1
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Tang T, Chen Y, Du Y, Yao B, Liu M. Effects of functional modules and bacterial clusters response on transmission performance of antibiotic resistance genes under antibiotic stress during anaerobic digestion of livestock wastewater. JOURNAL OF HAZARDOUS MATERIALS 2023; 441:129870. [PMID: 36063716 DOI: 10.1016/j.jhazmat.2022.129870] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/06/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
The formation and transmission of antibiotic resistance genes (ARGs) have attracted increasing attention. It is unclear whether the internal mechanisms by which antibiotics affect horizontal gene transfer (HGT) of ARGs during anaerobic digestion (AD) were influenced by dose and type. We investigated the effects of two major antibiotics (oxytetracycline, OTC, and sulfamethoxazole, SMX) on ARGs during AD according to antibiotic concentration in livestock wastewater influent. The low-dose antibiotic (0.5 mg/L) increased ROS and SOS responses, promoting the formation of ARGs. Meanwhile, low-dose antibiotics could also promote the spread of ARGs by promoting pili, communication responses, and the type IV secretion system (T4SS). However, different types and doses of antibiotics would lead to changes in the above functional modules and then affect the enrichment of ARGs. With the increasing dose of SMX, the advantages of pili and communication responses would gradually change. In the OTC system, low-dose has the strongest promoting ability in both pili and communication responses. Similarly, an increase in the dose of SMX would change T4SS from facilitation to inhibition, while OTC completely inhibits T4SS. Microbial and network analysis also revealed that low-dose antibiotics were more favorable for the growth of host bacteria.
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Affiliation(s)
- Taotao Tang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Ying Chen
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Ye Du
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Bing Yao
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Min Liu
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China.
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2
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Ping L, Ruxian J, Mengping Z, Pei J, Zhuoya L, Guosheng L, Zhenyu W, Hailei W. Whole-cell biosynthesis of cytarabine by an unnecessary protein-reduced Escherichia coli that coexpresses purine and uracil phosphorylase. Biotechnol Bioeng 2022; 119:1768-1780. [PMID: 35383880 DOI: 10.1002/bit.28098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 11/10/2022]
Abstract
Currently, whole-cell catalysts face challenges due to the complexity of reaction systems, although they have a cost advantage over pure enzymes. In this work, cytarabine was synthesized by purified purine phosphorylase 1 (PNP1) and uracil phosphorylase (UP), and the conversion of cytarabine from adenine arabinoside reached 72.3±4.3%. However, the synthesis was unsuccessful by whole-cell catalysis due to interference from unnecessary proteins (UNPs) in cells. Thus, we carried out a large-scale gene editing involving 377 genes in the genome of Escherichia coli to reduce the negative effect of UNPs on substrate conversion and cytarabine production. Finally, the PNP1 and UP activities of the obtained mutant were increased significantly compared with the parental strain, and more importantly, the conversion rate of cytarabine by whole-cell catalysis reached 67.4±2.5%. The lack of 148 proteins and down-regulation of 783 proteins caused by gene editing were equivalent to partial purification of the enzymes within cells, and thus, we provided inspiration to solve the problem caused by UNP interference, which is ubiquitous in the field of whole-cell catalysis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Li Ping
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Jing Ruxian
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Zhou Mengping
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Jia Pei
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Li Zhuoya
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Liu Guosheng
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Wang Zhenyu
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Wang Hailei
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China.,Advanced Environmental Biotechnology Center, Nanyang Technological University, Singapore, 637141, Singapore
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3
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Wang X, Peterson JH, Bernstein HD. Bacterial Outer Membrane Proteins Are Targeted to the Bam Complex by Two Parallel Mechanisms. mBio 2021; 12:e00597-21. [PMID: 33947759 PMCID: PMC8262991 DOI: 10.1128/mbio.00597-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/12/2021] [Indexed: 01/23/2023] Open
Abstract
