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Penner TV, Lorente Cobo N, Patel DT, Patel DH, Savchenko A, Brassinga AKC, Prehna G. Structural characterization of the Sel1-like repeat protein LceB from Legionella pneumophila. Protein Sci 2024; 33:e4889. [PMID: 38160319 PMCID: PMC10868440 DOI: 10.1002/pro.4889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Legionella are freshwater Gram-negative bacteria that in their normal environment infect protozoa. However, this adaptation also allows Legionella to infect human alveolar macrophages and cause pneumonia. Central to Legionella pathogenesis are more than 330 secreted effectors, of which there are nine core effectors that are conserved in all pathogenic species. Despite their importance, the biochemical function of several core effectors remains unclear. To address this, we have taken a structural approach to characterize the core effector of unknown function LceB, or Lpg1356, from Legionella pneumophila. Here, we solve an X-ray crystal structure of LceB using an AlphaFold model for molecular replacement. The experimental structure shows that LceB adopts a Sel1-like repeat (SLR) fold as predicted. However, the crystal structure captured multiple conformations of LceB, all of which differed from the AlphaFold model. A comparison of the predicted model and the experimental models suggests that LceB is highly flexible in solution. Additionally, the molecular analysis of LceB using its close structural homologs reveals sequence and structural motifs of known biochemical function. Specifically, LceB harbors a repeated KAAEQG motif that both stabilizes the SLR fold and is known to participate in protein-protein interactions with eukaryotic host proteins. We also observe that LceB forms several higher-order oligomers in solution. Overall, our results have revealed that LceB has conformational flexibility, self-associates, and contains a molecular surface for binding a target host-cell protein. Additionally, our data provides structural insights into the SLR family of proteins that remain poorly studied.
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Affiliation(s)
- Tiffany V Penner
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Neil Lorente Cobo
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Deepak T Patel
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Dhruvin H Patel
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | | | - Gerd Prehna
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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2
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Genetic Determinants of Salmonella Resistance to the Biofilm-Inhibitory Effects of a Synthetic 4-Oxazolidinone Analog. Appl Environ Microbiol 2020; 86:AEM.01120-20. [PMID: 32769186 DOI: 10.1128/aem.01120-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
Biofilms formed by Salmonella enterica are a frequent source of food supply contamination. Since biofilms are inherently resistant to disinfection, new agents capable of preventing biofilm formation are needed. Synthetic analogs of 4-oxazolidinone containing natural products have shown promise as antibiofilm compounds against Gram-positive bacteria. The purpose of our study was 2-fold: to establish the antibiofilm effects and mechanism of action of a synthetic 4-oxazolidinone analog (JJM-ox-3-70) and to establish mechanisms of resistance to this compound in Salmonella enterica serovar Typhimurium (S Typhimurium). JJM-ox-3-70 inhibited biofilm formation but had no effect on cell growth. The antibiofilm effects were linked to disruption of curli fimbriae and flagellar gene expression and alteration in swimming motility, suggesting an effect on multiple cellular processes. Using a 2-step screening approach of defined multigene and single-gene deletion mutant libraries, we identified 3 mutants that produced less biofilm in the presence of JJM-ox-3-70 than the isogenic WT, with phenotypes reversed by complementation in trans Genes responsible for S Typhimurium resistance to the compound included acrB, a component of the major drug efflux pump AcrAB-TolC, and two genes of unknown function (STM0437 and STM1292). The results of this study suggest that JJM-ox-3-70 inhibits biofilm formation by indirect inhibition of extracellular matrix production that may be linked to disruption of flagellar motility. Further work is needed to establish the role of the newly characterized genes as potential mechanisms of biofilm intrinsic antimicrobial resistance.IMPORTANCE Biofilms are resistant to killing by disinfectants and antimicrobials. S. enterica biofilms facilitate long-term host colonization and persistence in food processing environments. Synthetic analogs of 4-oxazolidinone natural products show promise as antibiofilm agents. Here, we show that a synthetic 4-oxazolidinone analog inhibits Salmonella biofilm through effects on both motility and biofilm matrix gene expression. Furthermore, we identify three genes that promote Salmonella resistance to the antibiofilm effects of the compound. This work provides insight into the mechanism of antibiofilm effects of a synthetic 4-oxazolidinone analog in Gram-negative bacteria and demonstrates new mechanisms of intrinsic antimicrobial resistance in Salmonella biofilms.
