23
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Outer Membrane Lipid Secretion and the Innate Immune Response to Gram-Negative Bacteria. Infect Immun 2020; 88:IAI.00920-19. [PMID: 32253250 DOI: 10.1128/iai.00920-19] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is an asymmetric lipid bilayer that consists of inner leaflet phospholipids and outer leaflet lipopolysaccharides (LPS). The asymmetric character and unique biochemistry of LPS molecules contribute to the OM's ability to function as a molecular permeability barrier that protects the bacterium against hazards in the environment. Assembly and regulation of the OM have been extensively studied for understanding mechanisms of antibiotic resistance and bacterial defense against host immunity; however, there is little knowledge on how Gram-negative bacteria release their OMs into their environment to manipulate their hosts. Discoveries in bacterial lipid trafficking, OM lipid homeostasis, and host recognition of microbial patterns have shed new light on how microbes secrete OM vesicles (OMVs) to influence inflammation, cell death, and disease pathogenesis. Pathogens release OMVs that contain phospholipids, like cardiolipins, and components of LPS molecules, like lipid A endotoxins. These multiacylated lipid amphiphiles are molecular patterns that are differentially detected by host receptors like the Toll-like receptor 4/myeloid differentiation factor 2 complex (TLR4/MD-2), mouse caspase-11, and human caspases 4 and 5. We discuss how lipid ligands on OMVs engage these pattern recognition receptors on the membranes and in the cytosol of mammalian cells. We then detail how bacteria regulate OM lipid asymmetry, negative membrane curvature, and the phospholipid-to-LPS ratio to control OMV formation. The goal is to highlight intersections between OM lipid regulation and host immunity and to provide working models for how bacterial lipids influence vesicle formation.
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Mushtaq S, Reynolds R, Gilmore MC, Esho O, Adkin R, García-Romero I, Chaudhry A, Horner C, Bartholomew TL, Valvano MA, Dry M, Murray J, Pichon B, Livermore DM. Inherent colistin resistance in genogroups of the Enterobacter cloacae complex: epidemiological, genetic and biochemical analysis from the BSAC Resistance Surveillance Programme. J Antimicrob Chemother 2020; 75:2452-2461. [DOI: 10.1093/jac/dkaa201] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/25/2020] [Accepted: 04/21/2020] [Indexed: 01/19/2023] Open
Abstract
AbstractBackgroundPolymyxins have re-entered use against problem Gram-negative bacteria. Resistance rates are uncertain, with estimates confounded by selective testing.MethodsThe BSAC Resistance Surveillance Programme has routinely tested colistin since 2010; we reviewed data up to 2017 for relevant Enterobacterales (n = 10 914). Unexpectedly frequent resistance was seen among the Enterobacter cloacae complex isolates (n = 1749); for these, we investigated relationships to species, genome, carbon source utilization and LPS structure.ResultsAnnual colistin resistance rates among E. cloacae complex isolates were 4.4%–20%, with a rising trend among bloodstream organisms; in contrast, annual rates for Escherichia coli and Klebsiella spp. (including K. aerogenes) generally remained <2%. WGS split the E. cloacae complex isolates into seven genogroup clusters, designated A–G. Among isolates assigned to genogroups A–D, 47/50 sequenced were colistin resistant, and many of those belonging to genogroups A–C identified as E. asburiae. Isolates belonging to genogroups E–G consistently identified as E. cloacae and were rarely (only 3/45 representatives sequenced) colistin resistant. Genogroups F and G, the predominant colistin-susceptible clusters, were metabolically distinct from other clusters, notably regarding utilization or not of l-fucose, formic acid, d-serine, adonitol, myo-inositol, l-lyxose and polysorbates. LPS from resistant organisms grown without colistin pressure lacked substitutions with 4-amino-arabinose or ethanolamine but was more structurally complex, with more molecular species present.ConclusionsColistin resistance is frequent in the E. cloacae complex and increasing among bloodstream isolates. It is associated with: (i) particular genomic and metabolic clusters; (ii) identification as E. asburiae; and (iii) with more complex LPS architectures.
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Affiliation(s)
- Shazad Mushtaq
- Antimicrobial Resistance & Healthcare Associated Infection Reference Unit, Public Health England, Colindale, London
| | - Rosy Reynolds
- British Society for Antimicrobial Chemotherapy, Birmingham, UK
- Department of Medical Microbiology, Southmead Hospital, Bristol, UK
- University of Bristol Medical School (Population Health Sciences), Canynge Hall, 39 Whatley Road, Bristol BS8 2PS, UK
| | - Michael C Gilmore
- The Wellcome-Wolfson Institute for Experimental Medicine, Queens University, Belfast, UK
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Olubukola Esho
- Department of Medical Microbiology, Norfolk and Norwich University Hospital, Norwich, UK
- Department of Clinical Microbiology and Infection Control, Royal Gwent Hospital, Cardiff Road, Newport, Gwent NP20 2UB, UK
| | - Rachael Adkin
- Antimicrobial Resistance & Healthcare Associated Infection Reference Unit, Public Health England, Colindale, London
| | | | - Aiysha Chaudhry
- Antimicrobial Resistance & Healthcare Associated Infection Reference Unit, Public Health England, Colindale, London
| | - Carolyne Horner
- British Society for Antimicrobial Chemotherapy, Birmingham, UK
| | - Toby L Bartholomew
- The Wellcome-Wolfson Institute for Experimental Medicine, Queens University, Belfast, UK
- Excerpta Medica BV, 90 Southwark Street, London SE1 0SW, UK
| | - Miguel A Valvano
- The Wellcome-Wolfson Institute for Experimental Medicine, Queens University, Belfast, UK
| | - Magdalena Dry
- Quotient Bio Analytical Sciences and HFL Sport Science, LGC Group, Fordham, UK
| | - John Murray
- Quotient Bio Analytical Sciences and HFL Sport Science, LGC Group, Fordham, UK
- Fisher Scientific Ltd, Bishop Meadow Road, Loughborough LE1 5RG, UK
| | - Bruno Pichon
- Antimicrobial Resistance & Healthcare Associated Infection Reference Unit, Public Health England, Colindale, London
| | - David M Livermore
- Antimicrobial Resistance & Healthcare Associated Infection Reference Unit, Public Health England, Colindale, London
- Norwich Medical School, University of East Anglia, Norwich, UK
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Huysmans GHM, Marx DC, Radford SE, Fleming KG. Determining the Free Energies of Outer Membrane Proteins in Lipid Bilayers. Methods Mol Biol 2020; 2168:217-232. [PMID: 33582994 DOI: 10.1007/978-1-0716-0724-4_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The thermodynamic stabilities of membrane proteins are of fundamental interest to provide a biophysical description of their structure-function relationships because energy determines conformational populations. In addition, structure-energy relationships can be exploited in membrane protein design and in synthetic biology. To determine the thermodynamic stability of a membrane protein, it is not sufficient to be able to unfold and refold the molecule: establishing path independence of this reaction is essential. Here we describe the procedures required to measure and verify path independence for the folding of outer membrane proteins in large unilamellar vesicles.