Membrane proteins that are integrated into the outer membrane of Gram-negative bacteria typically contain a unique "β barrel" structure that serves as a membrane spanning segment. A conserved "β signal" motif is located at the C terminus of the β barrel of many outer membrane proteins (OMPs), but the function of this sequence is unclear. We found that mutations in the β signal slightly delayed the assembly of three model Escherichia coli OMPs by reducing their affinity for the barrel assembly machinery (Bam) complex, a heterooligomer that catalyzes β barrel insertion, and led to the degradation of a fraction of the protein in the periplasm. Interestingly, the absence of the periplasmic chaperone SurA amplified the effect of the mutations and caused the complete degradation of the mutant proteins. In contrast, the absence of another periplasmic chaperone (Skp) suppressed the effect of the mutations and considerably enhanced the efficiency of assembly. Our results reveal the existence of two parallel OMP targeting mechanisms that rely on a cis-acting peptide (the β signal) and a trans-acting factor (SurA), respectively. Our results also challenge the long-standing view that periplasmic chaperones are redundant and provide evidence that they have specialized functions.IMPORTANCE Proteins that are embedded in the outer membrane of Gram-negative bacteria (OMPs) play an important role in protecting the cell from harmful chemicals. OMPs share a common architecture and often contain a conserved sequence motif (β motif) of unknown function. Although OMPs are escorted to the outer membrane by proteins called chaperones, the exact function of the chaperones is also unclear. Here, we show that the β motif and the chaperone SurA both target OMPs to the β barrel insertion machinery in the outer membrane. In contrast, the chaperone Skp delivers unintegrated OMPs to protein degradation complexes. Our results challenge the long-standing view that chaperones are functionally redundant and strongly suggest that they have specialized roles in OMP targeting and quality control.
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Affiliation(s)
- Xu Wang
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Janine H Peterson
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Harris D Bernstein
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
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4
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Li MF, Jia BB, Sun YY, Sun L. The Translocation and Assembly Module (TAM) of Edwardsiella tarda Is Essential for Stress Resistance and Host Infection. Front Microbiol 2020; 11:1743. [PMID: 32793174 PMCID: PMC7393178 DOI: 10.3389/fmicb.2020.01743] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/03/2020] [Indexed: 11/28/2022] Open
Abstract
Translocation and assembly module (TAM) is a protein channel known to mediate the secretion of virulence factors during pathogen infection. Edwardsiella tarda is a Gram-negative bacterium that is pathogenic to a wide range of farmed fish and other hosts including humans. In this study, we examined the function of the two components of the TAM, TamA and TamB, of E. tarda (named tamAEt and tamBEt, respectively). TamAEt was found to localize on the surface of E. tarda and be recognizable by TamAEt antibody. Compared to the wild type, the tamA and tamB knockouts, TX01ΔtamA and TX01ΔtamB, respectively, were significantly reduced in motility, flagella formation, invasion into host cells, intracellular replication, dissemination in host tissues, and inducing host mortality. The lost virulence capacities of TX01ΔtamA and TX01ΔtamB were restored by complementation with the tamAEt and tamBEt genes, respectively. Furthermore, TX01ΔtamA and TX01ΔtamB were significantly impaired in the ability to survive under low pH and oxidizing conditions, and were unable to maintain their internal pH balance and cellular structures in acidic environments, which led to increased susceptibility to lysozyme destruction. Taken together, these results indicate that TamAEt and TamBEt are essential for the virulence of E. tarda and required for E. tarda to survive under stress conditions.
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Affiliation(s)
- Mo-Fei Li
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Bei-Bei Jia
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuan-Yuan Sun
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Li Sun
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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5
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Stubenrauch CJ, Lithgow T. The TAM: A Translocation and Assembly Module of the β-Barrel Assembly Machinery in Bacterial Outer Membranes. EcoSal Plus 2019; 8. [DOI: 10.1128/ecosalplus.esp-0036-2018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Assembly of proteins into the outer membrane is an essential process in the cell biology of bacteria. The integration of β-barrel proteins into the outer membrane is mediated by a system referred to as the β-barrel assembly machinery (BAM) that includes two related proteins: BamA in the BAM complex and TamA in the TAM (translocation and assembly module). Here we review what is known about the TAM in terms of its function and the structural architecture of its two subunits, TamA and TamB. By linking the energy transduction possibilities in the inner membrane to TamA in the outer membrane, the TAM provides additional capability to the β-barrel assembly machinery. Conservation of the TAM across evolutionary boundaries, and the presence of hybrid BAM/TAM complexes in some bacterial lineages, adds insight to our growing understanding of how bacterial outer membranes are built.