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3
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Vazquez-Lopez J, Navarro-Garcia F. In silico Analyses of Core Proteins and Putative Effector and Immunity Proteins for T6SS in Enterohemorrhagic E. coli. Front Cell Infect Microbiol 2020; 10:195. [PMID: 32432054 PMCID: PMC7216683 DOI: 10.3389/fcimb.2020.00195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/14/2020] [Indexed: 12/29/2022] Open
Abstract
Shiga-toxin-producing Escherichia coli (STEC) has become an important pathogen that can cause diarrhea, hemorrhagic colitis and hemolytic uremic syndrome (HUS) in humans. Recent reports show that the type VI secretion system (T6SS) from EHEC is required to produce infection in a murine model and its expression has been related to a higher prevalence of HUS. In this work, we use bioinformatics analyses to identify the core genes of the T6SS and compared the differences between these components among the two published genomes for EHEC O157:H7 strain EDL933. Prototype strain EDL933 was further compared with other O157:H7 genomes. Unlike other typical T6SS effectors found in E. coli, we identified that there are several rhs family genes in EHEC, which could serve as T6SS effectors. In-silico and PCR analyses of the differences between rhs genes in the two existing genomes, allowed us to determine that the most recently published genome is more reliable to study the rhs genes. Analyzing the putative tridimensional structure of Rhs proteins, as well as the motifs found in their C-terminal end, allowed us to predict their possible functions. A phylogenetic analysis showed that the orphan rhs genes are more closely related between them than the rhs genes belonging to vgrG islands and that they are divided into three clades. Analyses of the downstream region of the rhs genes for identifying hypothetical immunity proteins showed that every gene has an associated small ORF (129-609 nucleotides). These genes could serve as immunity proteins as they had several interaction motifs as well as structural homology with other known immunity proteins. Our findings highlight the relevance of the T6SS in EHEC as well as the possible function of the Rhs effectors of EHEC O157:H7 during pathogenesis and bacterial competition, and the identification of novel effectors for the T6SS using a structural approach.
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Affiliation(s)
- Jaime Vazquez-Lopez
- Department of Cell Biology, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Mexico City, Mexico
| | - Fernando Navarro-Garcia
- Department of Cell Biology, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Mexico City, Mexico
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Wen H, Geng Z, Gao Z, She Z, Dong Y. Characterization of the Pseudomonas aeruginosa T6SS PldB immunity proteins PA5086, PA5087 and PA5088 explains a novel stockpiling mechanism. Acta Crystallogr F Struct Biol Commun 2020; 76:222-227. [PMID: 32356524 PMCID: PMC7193511 DOI: 10.1107/s2053230x2000566x] [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] [Received: 02/10/2020] [Accepted: 04/22/2020] [Indexed: 11/10/2022] Open
Abstract
The bacterial type VI secretion system (T6SS) secretes many toxic effectors to gain advantage in interbacterial competition and for eukaryotic host infection. The cognate immunity proteins of these effectors protect bacteria from their own effectors. PldB is a T6SS trans-kingdom effector in Pseudomonas aeruginosa that can infect both prokaryotic and eukaryotic cells. Three proteins, PA5086, PA5087 and PA5088, are employed to suppress the toxicity of PldB-family proteins. The structures of PA5087 and PA5088 have previously been reported, but the identification of further distinctions between these immunity proteins is needed. Here, the crystal structure of PA5086 is reported at 1.90 Å resolution. A structural comparison of the three PldB immunity proteins showed vast divergences in their electrostatic potential surfaces. This interesting phenomenon provides an explanation of the stockpiling mechanism of T6SS immunity proteins.