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Affiliation(s)
- Gerard H M Huysmans
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
| | - Dagan C Marx
- T C Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Karen G Fleming
- T C Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
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Tian W, Naveed H, Lin M, Liang J. GeTFEP: A general transfer free energy profile of transmembrane proteins. Protein Sci 2019; 29:469-479. [PMID: 31658402 DOI: 10.1002/pro.3763] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/20/2019] [Accepted: 10/23/2019] [Indexed: 01/06/2023]
Abstract
Free energy of transferring amino acid side-chains from aqueous environment into lipid bilayers, known as transfer free energy (TFE), provides important information on the thermodynamic stability of membrane proteins. In this study, we derived a TFE profile named General Transfer Free Energy Profile (GeTFEP) based on computation of the TFEs of 58 β-barrel membrane proteins (βMPs). The GeTFEP agrees well with experimentally measured and computationally derived TFEs. Analysis based on the GeTFEP shows that residues in different regions of the transmembrane (TM) segments of βMPs have different roles during the membrane insertion process. Results further reveal the importance of the sequence pattern of TM strands in stabilizing βMPs in the membrane environment. In addition, we show that GeTFEP can be used to predict the positioning and the orientation of βMPs in the membrane. We also show that GeTFEP can be used to identify structurally or functionally important amino acid residue sites of βMPs. Furthermore, the TM segments of α-helical membrane proteins can be accurately predicted with GeTFEP, suggesting that the GeTFEP is of general applicability in studying membrane protein.
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Affiliation(s)
- Wei Tian
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois
| | - Hammad Naveed
- Department of Computer Science, National University of Computer and Emerging Sciences (NUCES-FAST), Islamabad, Islamabad Capital Territory, Pakistan
| | - Meishan Lin
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois
| | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois
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Anandan A, Vrielink A. Structure and function of lipid A-modifying enzymes. Ann N Y Acad Sci 2019; 1459:19-37. [PMID: 31553069 DOI: 10.1111/nyas.14244] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/26/2019] [Accepted: 09/05/2019] [Indexed: 12/30/2022]
Abstract
Lipopolysaccharides are complex molecules found in the cell envelop of many Gram-negative bacteria. The toxic activity of these molecules has led to the terminology of endotoxins. They provide bacteria with structural integrity and protection from external environmental conditions, and they interact with host signaling receptors to induce host immune responses. Bacteria have evolved enzymes that act to modify lipopolysaccharides, particularly the lipid A region of the molecule, to enable the circumvention of host immune system responses. These modifications include changes to lipopolysaccharide by the addition of positively charged sugars, such as N-Ara4N, and phosphoethanolamine (pEtN). Other modifications include hydroxylation, acylation, and deacylation of fatty acyl chains. We review the two-component regulatory mechanisms for enzymes that carry out these modifications and provide details of the structures of four enzymes (PagP, PagL, pEtN transferases, and ArnT) that modify the lipid A portion of lipopolysaccharides. We focus largely on the three-dimensional structures of these enzymes, which provide an understanding of how their substrate binding and catalytic activities are mediated. A structure-function-based understanding of these enzymes provides a platform for the development of novel therapeutics to treat antibiotic resistance.
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Affiliation(s)
- Anandhi Anandan
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Alice Vrielink
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia, Australia
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Regulation of Gut Microbiota and Metabolic Endotoxemia with Dietary Factors. Nutrients 2019; 11:nu11102277. [PMID: 31547555 PMCID: PMC6835897 DOI: 10.3390/nu11102277] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 02/08/2023] Open
Abstract
Metabolic endotoxemia is a condition in which blood lipopolysaccharide (LPS) levels are elevated, regardless of the presence of obvious infection. It has been suggested to lead to chronic inflammation-related diseases such as obesity, type 2 diabetes mellitus, non-alcoholic fatty liver disease (NAFLD), pancreatitis, amyotrophic lateral sclerosis, and Alzheimer’s disease. In addition, it has attracted attention as a target for the prevention and treatment of these chronic diseases. As metabolic endotoxemia was first reported in mice that were fed a high-fat diet, research regarding its relationship with diets has been actively conducted in humans and animals. In this review, we summarize the relationship between fat intake and induction of metabolic endotoxemia, focusing on gut dysbiosis and the influx, kinetics, and metabolism of LPS. We also summarize the recent findings about dietary factors that attenuate metabolic endotoxemia, focusing on the regulation of gut microbiota. We hope that in the future, control of metabolic endotoxemia using dietary factors will help maintain human health.
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Intermembrane transport: Glycerophospholipid homeostasis of the Gram-negative cell envelope. Proc Natl Acad Sci U S A 2019; 116:17147-17155. [PMID: 31420510 PMCID: PMC6717313 DOI: 10.1073/pnas.1902026116] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
This perspective addresses recent advances in lipid transport across the Gram-negative inner and outer membranes. While we include a summary of previously existing literature regarding this topic, we focus on the maintenance of lipid asymmetry (Mla) pathway. Discovered in 2009 by the Silhavy group [J. C. Malinverni, T. J. Silhavy, Proc. Natl. Acad. Sci. U.S.A. 106, 8009–8014 (2009)], Mla has become increasingly appreciated for its role in bacterial cell envelope physiology. Through the work of many, we have gained an increasingly mechanistic understanding of the function of Mla via genetic, biochemical, and structural methods. Despite this, there is a degree of controversy surrounding the directionality in which Mla transports lipids. While the initial discovery and subsequent studies have posited that it mediated retrograde lipid transport (removing glycerophospholipids from the outer membrane and returning them to the inner membrane), others have asserted the opposite. This Perspective aims to lay out the evidence in an unbiased, yet critical, manner for Mla-mediated transport in addition to postulation of mechanisms for anterograde lipid transport from the inner to outer membranes.