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Affiliation(s)
- Christopher J. Stubenrauch
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton 3800, Australia
| | - Trevor Lithgow
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton 3800, Australia
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6
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Wang Y, Lu J, Mao L, Li J, Yuan Z, Bond PL, Guo J. Antiepileptic drug carbamazepine promotes horizontal transfer of plasmid-borne multi-antibiotic resistance genes within and across bacterial genera. THE ISME JOURNAL 2019; 13:509-522. [PMID: 30291330 PMCID: PMC6331567 DOI: 10.1038/s41396-018-0275-x] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/18/2018] [Accepted: 08/26/2018] [Indexed: 02/02/2023]
Abstract
Antibiotic resistance is a severe global threat for public health, causing around 700,000 deaths per year. Horizontal gene transfer (HGT) is one of the most significant pathways to disseminate antibiotic resistance. It is commonly acknowledged that sub-minimum inhibition concentrations of antibiotics are major contributors in promoting antibiotic resistance through HGT. Pharmaceuticals are occurring in our environments at increased levels, yet little is known whether non-antibiotic pharmaceuticals cause or accelerate the dissemination of antibiotic resistance. Here, we report for the first time that the antiepileptic drug, carbamazepine, promotes conjugative transfer of antibiotic resistance genes. It was seen that environmentally relevant concentrations of carbamazepine (e.g., 0.05 mg/L) significantly enhanced the conjugative transfer of multiresistance genes carried by plasmid within and across bacterial genera. The underlying mechanisms of the enhanced HGT were revealed by detecting oxidative stress and cell membrane permeability, in combination with MinION DNA sequencing, genome-wide RNA sequencing, and proteomic analysis. Carbamazepine induced a series of acute responses, including increased levels of reactive oxygen species, the SOS response; increased cell membrane permeability, and pilus generation. Expressional levels of genes related to these processes were significantly upregulated during carbamazepine exposure. Given that HGT occurs widely among different species in various environments, these findings are an early warning for a wide assessment of the roles of non-antibiotic pharmaceuticals in the spread of antibiotic resistance.
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Affiliation(s)
- Yue Wang
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Ji Lu
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Likai Mao
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Jie Li
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Philip L Bond
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia.
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7
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Bioinformatics Analysis and Functional Prediction of Transmembrane Proteins in Entamoeba histolytica. Genes (Basel) 2018; 9:genes9100499. [PMID: 30332795 PMCID: PMC6209943 DOI: 10.3390/genes9100499] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/09/2018] [Accepted: 09/12/2018] [Indexed: 12/18/2022] Open
Abstract
Entamoeba histolytica is an invasive, pathogenic parasite causing amoebiasis. Given that proteins involved in transmembrane (TM) transport are crucial for the adherence, invasion, and nutrition of the parasite, we conducted a genome-wide bioinformatics analysis of encoding proteins to functionally classify and characterize all the TM proteins in E. histolytica. In the present study, 692 TM proteins have been identified, of which 546 are TM transporters. For the first time, we report a set of 141 uncharacterized proteins predicted as TM transporters. The percentage of TM proteins was found to be lower in comparison to the free-living eukaryotes, due to the extracellular nature and functional diversification of the TM proteins. The number of multi-pass proteins is larger than the single-pass proteins; though both have their own significance in parasitism, multi-pass proteins are more extensively required as these are involved in acquiring nutrition and for ion transport, while single-pass proteins are only required at the time of inciting infection. Overall, this intestinal parasite implements multiple mechanisms for establishing infection, obtaining nutrition, and adapting itself to the new host environment. A classification of the repertoire of TM transporters in the present study augments several hints on potential methods of targeting the parasite for therapeutic benefits.