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Affiliation(s)
- Haiying Wen
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Zhi Geng
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Zengqiang Gao
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Zhun She
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Yuhui Dong
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
- University of Chinese Academy of Sciences, People’s Republic of China
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5
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Klebsiella pneumoniae type VI secretion system-mediated microbial competition is PhoPQ controlled and reactive oxygen species dependent. PLoS Pathog 2020; 16:e1007969. [PMID: 32191774 PMCID: PMC7108748 DOI: 10.1371/journal.ppat.1007969] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 03/31/2020] [Accepted: 02/17/2020] [Indexed: 12/21/2022] Open
Abstract
Klebsiella pneumoniae is recognized as an urgent threat to human health due to the increasing isolation of multidrug resistant strains. Hypervirulent strains are a major concern due to their ability to cause life-threating infections in healthy hosts. The type VI secretion system (T6SS) is widely implicated in microbial antagonism, and it mediates interactions with host eukaryotic cells in some cases. In silico search for genes orthologous to T6SS component genes and T6SS effector genes across 700 K. pneumoniae genomes shows extensive diversity in T6SS genes across the K. pneumoniae species. Temperature, oxygen tension, pH, osmolarity, iron levels, and NaCl regulate the expression of the T6SS encoded by a hypervirulent K. pneumoniae strain. Polymyxins and human defensin 3 also increase the activity of the T6SS. A screen for regulators governing T6SS uncover the correlation between the transcription of the T6SS and the ability to kill E. coli prey. Whereas H-NS represses the T6SS, PhoPQ, PmrAB, Hfq, Fur, RpoS and RpoN positively regulate the T6SS. K. pneumoniae T6SS mediates intra and inter species bacterial competition. This antagonism is only evident when the prey possesses an active T6SS. The PhoPQ two component system governs the activation of K. pneumoniae T6SS in bacterial competitions. Mechanistically, PhoQ periplasmic domain, and the acid patch within, is essential to activate K. pneumoniae T6SS. Klebsiella T6SS also mediates anti-fungal competition. We have delineated the contribution of each of the individual VgrGs in microbial competition and identified VgrG4 as a T6SS effector. The DUF2345 domain of VgrG4 is sufficient to intoxicate bacteria and yeast. ROS generation mediates the antibacterial effects of VgrG4, and the antitoxin Sel1E protects against the toxic activity of VgrG4. Our findings provide a better understanding of the regulation of the T6SS in bacterial competitions, and place ROS as an early event in microbial competition. Klebsiella pneumoniae has been singled out as an “urgent threat to human health” due to extremely drug resistant strains. Numerous studies investigate the molecular mechanisms underlying antibiotic resistance in K. pneumoniae, while others dissect the virulence strategies of this pathogen. However, there is still limited knowledge on the fitness of Klebsiella in the environment, and, particularly, the competition of Klebsiella with other species. Here, we demonstrate that Klebsiella exploits the type VI secretion system (T6SS) nanoweapon to kill bacterial competitors and fungi. K. pneumoniae perceives T6SS attacks from bacterial competitors, resulting in retaliation against the aggressive cell. The perception of the attack involved the sensor PhoPQ and led to the up-regulation of the T6SS. We identified one of the toxins deployed by the T6SS to antagonize other microbes and revealed how Klebsiella protects itself from this toxin. Our findings provide a better understanding of the T6SS role in microbial competition and uncover new aspects on how bacteria regulate T6SS-mediated microbial antagonism.