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Overcoming Iron Deficiency of an Escherichia coli tonB Mutant by Increasing Outer Membrane Permeability. J Bacteriol 2019; 201:JB.00340-19. [PMID: 31235517 DOI: 10.1128/jb.00340-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 06/21/2019] [Indexed: 01/20/2023] Open
Abstract
The intake of certain nutrients, including ferric ion, is facilitated by the outer membrane-localized transporters. Due to ferric insolubility at physiological pH, Escherichia coli secretes a chelator, enterobactin, outside the cell and then transports back the enterobactin-ferric complex via an outer membrane receptor protein, FepA, whose activity is dependent on the proton motive force energy transduced by the TonB-ExbBD complex of the inner membrane. Consequently, ΔtonB mutant cells grow poorly on a medium low in iron. Prolonged incubation of ΔtonB cells on low-iron medium yields faster-growing colonies that acquired suppressor mutations in the yejM (pbgA) gene, which codes for a putative inner-to-outer membrane cardiolipin transporter. Further characterization of suppressors revealed that they display hypersusceptibility to vancomycin, a large hydrophilic antibiotic normally precluded from entering E. coli cells, and leak periplasmic proteins into the culture supernatant, indicating a compromised outer membrane permeability barrier. All phenotypes were reversed by supplying the wild-type copy of yejM on a plasmid, suggesting that yejM mutations are solely responsible for the observed phenotypes. The deletion of all known cardiolipin synthase genes (clsABC) did not produce the phenotypes similar to mutations in the yejM gene, suggesting that the absence of cardiolipin from the outer membrane per se is not responsible for increased outer membrane permeability. Elevated lysophosphatidylethanolamine levels and the synthetic growth phenotype without pldA indicated that defective lipid homeostasis in the yejM mutant compromises outer membrane lipid asymmetry and permeability barrier to allow enterobactin intake, and that YejM has additional roles other than transporting cardiolipin.IMPORTANCE The work presented here describes a positive genetic selection strategy for isolating mutations that destabilize the outer membrane permeability barrier of E. coli Given the importance of the outer membrane in restricting the entry of antibiotics, characterization of the genes and their products that affect outer membrane integrity will enhance the understanding of bacterial membranes and the development of strategies to bypass the outer membrane barrier for improved drug efficacy.
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Lin Y, Zheng L, Bogdanov M. Measurement of Lysophospholipid Transport Across the Membrane Using Escherichia coli Spheroplasts. Methods Mol Biol 2019; 1949:165-180. [PMID: 30790256 DOI: 10.1007/978-1-4939-9136-5_13] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
In the inner membrane of Gram-negative bacteria lysophospholipid transporter (LplT) and the bifunctional acyl-acyl carrier protein (ACP) synthetase/2-acylglycerolphosphoethanolamine acyltransferase (Aas) form a glycerophospholipid remodeling system, which is capable of facilitating rapid retrograde translocation of lyso forms of phosphatidylethanolamine, phosphatidylglycerol, and cardiolipin across the cytoplasmic membrane. This coupled remodeling enzyme tandem provides an effective method for the measurement of substrate specificity of the lipid regeneration and lysophospholipid transport per se across the membrane. This chapter describes two distinct but complementary methods for the measurement of lysophospholipid transport across membrane using Escherichia coli spheroplasts.
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Affiliation(s)
- Yibin Lin
- Division of Infectious Diseases, Department of Pediatrics, Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA.
| | - Lei Zheng
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA.,Department of Biochemistry and Biotechnology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
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Li Z, Ye X, Liu M, Xia C, Zhang L, Luo X, Wang T, Chen Y, Zhao Y, Qiao Y, Huang Y, Cao H, Gu X, Fan J, Cui Z, Zhang Z. A novel outer membrane β-1,6-glucanase is deployed in the predation of fungi by myxobacteria. ISME JOURNAL 2019; 13:2223-2235. [PMID: 31065029 DOI: 10.1038/s41396-019-0424-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/03/2019] [Accepted: 04/08/2019] [Indexed: 12/20/2022]
Abstract
Myxobacterial predation on bacteria has been investigated for several decades. However, their predation on fungi has received less attention. Here, we show that a novel outer membrane β-1,6-glucanase GluM from Corallococcus sp. strain EGB is essential for initial sensing and efficient decomposition of fungi during predation. GluM belongs to an unstudied family of outer membrane β-barrel proteins with potent specific activity up to 24,000 U/mg, whose homologs extensively exist in myxobacteria. GluM was able to digest fungal cell walls efficiently and restrict Magnaporthe oryzae infection of rice plants. Genetic complementation with gluM restored the fungal predation ability of Myxococcus xanthus CL1001, which was abolished by the disruption of gluM homolog oar. The inability to prey on fungi with cell walls that lack β-1,6-glucans indicates that β-1,6-glucans are targeted by GluM. Our results demonstrate that GluM confers myxobacteria with the ability to feed on fungi, and provide new insights for understanding predator-prey interactions. Considering the attack mode of GluM, we suggest that β-1,6-glucan is a promising target for the development of novel broad-spectrum antifungal agents.
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Affiliation(s)
- Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, China
| | - Muxing Liu
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects of Chinese Ministry of Agriculture, College of Plant Protection, Nanjing Agriculture University, 210095, Nanjing, China
| | - Chengyao Xia
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, China
| | - Lei Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, China
| | - Xue Luo
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, China
| | - Ting Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, China
| | - Yue Chen
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, 410125, Changsha, China
| | - Yuqiang Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, China
| | - Yan Qiao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, China
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, China
| | - Xiangyang Gu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, China
| | - Jiaqin Fan
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects of Chinese Ministry of Agriculture, College of Plant Protection, Nanjing Agriculture University, 210095, Nanjing, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, China.
| | - Zhengguang Zhang
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects of Chinese Ministry of Agriculture, College of Plant Protection, Nanjing Agriculture University, 210095, Nanjing, China.