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8
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Sugimoto S, Arita-Morioka KI, Terao A, Yamanaka K, Ogura T, Mizunoe Y. Multitasking of Hsp70 chaperone in the biogenesis of bacterial functional amyloids. Commun Biol 2018; 1:52. [PMID: 30271935 PMCID: PMC6123696 DOI: 10.1038/s42003-018-0056-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/19/2018] [Indexed: 11/21/2022] Open
Abstract
Biofilms are intricate communities of microorganisms embedded in a self-produced matrix of extracellular polymer, which provides microbes survival advantages in stressful environments and can cause chronic infections in humans. Curli are functional amyloids that assemble on the extracellular surface of enteric bacteria such as Escherichia coli during biofilm development and colonization. The molecular chaperone DnaK, a bacterial Hsp70 homologue, promotes curli biogenesis via unknown mechanism(s). Here we show that DnaK increases the expression of CsgA and CsgB—the major and minor structural components of curli, respectively—via a quantity and quality control of RpoS, a stationary phase-specific alternative sigma factor regulating bacterial transcription, and CsgD, the master transcriptional regulator of curli formation. DnaK also keeps CsgA and CsgB in a translocation-competent state by binding to their signal peptides prone to aggregation. Our findings suggest that DnaK controls the homoeostasis of curli biogenesis at multiple stages to organize the biofilm matrix. Shinya Sugimoto et al. demonstrate how molecular chaperone DnaK regulates biofilm formation through the production of curli, which anchor enteric bacteria to the biofilm. This finding provides mechanistic insights into the development of anti-biofilm agents as antibiotics.
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Affiliation(s)
- Shinya Sugimoto
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan. .,Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan.
| | - Ken-Ichi Arita-Morioka
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-Ku, Kumamoto, 860-0811, Japan.,Advanced Science Research Center, Fukuoka Dental College, 2-15-1 Tamura, Sawara-Ku, Fukuoka, 814-0193, Japan
| | - Akari Terao
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
| | - Kunitoshi Yamanaka
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-Ku, Kumamoto, 860-0811, Japan
| | - Teru Ogura
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-Ku, Kumamoto, 860-0811, Japan
| | - Yoshimitsu Mizunoe
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan.,Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-Ku, Tokyo, 105-8461, Japan
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9
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Applications of solid-state NMR to membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1577-1586. [PMID: 28709996 DOI: 10.1016/j.bbapap.2017.07.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/30/2017] [Accepted: 07/07/2017] [Indexed: 11/23/2022]
Abstract
Membrane proteins mediate flow of molecules, signals, and energy between cells and intracellular compartments. Understanding membrane protein function requires a detailed understanding of the structural and dynamic properties involved. Lipid bilayers provide a native-like environment for structure-function investigations of membrane proteins. In this review we give a general discourse on the recent progress in the field of solid-state NMR of membrane proteins. Solid-state NMR is a variation of NMR spectroscopy that is applicable to molecular systems with restricted mobility, such as high molecular weight proteins and protein complexes, supramolecular assemblies, or membrane proteins in a phospholipid environment. We highlight recent advances in applications of solid-state NMR to membrane proteins, specifically focusing on the recent developments in the field of Dynamic Nuclear Polarization, proton detection, and solid-state NMR applications in situ (in cell membranes). This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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10
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The Ruler Protein EscP of the Enteropathogenic Escherichia coli Type III Secretion System Is Involved in Calcium Sensing and Secretion Hierarchy Regulation by Interacting with the Gatekeeper Protein SepL. mBio 2017; 8:mBio.01733-16. [PMID: 28049143 PMCID: PMC5210495 DOI: 10.1128/mbio.01733-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The type III secretion system (T3SS) is a multiprotein complex that plays a central role in the virulence of many Gram-negative bacterial pathogens. To ensure that effector proteins are efficiently translocated into the host cell, bacteria must be able to sense their contact with the host cell. In this study, we found that EscP, which was previously shown to function as the ruler protein of the enteropathogenic Escherichia coli T3SS, is also involved in the switch from the secretion of translocator proteins to the secretion of effector proteins. In addition, we demonstrated that EscP can interact with the gatekeeper protein SepL and that the EscP-SepL complex dissociates upon a calcium concentration drop. We suggest a model in which bacterial contact with the host cell is accompanied by a drop in the calcium concentration that causes SepL-EscP complex dissociation and triggers the secretion of effector proteins. IMPORTANCE The emergence of multidrug-resistant bacterial strains, especially those of pathogenic bacteria, has serious medical and clinical implications. At the same time, the development and approval of new antibiotics have been limited for years. Recently, antivirulence drugs have received considerable attention as a novel antibiotic strategy that specifically targets bacterial virulence rather than growth, an approach that applies milder evolutionary pressure on the bacteria to develop resistance. A highly attractive target for the development of antivirulence compounds is the type III secretion system, a specialized secretory system possessed by many Gram-negative bacterial pathogens for injecting virulence factors (effectors) into host cells. In this study, we shed light on the molecular mechanism that allows bacteria to sense their contact with the host cell and to respond with the timed secretion of effector proteins. Understanding this critical step for bacterial virulence may provide a new therapeutic strategy.