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Brunkard JO, Xu M, Scarpin MR, Chatterjee S, Shemyakina EA, Goodman HM, Zambryski P. TOR dynamically regulates plant cell-cell transport. Proc Natl Acad Sci U S A 2020; 117:5049-5058. [PMID: 32051250 PMCID: PMC7060719 DOI: 10.1073/pnas.1919196117] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The coordinated redistribution of sugars from mature "source" leaves to developing "sink" leaves requires tight regulation of sugar transport between cells via plasmodesmata (PD). Although fundamental to plant physiology, the mechanisms that control PD transport and thereby support development of new leaves have remained elusive. From a forward genetic screen for altered PD transport, we discovered that the conserved eukaryotic glucose-TOR (TARGET OF RAPAMYCIN) metabolic signaling network restricts PD transport in leaves. Genetic approaches and chemical or physiological treatments to either promote or disrupt TOR activity demonstrate that glucose-activated TOR decreases PD transport in leaves. We further found that TOR is significantly more active in mature leaves photosynthesizing excess sugars than in young, growing leaves, and that this increase in TOR activity correlates with decreased rates of PD transport. We conclude that leaf cells regulate PD trafficking in response to changing carbohydrate availability monitored by the TOR pathway.
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Affiliation(s)
- Jacob O Brunkard
- Department of Plant and Microbial Biology, University of California, Berkeley CA 94720;
- Plant Gene Expression Center, US Department of Agriculture, Agricultural Research Service, Albany, CA 94710
- Innovative Genomics Institute, Berkeley, CA 94720
| | - Min Xu
- Department of Plant and Microbial Biology, University of California, Berkeley CA 94720
- Department of Biology, Northwest University, 710069 Xi'an, China
| | - M Regina Scarpin
- Department of Plant and Microbial Biology, University of California, Berkeley CA 94720
- Plant Gene Expression Center, US Department of Agriculture, Agricultural Research Service, Albany, CA 94710
| | - Snigdha Chatterjee
- Department of Plant and Microbial Biology, University of California, Berkeley CA 94720
- Plant Gene Expression Center, US Department of Agriculture, Agricultural Research Service, Albany, CA 94710
- Innovative Genomics Institute, Berkeley, CA 94720
| | - Elena A Shemyakina
- Department of Plant and Microbial Biology, University of California, Berkeley CA 94720
- Plant Gene Expression Center, US Department of Agriculture, Agricultural Research Service, Albany, CA 94710
| | - Howard M Goodman
- Department of Plant and Microbial Biology, University of California, Berkeley CA 94720
| | - Patricia Zambryski
- Department of Plant and Microbial Biology, University of California, Berkeley CA 94720;
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7
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Sakuma M, Nishikawa S, Inaba S, Nishigaki T, Kojima S, Homma M, Imada K. Structure of the periplasmic domain of SflA involved in spatial regulation of the flagellar biogenesis of Vibrio reveals a TPR/SLR-like fold. J Biochem 2019; 166:197-204. [PMID: 30989194 DOI: 10.1093/jb/mvz027] [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: 12/21/2018] [Accepted: 04/09/2019] [Indexed: 11/13/2022] Open
Abstract
Bacteria have evolved various types of flagellum, an organella for bacterial motility, to adapt to their habitat environments. The number and the spatial arrangement of the flagellum are precisely controlled to optimize performance of each type of the flagellar system. Vibrio alginolyticus has a single sheathed flagellum at the cell pole for swimming. SflA is a regulator protein to prevent peritrichous formation of the sheathed flagellum, and consists of an N-terminal periplasmic region, a transmembrane helix, and a C-terminal cytoplasmic region. Whereas the cytoplasmic region has been characterized to be essential for inhibition of the peritrichous growth, the role of the N-terminal region is still unclear. We here determined the structure of the N-terminal periplasmic region of SflA (SflAN) at 1.9-Å resolution. The core of SflAN forms a domain-swapped dimer with tetratricopeptide repeat (TPR)/Sel1-like repeat (SLR) motif, which is often found in the domains responsible for protein-protein interaction in various proteins. The structural similarity and the following mutational analysis based on the structure suggest that SflA binds to unknown partner protein by SflAN and the binding signal is important for the precise control of the SflA function.