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Izzo L, Matrella S, Mella M, Benvenuto G, Vigliotta G. Escherichia coli as a Model for the Description of the Antimicrobial Mechanism of a Cationic Polymer Surface: Cellular Target and Bacterial Contrast Response. ACS APPLIED MATERIALS & INTERFACES 2019; 11:15332-15343. [PMID: 30950609 DOI: 10.1021/acsami.9b02903] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this study, we use Escherichia coli as a model to investigate the antimicrobial mechanism of a film made of a copolymer based on monomethylether poly(ethylene glycol), methyl methacrylate, and 2-dimethyl(aminoethyl) methacrylate, whose surface is active towards Gram-negative and Gram-positive bacteria. The polymer contains not quaternized amino groups that can generate a charged surface by protonation when in contact with water. For this purpose, we adopted a dual strategy based on the analysis of cell damage caused by contact with the polymer surface and on the evaluation of the cell response to the surface toxic action. The lithic effect on the protoplasts of E. coli showed that the polymer surface can affect the structure of cytoplasmic membranes, while assays of calcein leakage from large unilamellar vesicles at different phospholipid compositions indicated that action on membranes does not need a functionally active cell. On the other hand, the significant increase in sensitivity to actinomycin D demonstrates that the polymer interferes also with the structure of the outer membrane, modifying its permeability. The study on gene expression, based on the analysis of the transcripts in a temporal window where the contact with the polymer is not lethal and the damage is reversible, showed that some key genes of the synthesis and maintenance of the outer membrane structure ( fabR, fadR, fabA, waaA, waaC, kdsA, pldA, and pagP), as well as regulators of cellular response to oxidative stress ( soxS), are more expressed when bacteria are exposed to the polymer surface. All together these results identified the outer membrane as the main cellular target of the antimicrobial surface and indicated a specific cellular response to damage, providing more information on the antimicrobial mechanism. In this perspective, data reported here could play a pivotal role in a microbial growth control strategy based not only on the structural improvements of the materials but also on the possibility of intervening on the cellular pathways involved in the contrast reaction to these and other polymers with similar mechanisms.
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Affiliation(s)
- Lorella Izzo
- Dipartimento di Biotecnologie e Scienze della Vita , Università degli Studi dell'Insubria , Via J.H. Dunant, 3 , 21100 Varese , Italy
| | - Simona Matrella
- Dipartimento di Chimica e Biologia "A. Zambelli" , Università degli Studi di Salerno , Via Giovanni Paolo II, 132 , 84084 Fisciano , Salerno , Italy
| | - Massimo Mella
- Dipartimento di Scienza ed Alta Tecnologia , Università degli Studi dell'Insubria , via Valleggio, 11 , 22100 Como , Italy
| | | | - Giovanni Vigliotta
- Dipartimento di Chimica e Biologia "A. Zambelli" , Università degli Studi di Salerno , Via Giovanni Paolo II, 132 , 84084 Fisciano , Salerno , Italy
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Lo Sciuto A, Martorana AM, Fernández-Piñar R, Mancone C, Polissi A, Imperi F. Pseudomonas aeruginosa LptE is crucial for LptD assembly, cell envelope integrity, antibiotic resistance and virulence. Virulence 2019; 9:1718-1733. [PMID: 30354941 PMCID: PMC7204523 DOI: 10.1080/21505594.2018.1537730] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Lipopolysaccharide (LPS) is an essential structural component of the outer membrane (OM) of most Gram-negative bacteria. In the model organism Escherichia coli, LPS transport to the OM requires seven essential proteins (LptABCDEFG) that form a continuous bridge across the cell envelope. In Pseudomonas aeruginosa the recently-demonstrated essentiality of LptD and LptH, the P. aeruginosa LptA homologue, confirmed the crucial role of the Lpt system and, thus, of LPS in OM biogenesis in this species. Surprisingly, independent high-throughput transposon mutagenesis studies identified viable P. aeruginosa insertion mutants in the lptE gene, suggesting that it might be dispensable for bacterial growth. To test this hypothesis, we generated an lptE conditional mutant in P. aeruginosa PAO1. LptE depletion only slightly impairs P. aeruginosa growth in vitro. Conversely, LptE is important for cell envelope stability, antibiotic resistance and virulence in an insect model. Interestingly, the maturation and OM localization of LPS is only marginally affected in LptE-depleted cells, while the levels of the OM component LptD are strongly reduced. This suggests that P. aeruginosa LptE might not be directly involved in LPS transport, although it is clearly essential for the maturation and/or stability of LptD. While poor functionality of LptD caused by LptE depletion is somehow tolerated by P. aeruginosa, this has a high cost in terms of cell integrity, drug resistance and virulence, highlighting LptE function(s) as an interesting target to weaken P. aeruginosa defenses and reduce its infectivity.
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Affiliation(s)
- Alessandra Lo Sciuto
- a Department of Biology and Biotechnology Charles Darwin , Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti , Rome , Italy
| | - Alessandra M Martorana
- b Department of Pharmacological and Biomolecular Sciences , University of Milan , Milan , Italy
| | - Regina Fernández-Piñar
- a Department of Biology and Biotechnology Charles Darwin , Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti , Rome , Italy
| | - Carmine Mancone
- c Department of Cellular Biotechnologies and Haematology , Sapienza University of Rome , Rome , Italy
| | - Alessandra Polissi
- b Department of Pharmacological and Biomolecular Sciences , University of Milan , Milan , Italy
| | - Francesco Imperi
- a Department of Biology and Biotechnology Charles Darwin , Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti , Rome , Italy
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Baarda BI, Zielke RA, Le Van A, Jerse AE, Sikora AE. Neisseria gonorrhoeae MlaA influences gonococcal virulence and membrane vesicle production. PLoS Pathog 2019; 15:e1007385. [PMID: 30845186 PMCID: PMC6424457 DOI: 10.1371/journal.ppat.1007385] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 03/19/2019] [Accepted: 02/11/2019] [Indexed: 02/07/2023] Open
Abstract
The six-component maintenance of lipid asymmetry (Mla) system is responsible for retrograde transport of phospholipids, ensuring the barrier function of the Gram-negative cell envelope. Located within the outer membrane, MlaA (VacJ) acts as a channel to shuttle phospholipids from the outer leaflet. We identified Neisseria gonorrhoeae MlaA (ngo2121) during high-throughput proteomic mining for potential therapeutic targets against this medically important human pathogen. Our follow-up phenotypic microarrays revealed that lack of MlaA results in a complex sensitivity phenome. Herein we focused on MlaA function in cell envelope biogenesis and pathogenesis. We demonstrate the existence of two MlaA classes among 21 bacterial species, characterized by the presence or lack of a lipoprotein signal peptide. Purified truncated N. gonorrhoeae MlaA elicited antibodies that cross-reacted with a panel of different Neisseria. Little is known about MlaA expression; we provide the first evidence that MlaA levels increase in stationary phase and under anaerobiosis but decrease during iron starvation. Lack of MlaA resulted in higher cell counts during conditions mimicking different host niches; however, it also significantly decreased colony size. Antimicrobial peptides such as polymyxin B exacerbated the size difference while human defensin was detrimental to mutant viability. Consistent with the proposed role of MlaA in vesicle biogenesis, the ΔmlaA mutant released 1.7-fold more membrane vesicles. Comparative proteomics of cell envelopes and native membrane vesicles derived from ΔmlaA and wild type bacteria revealed enrichment of TadA–which recodes proteins through mRNA editing–as well as increased levels of adhesins and virulence factors. MlaA-deficient gonococci significantly outcompeted (up to 16-fold) wild-type bacteria in the murine lower genital tract, suggesting the growth advantage or increased expression of virulence factors afforded by inactivation of mlaA is advantageous in vivo. Based on these results, we propose N. gonorrhoeae restricts MlaA levels to modulate cell envelope homeostasis and fine-tune virulence. The Gram-negative outer membrane is a formidable barrier, primarily because of its asymmetric composition. A layer of lipopolysaccharide is exposed to the external environment and phospholipids are on the internal face of the outer membrane. MlaA is part of a bacterial system that prevents phospholipid accumulation within the lipopolysaccharide layer. If MlaA is removed, membrane asymmetry is disrupted and bacteria become more vulnerable to certain antimicrobials. Neisseria gonorrhoeae causes millions of infections worldwide annually. A growing number are resistant to available antibiotics. Improving our understanding of gonococcal pathogenicity and basic biological processes is required to facilitate the discovery of new weapons against gonorrhea. We investigated the role of MlaA in N. gonorrhoeae and found that when MlaA was absent, bacteria were more sensitive to antibiotics and human defensins. However, the mutant bacteria produced more membrane vesicles–packages of proteins wrapped in membrane material. Mutant vesicles and cell envelopes were enriched in proteins that contribute to disease. These alterations significantly increased mutant fitness during experimental infection of the female mouse genital tract. Our results provide new insights into the processes N. gonorrhoeae uses to fine-tune its ability to stay fit in the hostile environment of the genital tract.