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11
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Yan R, Wang X, Huang L, Tian Y, Cai W. Transmembrane region prediction by using sequence-derived features and machine learning methods. RSC Adv 2017. [DOI: 10.1039/c7ra03883f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Membrane proteins are central to carrying out impressive biological functions.
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Affiliation(s)
- Renxiang Yan
- School of Biological Sciences and Engineering
- Fuzhou University
- Fuzhou 350108
- China
| | - Xiaofeng Wang
- College of Mathematics and Computer Science
- Shanxi Normal University
- Linfen 041004
- China
| | - Lanqing Huang
- School of Biological Sciences and Engineering
- Fuzhou University
- Fuzhou 350108
- China
| | - Yarong Tian
- School of Biological Sciences and Engineering
- Fuzhou University
- Fuzhou 350108
- China
| | - Weiwen Cai
- School of Biological Sciences and Engineering
- Fuzhou University
- Fuzhou 350108
- China
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12
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Bosák J, Micenková L, Doležalová M, Šmajs D. Colicins U and Y inhibit growth of Escherichia coli strains via recognition of conserved OmpA extracellular loop 1. Int J Med Microbiol 2016; 306:486-494. [PMID: 27510856 DOI: 10.1016/j.ijmm.2016.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/28/2016] [Accepted: 07/31/2016] [Indexed: 01/04/2023] Open
Abstract
Interactions of colicins U and Y with the OmpA (Outer membrane protein A) receptor molecule were studied using site-directed mutagenesis and colicin binding assay. A systematic mutagenesis of the colicin-susceptible OmpA sequence from Escherichia coli (OmpAEC) to the colicin-resistant OmpA sequence from Serratia marcescens (OmpASM) was performed in regions corresponding to extracellular OmpA loops 1-4. Susceptibility to colicins U and Y was significantly affected by the OmpA mutation in loop 1. As with functional analysis, a decrease in binding capacity of His-tagged colicin U was found for recombinant OmpA with a mutated segment in loop 1 compared to control OmpAEC. To verify the importance of the identified amino acid residues in OmpA loop 1, we introduced loop 1 from OmpAEC into OmpASM, which resulted in the substantial increase of susceptibility to colicins U and Y. In addition, colicins U and Y were tested against a panel of 118 bacteriocin non-producing strains of four Escherichia species, including E. coli (39 strains), E. fergusonii (10 strains), E. hermannii (42 strains), and E. vulneris (27 strains). A majority (82%) of E. coli strains was susceptible to colicins U and Y. Interestingly, colicins U and Y also inhibited all of the 30 tested multidrug-resistant E. coli O25b-ST131 isolates. These findings, together with the fact that OmpA loop 1 is important for bacterial virulence and is evolutionary conserved, offer the potential of using colicins U and Y as specific anti-OmpA loop 1 directed antibacterial proteins.
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Affiliation(s)
- Juraj Bosák
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic
| | - Lenka Micenková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic
| | - Magda Doležalová
- Department of Environment Protection Engineering, Faculty of Technology, Tomas Bata University in Zlín, T. G. Masaryk square 275, Zlín, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic.