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Affiliation(s)
- Mayuko Sakuma
- Radioisotope Research Center, Graduate School of Science, Nagoya University, Chikusa-Ku, Furocho, Nagoya, Japan.,Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Furocho, Nagoya, Japan
| | - Shoji Nishikawa
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Machikaneyama 1-1, Toyonaka, Japan
| | - Satoshi Inaba
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Furocho, Nagoya, Japan
| | - Takehiko Nishigaki
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Furocho, Nagoya, Japan
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Furocho, Nagoya, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Furocho, Nagoya, Japan
| | - Katsumi Imada
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Machikaneyama 1-1, Toyonaka, Japan
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8
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Mohanraj K, Wasilewski M, Benincá C, Cysewski D, Poznanski J, Sakowska P, Bugajska Z, Deckers M, Dennerlein S, Fernandez‐Vizarra E, Rehling P, Dadlez M, Zeviani M, Chacinska A. Inhibition of proteasome rescues a pathogenic variant of respiratory chain assembly factor COA7. EMBO Mol Med 2019; 11:emmm.201809561. [PMID: 30885959 PMCID: PMC6505684 DOI: 10.15252/emmm.201809561] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Nuclear and mitochondrial genome mutations lead to various mitochondrial diseases, many of which affect the mitochondrial respiratory chain. The proteome of the intermembrane space (IMS) of mitochondria consists of several important assembly factors that participate in the biogenesis of mitochondrial respiratory chain complexes. The present study comprehensively analyzed a recently identified IMS protein cytochrome c oxidase assembly factor 7 (COA7), or RESpiratory chain Assembly 1 (RESA1) factor that is associated with a rare form of mitochondrial leukoencephalopathy and complex IV deficiency. We found that COA7 requires the mitochondrial IMS import and assembly (MIA) pathway for efficient accumulation in the IMS We also found that pathogenic mutant versions of COA7 are imported slower than the wild-type protein, and mislocalized proteins are degraded in the cytosol by the proteasome. Interestingly, proteasome inhibition rescued both the mitochondrial localization of COA7 and complex IV activity in patient-derived fibroblasts. We propose proteasome inhibition as a novel therapeutic approach for a broad range of mitochondrial pathologies associated with the decreased levels of mitochondrial proteins.
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Affiliation(s)
- Karthik Mohanraj
- Laboratory of Mitochondrial BiogenesisCentre of New TechnologiesUniversity of WarsawWarsawPoland,ReMedy International Research Agenda UnitCentre of New TechnologiesUniversity of WarsawWarsawPoland,Laboratory of Mitochondrial BiogenesisInternational Institute of Molecular and Cell BiologyWarsawPoland
| | - Michal Wasilewski
- Laboratory of Mitochondrial BiogenesisCentre of New TechnologiesUniversity of WarsawWarsawPoland,Laboratory of Mitochondrial BiogenesisInternational Institute of Molecular and Cell BiologyWarsawPoland
| | | | - Dominik Cysewski
- Mass Spectrometry LabDepartment of BiophysicsInstitute of Biochemistry and BiophysicsWarsawPoland
| | - Jaroslaw Poznanski
- Department of BiophysicsInstitute of Biochemistry and BiophysicsWarsawPoland
| | - Paulina Sakowska
- Laboratory of Mitochondrial BiogenesisInternational Institute of Molecular and Cell BiologyWarsawPoland
| | - Zaneta Bugajska
- Laboratory of Mitochondrial BiogenesisCentre of New TechnologiesUniversity of WarsawWarsawPoland
| | - Markus Deckers
- Department of Cellular BiochemistryUniversity of GöttingenGöttingenGermany
| | - Sven Dennerlein
- Department of Cellular BiochemistryUniversity of GöttingenGöttingenGermany
| | | | - Peter Rehling
- Department of Cellular BiochemistryUniversity of GöttingenGöttingenGermany,Max Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Michal Dadlez
- Mass Spectrometry LabDepartment of BiophysicsInstitute of Biochemistry and BiophysicsWarsawPoland
| | - Massimo Zeviani
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Agnieszka Chacinska