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Affiliation(s)
- Benjamin I. Baarda
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
| | - Ryszard A. Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
| | - Adriana Le Van
- Department of Microbiology and Immunology, F. Edward Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Ann E. Jerse
- Department of Microbiology and Immunology, F. Edward Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America
- * E-mail:
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Abstract
Gram-negative bacteria have an outer membrane that is positioned at the frontline of the cell's interaction with the environment and that serves as a barrier against noxious molecules including many antibiotics. This protective function mainly relies on lipopolysaccharide, a complex glycolipid located in the outer leaflet of the outer membrane. In this chapter we will first summarize lipopolysaccharide structure, functions and biosynthetic pathway and then we will discuss how it is transported and assembled to the cell surface. This is a remarkably complex process, as amphipathic lipopolysaccharide molecules must traverse three different cellular compartments to reach their final destination.
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Comparative Analysis of TM and Cytoplasmic β-barrel Conformations Using Joint Descriptor. Sci Rep 2018; 8:14185. [PMID: 30242187 PMCID: PMC6155101 DOI: 10.1038/s41598-018-32136-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/16/2018] [Indexed: 01/01/2023] Open
Abstract
Macroscopic descriptors have become valuable as coarse-grained features of complex proteins and are complementary to microscopic descriptors. Proteins macroscopic geometric features provide effective clues in the quantification of distant similarity and close dissimilarity searches for structural comparisons. In this study, we performed a systematic comparison of β-barrels, one of the important classes of protein folds in various transmembrane (TM) proteins against cytoplasmic barrels to estimate the conformational features using a joint-based descriptor. The approach uses joint coordinates and dihedral angles (β and γ) based on the β-strand joints and loops to determine the arrangements and propensities at the local and global levels. We then confirmed that there is a clear preference in the overall β and γ distribution, arrangements of β-strands and loops, signature patterns, and the number of strand effects between TM and cytoplasmic β-barrel geometries. As a robust and simple approach, we determine that the joint-based descriptor could provide a reliable static structural comparison aimed at macroscopic level between complex protein conformations.
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38
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Abstract
Biofilms are often described as protective shelters that preserve bacteria from hostile surroundings. However, biofilm bacteria are also exposed to various stresses and need to adjust to the heterogeneous physicochemical conditions prevailing within biofilms. In Gram-negative bacteria, such adaptations can result in modifications of the lipopolysaccharide, a major component of the outer membrane characterized by a highly dynamic structure responding to environmental changes. We previously showed that Gram-negative biofilm bacteria undergo an increase in lipid A palmitoylation mediated by the PagP enzyme, contributing to increased resistance to host defenses. Here we describe a regulatory pathway leading to transcriptional induction of pagP in response to specific conditions created in the biofilm environment. We show that pagP expression is induced via the Rcs envelope stress system independently of the Rcs phosphorelay cascade and that it requires the GadE auxiliary regulator. Moreover, we identify an increase in osmolarity (i.e., ionic stress) as a signal able to induce pagP expression in an RcsB-dependent manner. Consistently, we show that the biofilm is a hyperosmolar environment and that RcsB-dependent pagP induction can be dampened in the presence of an osmoprotectant. These results provide new insights into the adaptive mechanisms of bacterial differentiation in biofilm.IMPORTANCE The development of the dense bacterial communities called biofilms creates a highly heterogeneous environment in which bacteria are subjected to a variety of physicochemical stresses. We investigated the mechanisms of a widespread and biofilm-associated chemical modification of the lipopolysaccharide (LPS), a major component of all Gram-negative bacterial outer membranes. This modification corresponds to the incorporation, mediated by the enzyme PagP, of a palmitate chain into lipid A (palmitoylation) that reduces bacterial recognition by host immune responses. Using biochemical and genetic approaches, we demonstrate that a significant part of biofilm-associated lipid A palmitoylation is triggered upon induction of pagP transcription by the hyperosmolar biofilm environment. pagP induction is regulated by RcsB, the response regulator of the Rcs stress response pathway, and is not observed under planktonic conditions. Our report provides new insights into how physiological adaptations to local biofilm microenvironments can contribute to decreases in susceptibility to antimicrobial agents and host immune defenses.