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13
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Joseph NMS, Ho KL, Tey BT, Tan CS, Shafee N, Tan WS. Production of the virus-like particles of nipah virus matrix protein inPichia pastorisas diagnostic reagents. Biotechnol Prog 2016; 32:1038-45. [DOI: 10.1002/btpr.2279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 02/03/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Narcisse MS Joseph
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences; Universiti Putra Malaysia; UPM Serdang Selangor 43400 Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences; Universiti Putra Malaysia; UPM Serdang Selangor 43400 Malaysia
| | - Beng Ti Tey
- Multidisciplinary Platform of Advance Engineering; Monash University Malaysia; Bandar Sunway Selangor 46150 Malaysia
- Discipline of Chemical Engineering, School of Engineering, Monash University Malaysia; Bandar Sunway Selangor 46150 Malaysia
| | - Chon Seng Tan
- Biotechnology Research Centre, Malaysia Agricultural Research and Development Institute (MARDI); Serdang Selangor 43400 Malaysia
| | - Norazizah Shafee
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences; Universiti Putra Malaysia; UPM Serdang Selangor 43400 Malaysia
| | - Wen Siang Tan
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences; Universiti Putra Malaysia; UPM Serdang Selangor 43400 Malaysia
- Institute of Bioscience, Universiti Putra Malaysia; UPM Serdang Selangor 43400 Malaysia
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14
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Kim J, Kagawa A, Kurasaki K, Ataie N, Cho IK, Li QX, Ng HL. Large-scale identification of membrane proteins with properties favorable for crystallization. Protein Sci 2015; 24:1756-63. [PMID: 26257393 DOI: 10.1002/pro.2766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/04/2015] [Indexed: 12/27/2022]
Abstract
Membrane protein crystallography is notoriously difficult due to challenges in protein expression and issues of degradation and structural stability. We have developed a novel method for large-scale screening of native sources for integral membrane proteins that have intrinsic biochemical properties favorable for crystallization. Highly expressed membrane proteins that are thermally stable and nonaggregating in detergent solutions were identified by mass spectrometry from Escherichia coli, Saccharomyces cerevisiae, and Sus scrofa cerebrum. Many of the membrane proteins identified had been crystallized previously, supporting the promise of the approach. Most identified proteins have known functions and include high-value targets such as transporters and ATPases. To validate the method, we recombinantly expressed and purified the yeast protein, Yop1, which is responsible for endoplasmic reticulum curvature. We demonstrate that Yop1 can be purified with the detergent dodecylmaltoside without aggregating.
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Affiliation(s)
- Jared Kim
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, 96822
| | - Allison Kagawa
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, 96822
| | - Kellie Kurasaki
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, 96822
| | - Niloufar Ataie
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, 96822
| | - Il Kyu Cho
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii, 96822
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii, 96822
| | - Ho Leung Ng
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, 96822.,University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii, 96822
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15
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Dunstan RA, Hay ID, Wilksch JJ, Schittenhelm RB, Purcell AW, Clark J, Costin A, Ramm G, Strugnell RA, Lithgow T. Assembly of the secretion pores GspD, Wza and CsgG into bacterial outer membranes does not require the Omp85 proteins BamA or TamA. Mol Microbiol 2015; 97:616-29. [DOI: 10.1111/mmi.13055] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2015] [Indexed: 01/07/2023]
Affiliation(s)
- Rhys A. Dunstan
- Department of Microbiology; Monash University; Clayton Vic. 3800 Australia
- Department of Biochemistry and Molecular Biology; Monash University; Clayton Vic. 3800 Australia
| | - Iain D. Hay
- Department of Microbiology; Monash University; Clayton Vic. 3800 Australia
| | - Jonathan J. Wilksch
- Department of Microbiology & Immunology; The Peter Doherty Institute for Infection and Immunity; University of Melbourne; Parkville Vic. 3052 Australia
| | - Ralf B. Schittenhelm
- Department of Biochemistry and Molecular Biology; Monash University; Clayton Vic. 3800 Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology; Monash University; Clayton Vic. 3800 Australia
| | - Joan Clark
- Department of Biochemistry and Molecular Biology; Monash University; Clayton Vic. 3800 Australia
| | - Adam Costin
- Department of Biochemistry and Molecular Biology; Monash University; Clayton Vic. 3800 Australia
| | - Georg Ramm
- Department of Biochemistry and Molecular Biology; Monash University; Clayton Vic. 3800 Australia