- Laboratory of Mitochondrial BiogenesisCentre of New TechnologiesUniversity of WarsawWarsawPoland,ReMedy International Research Agenda UnitCentre of New TechnologiesUniversity of WarsawWarsawPoland,Laboratory of Mitochondrial BiogenesisInternational Institute of Molecular and Cell BiologyWarsawPoland
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9
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Cretich M, Gori A, D'Annessa I, Chiari M, Colombo G. Peptides for Infectious Diseases: From Probe Design to Diagnostic Microarrays. Antibodies (Basel) 2019; 8:E23. [PMID: 31544829 PMCID: PMC6640701 DOI: 10.3390/antib8010023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 02/28/2019] [Accepted: 03/04/2019] [Indexed: 01/03/2023] Open
Abstract
Peptides and peptidomimetics have attracted revived interest regarding their applications in chemical biology over the last few years. Their chemical versatility, synthetic accessibility and the ease of storage and management compared to full proteins have made peptides particularly interesting in diagnostic applications, where they proved to efficiently recapitulate the molecular recognition properties of larger protein antigens, and were proven to be able to capture antibodies circulating in the plasma and serum of patients previously exposed to bacterial or viral infections. Here, we describe the development, integration and application of strategies for computational prediction and design, advanced chemical synthesis, and diagnostic deployment in multiplexed assays of peptide-based materials which are able to bind antibodies of diagnostic as well as therapeutic interest. By presenting successful applications of such an integrated strategy, we argue that they will have an ever-increasing role in both basic and clinical realms of research, where important advances can be expected in the next few years.
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Affiliation(s)
- Marina Cretich
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
| | - Alessandro Gori
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
| | - Ilda D'Annessa
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
| | - Marcella Chiari
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
| | - Giorgio Colombo
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 12, 27100 Pavia, Italy.
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10
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Voth KA, Chung IYW, van Straaten K, Li L, Boniecki MT, Cygler M. The structure of Legionella effector protein LpnE provides insights into its interaction with Oculocerebrorenal syndrome of Lowe (OCRL) protein. FEBS J 2018; 286:710-725. [PMID: 30479037 DOI: 10.1111/febs.14710] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/18/2018] [Accepted: 11/23/2018] [Indexed: 12/17/2022]
Abstract
Legionella pneumophila is a freshwater bacterium that replicates in predatory amoeba and alveolar macrophage. The ability of L. pneumophila to thrive in eukaryotic host cells is conferred by the Legionella containing vacuole (LCV). Formation and intracellular trafficking of the LCV are governed by an arsenal of effector proteins, many of which are secreted by the Icm/Dot Type 4 Secretion System. One such effector, known as LpnE (L. pneumophila Entry), has been implicated in facilitating bacterial entry into host cells, LCV trafficking, and substrate translocation. LpnE belongs to a subfamily of tetratricopeptide repeat proteins known as Sel1-like repeats (SLRs). All eight of the predicted SLRs in LpnE are required to promote host cell invasion. Herein, we report that LpnE(1-375) localizes to cis-Golgi in HEK293 cells via its signal peptide (aa 1-22). We further verify the interaction of LpnE(73-375) and LpnE(22-375) with Oculocerebrorenal syndrome of Lowe protein (OCRL) residues 10-208, restricting the known interacting residues for both proteins. To further characterize the SLR region of LpnE, we solved the crystal structure of LpnE(73-375) to 1.75Å resolution. This construct comprises all SLRs, which are arranged in a superhelical fold. The α-helices forming the inner concave surface of the LpnE superhelix suggest a potential protein-protein interaction interface. DATABASE: Coordinates and structure factors were deposited in the Protein Data Bank with the accession number 6DEH.