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Stead CM, Cockrell DC, Beare PA, Miller HE, Heinzen RA. A Coxiella burnetii phospholipase A homolog pldA is required for optimal growth in macrophages and developmental form lipid remodeling. BMC Microbiol 2018; 18:33. [PMID: 29661138 PMCID: PMC5902883 DOI: 10.1186/s12866-018-1181-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/09/2018] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Many gram-negative bacteria produce an outer membrane phospholipase A (PldA) that plays an important role in outer membrane function and is associated with virulence. RESULTS In the current study, we characterized a pldA mutant of Coxiella burnetii, an intracellular gram-negative pathogen and the agent of human Q fever. The C. burnetti pldA open reading frame directs synthesis of a protein with conserved PldA active site residues. A C. burnetii ΔpldA deletion mutant had a significant growth defect in THP-1 macrophages, but not axenic medium, that was rescued by complementation. Thin layer chromatography was employed to assess whether pldA plays a role in remodeling membrane lipids during C. burnetii morphological differentiation. Extracted lipids were analyzed from replicating, logarithmic phase large cell variants (LCVs), non-replicating, stationary phase small cell variants (SCVs), and a mixture of LCVs and SCVs. Similar to Escherichia coli, all three forms contained cardiolipin (CL), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). However, PE and PG were present in lower quantities in the SCV while three additional lipid species were present in higher quantities. Co-migration with standards tentatively identified two of the three SCV-enriched lipids as lyso-phosphatidylethanolamine, a breakdown product of PE, and free fatty acids, which are generally toxic to bacteria. Developmental form lipid modifications required the activity of PldA. CONCLUSIONS Collectively, these results indicate developmentally-regulated lipid synthesis by C. burnetii contributes to colonization of macrophages and may contribute to the environmental stability and the distinct biological properties of the SCV.
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Affiliation(s)
- Christopher M. Stead
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana USA
- Department of Chemistry, New Mexico Highlands University, Las Vegas, New Mexico USA
| | - Diane C. Cockrell
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana USA
| | - Paul A. Beare
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana USA
| | - Heather E. Miller
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana USA
| | - Robert A. Heinzen
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana USA
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Abstract
The outer membrane (OM) bilayer of Gram-negative bacteria is biologically unique in its asymmetrical organization of lipids, with an inner leaflet composed of glycerophospholipids (PLs) and a surface-exposed outer leaflet composed of lipopolysaccharide (LPS). This lipid organization is integral to the OM’s barrier properties. Perturbations of the outer leaflet by antimicrobial peptides or defects in LPS biosynthesis or transport to the OM cause a compensatory flipping of PLs to the outer leaflet. As a result, lipid asymmetry is disrupted and OM integrity is compromised. Recently, we identified an Escherichia coli mutant that exhibits aberrant accumulation of surface PLs accompanied by a cellular increase in LPS production. Remarkably, the observed hyperproduction of LPS is PldA dependent. Here we provide evidence that the fatty acids generated by PldA at the OM are transported into the cytoplasm and simultaneously activated by thioesterification to coenzyme A (CoA) by FadD. The acyl-CoAs produced ultimately inhibit LpxC degradation by FtsH. The increased levels of LpxC, the enzyme that catalyzes the first committed step in LPS biosynthesis, increases the amount of LPS produced. Our data suggest that PldA acts as a sensor for lipid asymmetry in the OM. PldA protects the OM barrier by both degrading mislocalized PLs and generating lipid second messengers that enable long-distance signaling that prompts the cell to restore homeostasis at a distant organelle. The outer membrane of Gram-negative bacteria is an effective permeability barrier that protects the cell from toxic agents, including antibiotics. Barrier defects are often manifested by phospholipids present in the outer leaflet of this membrane that take up space normally occupied by lipopolysaccharide. We have discovered a signaling mechanism that operates across the entire cell envelope used by the cell to detect these outer membrane defects. A phospholipase, PldA, that functions to degrade these mislocalized phospholipids has a second, equally important function as a sensor. The fatty acids produced by hydrolysis of the phospholipids act as second messengers to signal the cell that more lipopolysaccharide is needed. These fatty acids diffuse across the periplasm and are transported into the cytoplasm by a process that attaches coenzyme A. The acyl-CoA molecule produces signals to inhibit the degradation of the critical enzyme LpxC by the ATP-dependent protease FtsH, increasing lipopolysaccharide production.
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41
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Abstract
[Formula: see text]-Barrel membrane proteins ([Formula: see text]MPs) play important roles, but knowledge of their structures is limited. We have developed a method to predict their 3D structures. We predict strand registers and construct transmembrane (TM) domains of [Formula: see text]MPs accurately, including proteins for which no prediction has been attempted before. Our method also accurately predicts structures from protein families with a limited number of sequences and proteins with novel folds. An average main-chain rmsd of 3.48 Å is achieved between predicted and experimentally resolved structures of TM domains, which is a significant improvement ([Formula: see text]3 Å) over a recent study. For [Formula: see text]MPs with NMR structures, the deviation between predictions and experimentally solved structures is similar to the difference among the NMR structures, indicating excellent prediction accuracy. Moreover, we can now accurately model the extended [Formula: see text]-barrels and loops in non-TM domains, increasing the overall coverage of structure prediction by [Formula: see text]%. Our method is general and can be applied to genome-wide structural prediction of [Formula: see text]MPs.
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42
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Powers MJ, Trent MS. Expanding the paradigm for the outer membrane: Acinetobacter baumannii in the absence of endotoxin. Mol Microbiol 2017; 107:47-56. [PMID: 29114953 DOI: 10.1111/mmi.13872] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2017] [Indexed: 12/30/2022]
Abstract
Asymmetry in the outer membrane has long defined the cell envelope of Gram-negative bacteria. This asymmetry, with lipopolysaccharide (LPS) or lipooligosaccharide (LOS) exclusively in the outer leaflet of the membrane, establishes an impermeable barrier that protects the cell from a number of stressors in the environment. Work done over the past 5 years has shown that Acinetobacter baumannii has the remarkable capability to survive with inactivated production of lipid A biosynthesis and the absence of LOS in its outer membrane. The implications of LOS-deficient A. baumannii are far-reaching - from impacts on cell envelope biogenesis and maintenance, bacterial physiology, antibiotic resistance and virulence. This review examines recent work that has contributed to our understanding of LOS-deficiency and compares it to studies done on Neisseria meningitidis and Moraxella catarrhalis; the two other organisms with this capability.
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Affiliation(s)
- Matthew Joseph Powers
- Department of Infectious Diseases, University of Georgia, 510 DW Brooks Drive, Athens, GA 30602, USA.,Department of Microbiology, University of Georgia, Athens, GA, USA
| | - M Stephen Trent
- Department of Infectious Diseases, University of Georgia, 510 DW Brooks Drive, Athens, GA 30602, USA
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43
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Chaturvedi D, Mahalakshmi R. Transmembrane β-barrels: Evolution, folding and energetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2467-2482. [PMID: 28943271 DOI: 10.1016/j.bbamem.2017.09.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/16/2017] [Accepted: 09/19/2017] [Indexed: 12/23/2022]
Abstract
The biogenesis of transmembrane β-barrels (outer membrane proteins, or OMPs) is an elaborate multistep orchestration of the nascent polypeptide with translocases, barrel assembly machinery, and helper chaperone proteins. Several theories exist that describe the mechanism of chaperone-assisted OMP assembly in vivo and unassisted (spontaneous) folding in vitro. Structurally, OMPs of bacterial origin possess even-numbered strands, while mitochondrial β-barrels are even- and odd-stranded. Several underlying similarities between prokaryotic and eukaryotic β-barrels and their folding machinery are known; yet, the link in their evolutionary origin is unclear. While OMPs exhibit diversity in sequence and function, they share similar biophysical attributes and structure. Similarly, it is important to understand the intricate OMP assembly mechanism, particularly in eukaryotic β-barrels that have evolved to perform more complex functions. Here, we deliberate known facets of β-barrel evolution, folding, and stability, and attempt to highlight outstanding questions in β-barrel biogenesis and proteostasis.
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Affiliation(s)
- Deepti Chaturvedi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India.
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India.
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Vollan HS, Tannæs T, Caugant DA, Vriend G, Bukholm G. Outer membrane phospholipase A's roles in Helicobacter pylori acid adaptation. Gut Pathog 2017; 9:36. [PMID: 28616083 PMCID: PMC5469174 DOI: 10.1186/s13099-017-0184-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/08/2017] [Indexed: 02/08/2023] Open
Abstract
Background The pH of the human gastric mucosa varies around 2.5 so that only bacteria with strong acidic stress tolerance can colonize it. The ulcer causing Helicobacter pylori thrives in the gastric mucosa. We analyse the roles of the key outer membrane protein OMPLA in its roles in acid tolerance. Results The homology model of Helicobacter pylori outer membrane phospholipase A (OMPLA) reveals a twelve stranded β-barrel with a pore that allows molecules to pass with a diameter up to 4 Å. Structure based multiple sequence alignments revealed the functional roles of many amino acids, and led to the suggestion that OMPLA has multiple functions. Besides its role as phospholipase it lets urea enter and ammonium exit the periplasm. Combined with an extensive literature study, our work leads to a comprehensive model for H. pylori’s acid tolerance. This model is based on the conversion of urea into ammonium, and it includes multiple roles for OMPLA and involves two hitherto little studied membrane channels in the OMPLA operon. Conclusion The three-dimensional model of OMPLA predicts a transmembrane pore that can aid H. pylori’s acid tolerance through urea influx and ammonium efflux. After urea passes through OMPLA into the periplasm, it passes through the pH-gated inner membrane channel UreI into the cytoplasm where urease hydrolyses it into NH3 and CO2. Most of the NH3 becomes NH4+ that is likely to need an inner membrane channel to reach the periplasm. Two genes that are co-regulated with OMPLA in gastric Helicobacter operons could aid this transport. The NH4+ that might leave the cell through the OMPLA pore has been implicated in H. pylor’s pathogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s13099-017-0184-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hilde S Vollan
- Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital and University of Oslo, PO box 28, 1478 Lørenskog, Norway.,Norwegian Institute of Public Health, Box 4404, Nydalen, 0403 Oslo, Norway
| | - Tone Tannæs
- Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital and University of Oslo, PO box 28, 1478 Lørenskog, Norway
| | - Dominique A Caugant
- Norwegian Institute of Public Health, Box 4404, Nydalen, 0403 Oslo, Norway.,Department of Community Medicine and Global Health, Faculty of Medicine, University of Oslo, P.O. Box 1130, Blindern, 0318 Oslo, Norway
| | - Gert Vriend
- CMBI, Radboudumc, 6525 GA Nijmegen, The Netherlands
| | - Geir Bukholm
- Norwegian Institute of Public Health, Box 4404, Nydalen, 0403 Oslo, Norway.,Norwegian University of Life Sciences, PO Box 5003, 1430 Ås, Norway
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45
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Bhat IA, Jain R, Siddiqui MM, Saini DK, Mukherjee PS. Water-Soluble Pd 8L 4 Self-assembled Molecular Barrel as an Aqueous Carrier for Hydrophobic Curcumin. Inorg Chem 2017; 56:5352-5360. [PMID: 28394128 DOI: 10.1021/acs.inorgchem.7b00449] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A tetrafacial water-soluble molecular barrel (1) was synthesized by coordination driven self-assembly of a symmetrical tetrapyridyl donor (L) with a cis-blocked 90° acceptor [cis-(en)Pd(NO3)2] (en = ethane-1,2-diamine). The open barrel structure of (1) was confirmed by single crystal X-ray diffraction. The presence of a hydrophobic cavity with large windows makes it an ideal candidate for encapsulation and carrying hydrophobic drug like curcumin in an aqueous medium. The barrel (1) encapsulates curcumin inside its molecular cavity and protects highly photosensitive curcumin from photodegradation. The photostability of encapsulated curcumin is due to the absorption of a high proportion of the incident photons by the aromatic walls of 1 with a high absorption cross-sectional area, which helps the walls to shield the guest even against sunlight/UV radiations. As compared to free curcumin in water, we noticed a significant increase in solubility as well as cellular uptake of curcumin upon encapsulation inside the water-soluble molecular barrel (1) in aqueous medium. Fluorescence imaging confirmed that curcumin was delivered into HeLa cancer cells by the aqueous barrel (1) with the retention of its potential anticancer activity. While free curcumin is inactive toward cancer cells in aqueous medium at room temperature due to negligible solubility, the determined IC50 value of ∼14 μM for curcumin in aqueous medium in the presence of the barrel (1) reflects the efficiency of the barrel as a potential curcumin carrier in aqueous medium without any other additives. Thus, two major challenges of increasing the bioavailability and stability of curcumin in aqueous medium even in the presence of UV light have been addressed by using a new supramolecular water-soluble barrel (1) as a drug carrier.