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Affiliation(s)
- Kevin A Voth
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Canada
| | - Ivy Yeuk Wah Chung
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Canada
| | - Karin van Straaten
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Canada
| | - Lei Li
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Canada
| | - Michal T Boniecki
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Canada
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11
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Yang XY, Li ZQ, She Z, Geng Z, Xu JH, Gao ZQ, Dong YH. Structural analysis of Pseudomonas aeruginosa H3-T6SS immunity proteins. FEBS Lett 2016; 590:2787-96. [PMID: 27397502 DOI: 10.1002/1873-3468.12291] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 05/31/2016] [Accepted: 06/27/2016] [Indexed: 01/13/2023]
Abstract
The Pseudomonas aeruginosa PldB protein is a transkingdom effector secreted by the Type VI Secretion System (T6SS). PA5088, PA5087, and PA5086 are three immunity proteins that can suppress the virulence of PldB. We report the crystal structures of PA5088 and PA5087 at 2.0 and 2.1 Å resolution, respectively. PA5088 and PA5087 both consist of several Sel1-like Repeats (SLRs) and form super-ring folds. Our structural analysis of these proteins revealed key differences among PA5088, PA5087, and their homologs. Our docking experiments have shed light on the putative interaction mechanism of their function as phospholipase D inhibitors.
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Affiliation(s)
- Xiao-Yun Yang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Zong-Qiang Li
- College of Life Science and Technology, Huazhong Agriculture University, Wuhan, China
| | - Zhun She
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Zhi Geng
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Jian-Hua Xu
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Zeng-Qiang Gao
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Yu-Hui Dong
- Multidiscipline Research Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
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12
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Kress-Bennett JM, Hiller NL, Eutsey RA, Powell E, Longwell MJ, Hillman T, Blackwell T, Byers B, Mell JC, Post JC, Hu FZ, Ehrlich GD, Janto BA. Identification and Characterization of msf, a Novel Virulence Factor in Haemophilus influenzae. PLoS One 2016; 11:e0149891. [PMID: 26977929 PMCID: PMC4792463 DOI: 10.1371/journal.pone.0149891] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 02/05/2016] [Indexed: 12/11/2022] Open
Abstract
Haemophilus influenzae is an opportunistic pathogen. The emergence of virulent, non-typeable strains (NTHi) emphasizes the importance of developing new interventional targets. We screened the NTHi supragenome for genes encoding surface-exposed proteins suggestive of immune evasion, identifying a large family containing Sel1-like repeats (SLRs). Clustering identified ten SLR-containing gene subfamilies, each with various numbers of SLRs per gene. Individual strains also had varying numbers of SLR-containing genes from one or more of the subfamilies. Statistical genetic analyses of gene possession among 210 NTHi strains typed as either disease or carriage found a significant association between possession of the SlrVA subfamily (which we have termed, macrophage survival factor, msf) and the disease isolates. The PittII strain contains four chromosomally contiguous msf genes. Deleting all four of these genes (msfA1-4) (KO) resulted in a highly significant decrease in phagocytosis and survival in macrophages; which was fully complemented by a single copy of the msfA1 gene. Using the chinchilla model of otitis media and invasive disease, the KO strain displayed a significant decrease in fitness compared to the WT in co-infections; and in single infections, the KO lost its ability to invade the brain. The singly complemented strain showed only a partial ability to compete with the WT suggesting gene dosage is important in vivo. The transcriptional profiles of the KO and WT in planktonic growth were compared using the NTHi supragenome array, which revealed highly significant changes in the expression of operons involved in virulence and anaerobiosis. These findings demonstrate that the msfA1-4 genes are virulence factors for phagocytosis, persistence, and trafficking to non-mucosal sites.