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Affiliation(s)
- Imtiyaz Ahmad Bhat
- Department of Inorganic and Physical Chemistry, Indian Institute of Science , Bangalore 560012, India
| | - Ruchi Jain
- Department of Molecular Reproduction, Development and Genetics and Centre for Biosystems Science and Engineering, Indian Institute of Science , Bangalore 560012, India
| | - Mujahuddin M Siddiqui
- Department of Inorganic and Physical Chemistry, Indian Institute of Science , Bangalore 560012, India
| | - Deepak K Saini
- Department of Molecular Reproduction, Development and Genetics and Centre for Biosystems Science and Engineering, Indian Institute of Science , Bangalore 560012, India
| | - Partha Sarathi Mukherjee
- Department of Inorganic and Physical Chemistry, Indian Institute of Science , Bangalore 560012, India
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46
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Real-time Visualization of Phospholipid Degradation by Outer Membrane Phospholipase A using High-Speed Atomic Force Microscopy. J Mol Biol 2017; 429:977-986. [DOI: 10.1016/j.jmb.2017.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/28/2017] [Accepted: 03/01/2017] [Indexed: 11/17/2022]
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47
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Dufrisne MB, Petrou VI, Clarke OB, Mancia F. Structural basis for catalysis at the membrane-water interface. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1368-1385. [PMID: 27913292 DOI: 10.1016/j.bbalip.2016.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 11/27/2022]
Abstract
The membrane-water interface forms a uniquely heterogeneous and geometrically constrained environment for enzymatic catalysis. Integral membrane enzymes sample three environments - the uniformly hydrophobic interior of the membrane, the aqueous extramembrane region, and the fuzzy, amphipathic interfacial region formed by the tightly packed headgroups of the components of the lipid bilayer. Depending on the nature of the substrates and the location of the site of chemical modification, catalysis may occur in each of these environments. The availability of structural information for alpha-helical enzyme families from each of these classes, as well as several beta-barrel enzymes from the bacterial outer membrane, has allowed us to review here the different ways in which each enzyme fold has adapted to the nature of the substrates, products, and the unique environment of the membrane. Our focus here is on enzymes that process lipidic substrates. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
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Affiliation(s)
- Meagan Belcher Dufrisne
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Vasileios I Petrou
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Oliver B Clarke
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.
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48
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Sperandeo P, Martorana AM, Polissi A. Lipopolysaccharide biogenesis and transport at the outer membrane of Gram-negative bacteria. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1451-1460. [PMID: 27760389 DOI: 10.1016/j.bbalip.2016.10.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 01/10/2023]
Abstract
The outer membrane (OM) of Gram-negative bacteria is an asymmetric lipid bilayer containing a unique glycolipid, lipopolysaccharide (LPS) in its outer leaflet. LPS molecules confer to the OM peculiar permeability barrier properties enabling Gram-negative bacteria to exclude many toxic compounds, including clinically useful antibiotics, and to survive harsh environments. Transport of LPS poses several problems to the cells due to the amphipatic nature of this molecule. In this review we summarize the current knowledge on the LPS transport machinery, discuss the challenges associated with this process and present the solutions that bacterial cells have evolved to address the problem of LPS transport and assembly at the cell surface. Finally, we discuss how knowledge on LPS biogenesis can be translated for the development of novel antimicrobial therapies. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
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Affiliation(s)
- Paola Sperandeo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy.
| | - Alessandra M Martorana
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Alessandra Polissi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy.
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49
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Wang X, Jiang F, Zheng J, Chen L, Dong J, Sun L, Zhu Y, Liu B, Yang J, Yang G, Jin Q. The outer membrane phospholipase A is essential for membrane integrity and type III secretion in Shigella flexneri. Open Biol 2016; 6:rsob.160073. [PMID: 27655730 PMCID: PMC5043575 DOI: 10.1098/rsob.160073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 08/31/2016] [Indexed: 12/11/2022] Open
Abstract
Outer membrane phospholipase A (OMPLA) is an enzyme located in the outer membrane of Gram-negative bacteria. OMPLA exhibits broad substrate specificity, and some of its substrates are located in the cellular envelope. Generally, the enzymatic activity can only be induced by perturbation of the cell envelope integrity through diverse methods. Although OMPLA has been thoroughly studied as a membrane protein in Escherichia coli and is constitutively expressed in many other bacterial pathogens, little is known regarding the functions of OMPLA during the process of bacterial infection. In this study, the proteomic and transcriptomic data indicated that OMPLA in Shigella flexneri, termed PldA, both stabilizes the bacterial membrane and is involved in bacterial infection under ordinary culture conditions. A series of physiological assays substantiated the disorganization of the bacterial outer membrane and the periplasmic space in the ΔpldA mutant strain. Furthermore, the ΔpldA mutant strain showed decreased levels of type III secretion system expression, contributing to the reduced internalization efficiency in host cells. The results of this study support that PldA, which is widespread across Gram-negative bacteria, is an important factor for the bacterial life cycle, particularly in human pathogens.
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Affiliation(s)
- Xia Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Feng Jiang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Jianhua Zheng
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Lihong Chen
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Jie Dong
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Lilian Sun
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Yafang Zhu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Bo Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Jian Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Guowei Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
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Iyer BR, Mahalakshmi R. Distinct Structural Elements Govern the Folding, Stability, and Catalysis in the Outer Membrane Enzyme PagP. Biochemistry 2016; 55:4960-70. [PMID: 27525547 DOI: 10.1021/acs.biochem.6b00678] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The outer membrane enzyme PagP is indispensable for lipid A palmitoylation in Gram-negative bacteria and has been implicated in resistance to host immune defenses. PagP possesses an unusual structure for an integral membrane protein, with a highly dynamic barrel domain that is tilted with respect to the membrane normal. In addition, it contains an N-terminal amphipathic helix. Recent functional and structural studies have shown that these molecular factors are critical for PagP to carry out its function in the challenging environment of the bacterial outer membrane. However, the precise contributions of the N-helix to folding and stability and residues that can influence catalytic rates remain to be addressed. Here, we identify a sequence-dependent stabilizing role for the N-terminal helix of PagP in the measured thermodynamic stability of the barrel. Using chimeric barrel sequences, we show that the Escherichia coli PagP N-terminal helix confers 2-fold greater stability to the Salmonella typhimurium barrel. Further, we find that the W78F substitution in S. typhimurium causes a nearly 20-fold increase in the specific activity in vitro for the phospholipase reaction, compared to that of E. coli PagP. Here, phenylalanine serves as a key regulator of catalysis, possibly by increasing the reaction rate. Through coevolution analysis, we detect an interaction network between seemingly unrelated segments of this membrane protein. Exchanging the structural and functional features between homologous PagP enzymes from E. coli and S. typhimurium has provided us with an understanding of the molecular factors governing PagP stability and function.
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Affiliation(s)
- Bharat Ramasubramanian Iyer
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research , Bhopal 462066, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research , Bhopal 462066, India
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