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Affiliation(s)
- Jennifer M. Kress-Bennett
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - N. Luisa Hiller
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Rory A. Eutsey
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Evan Powell
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Mark J. Longwell
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Todd Hillman
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Tenisha Blackwell
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Barbara Byers
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Joshua C. Mell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - J. Christopher Post
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Otolaryngology, Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, Pennsylvania, United States of America
| | - Fen Z. Hu
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Otolaryngology, Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, Pennsylvania, United States of America
| | - Garth D. Ehrlich
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Otolaryngology, Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, Pennsylvania, United States of America
| | - Benjamin A. Janto
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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13
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Wiech EM, Cheng HP, Singh SM. Molecular modeling and computational analyses suggests that the Sinorhizobium meliloti periplasmic regulator protein ExoR adopts a superhelical fold and is controlled by a unique mechanism of proteolysis. Protein Sci 2015; 24:319-27. [PMID: 25492513 PMCID: PMC4353358 DOI: 10.1002/pro.2616] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 12/12/2022]
Abstract
The Sinorhizobium meliloti periplasmic ExoR protein and the ExoS/ChvI two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. In the absence of crystal structures, understanding the molecular mechanism of interaction between ExoR and the ExoS sensor, which is believed to drive the key regulatory step in the invasion process, remains a major challenge. In this study, we present a theoretical structural model of the active form of ExoR protein, ExoRm , generated using computational methods. Our model suggests that ExoR possesses a super-helical fold comprising 12 α-helices forming six Sel1-like repeats, including two that were unidentified in previous studies. This fold is highly conducive to mediating protein-protein interactions and this is corroborated by the identification of putative protein binding sites on the surface of the ExoRm protein. Our studies reveal two novel insights: (a) an extended conformation of the third Sel1-like repeat that might be important for ExoR regulatory function and (b) a buried proteolytic site that implies a unique proteolytic mechanism. This study provides new and interesting insights into the structure of S. meliloti ExoR, lays the groundwork for elaborating the molecular mechanism of ExoRm cleavage, ExoRm -ExoS interactions, and studies of ExoR homologs in other bacterial host interactions.
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Affiliation(s)
- Eliza M Wiech
- Department of Biology, The Graduate Center of the City University of New YorkNew York, New York, 10016
- Department of Biology, Brooklyn College, The City University of New YorkBrooklyn, New York, 11210
| | - Hai-Ping Cheng
- Department of Biology, The Graduate Center of the City University of New YorkNew York, New York, 10016
- Biological Sciences Department, Lehman College, The City University of New YorkBronx, New York, 10468
| | - Shaneen M Singh
- Department of Biology, The Graduate Center of the City University of New YorkNew York, New York, 10016
- Department of Biology, Brooklyn College, The City University of New YorkBrooklyn, New York, 11210
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14
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Jeong H, Lee H, Lee C. Crystallization and preliminary X-ray diffraction analysis of the Sel1-like repeats of SEL1L. Acta Crystallogr F Struct Biol Commun 2014; 70:1624-7. [PMID: 25484212 PMCID: PMC4259226 DOI: 10.1107/s2053230x14023115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/20/2014] [Indexed: 01/03/2023] Open
Abstract
Terminally misfolded or unassembled proteins are selectively recognized and cleared by the ER-associated degradation (ERAD) pathway. Suppressor/enhancer of lin-12-like (SEL1L), a component of the dislocation machinery containing the E3 ubiquitin ligase Hrd1, plays an important role in selecting and transporting ERAD substrates for degradation in the endoplasmic reticulum. In this study, the purification, crystallization and preliminary X-ray diffraction analysis of recombinant mouse SEL1L (residues 348-533) are reported. The crystals were obtained by the hanging-drop vapour-diffusion method at pH 8.5 and 277 K using 30% 2-propanol as a precipitant. Optimized crystals diffracted to 3.3 Å resolution at a synchrotron-radiation source. Preliminary X-ray diffraction analysis revealed that the crystals belonged to space group P21 and contained four molecules per asymmetric unit, with a solvent content of 44%.
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Affiliation(s)
- Hanbin Jeong
- School of Life Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 689-798, Republic of Korea
| | - Hakbong Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 689-798, Republic of Korea
| | - Changwook Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 689-798, Republic of Korea
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