| | - Richard A. Strugnell
- Department of Microbiology & Immunology; The Peter Doherty Institute for Infection and Immunity; University of Melbourne; Parkville Vic. 3052 Australia
| | - Trevor Lithgow
- Department of Microbiology; Monash University; Clayton Vic. 3800 Australia
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16
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Molina F, López-Acedo E, Tabla R, Roa I, Gómez A, Rebollo JE. Improved detection of Escherichia coli and coliform bacteria by multiplex PCR. BMC Biotechnol 2015; 15:48. [PMID: 26040540 PMCID: PMC4453288 DOI: 10.1186/s12896-015-0168-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/17/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The presence of coliform bacteria is routinely assessed to establish the microbiological safety of water supplies and raw or processed foods. Coliforms are a group of lactose-fermenting Enterobacteriaceae, which most likely acquired the lacZ gene by horizontal transfer and therefore constitute a polyphyletic group. Among this group of bacteria is Escherichia coli, the pathogen that is most frequently associated with foodborne disease outbreaks and is often identified by β-glucuronidase enzymatic activity or by the redundant detection of uidA by PCR. Because a significant fraction of essential E. coli genes are preserved throughout the bacterial kingdom, alternative oligonucleotide primers for specific E. coli detection are not easily identified. RESULTS In this manuscript, two strategies were used to design oligonucleotide primers with differing levels of specificity for the simultaneous detection of total coliforms and E. coli by multiplex PCR. A consensus sequence of lacZ and the orphan gene yaiO were chosen as targets for amplification, yielding 234 bp and 115 bp PCR products, respectively. CONCLUSIONS The assay designed in this work demonstrated superior detection ability when tested with lab collection and dairy isolated lactose-fermenting strains. While lacZ amplicons were found in a wide range of coliforms, yaiO amplification was highly specific for E. coli. Additionally, yaiO detection is non-redundant with enzymatic methods.
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Affiliation(s)
- Felipe Molina
- Área de Genética, Departamento de Bioquímica y Biologia Molecular y Genética, Universidad de Extremadura, Badajoz, Spain.
| | - Elena López-Acedo
- Área de Genética, Departamento de Bioquímica y Biologia Molecular y Genética, Universidad de Extremadura, Badajoz, Spain.
| | - Rafael Tabla
- Dairy products, Technological institute of Food and Agriculture, Badajoz, Spain.
| | - Isidro Roa
- Dairy products, Technological institute of Food and Agriculture, Badajoz, Spain.
| | - Antonia Gómez
- Dairy products, Technological institute of Food and Agriculture, Badajoz, Spain.
| | - José E Rebollo
- Área de Genética, Departamento de Bioquímica y Biologia Molecular y Genética, Universidad de Extremadura, Badajoz, Spain.
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17
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Brown LS, Ladizhansky V. Membrane proteins in their native habitat as seen by solid-state NMR spectroscopy. Protein Sci 2015; 24:1333-46. [PMID: 25973959 DOI: 10.1002/pro.2700] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 12/21/2022]
Abstract
Membrane proteins play many critical roles in cells, mediating flow of material and information across cell membranes. They have evolved to perform these functions in the environment of a cell membrane, whose physicochemical properties are often different from those of common cell membrane mimetics used for structure determination. As a result, membrane proteins are difficult to study by traditional methods of structural biology, and they are significantly underrepresented in the protein structure databank. Solid-state Nuclear Magnetic Resonance (SSNMR) has long been considered as an attractive alternative because it allows for studies of membrane proteins in both native-like membranes composed of synthetic lipids and in cell membranes. Over the past decade, SSNMR has been rapidly developing into a major structural method, and a growing number of membrane protein structures obtained by this technique highlights its potential. Here we discuss membrane protein sample requirements, review recent progress in SSNMR methodologies, and describe recent advances in characterizing membrane proteins in the environment of a cellular membrane.
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Affiliation(s)
- Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Vladimir Ladizhansky
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
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18
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Sala A, Bordes P, Genevaux P. Multitasking SecB chaperones in bacteria. Front Microbiol 2014; 5:666. [PMID: 25538690 PMCID: PMC4257090 DOI: 10.3389/fmicb.2014.00666] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/17/2014] [Indexed: 12/17/2022] Open
Abstract
Protein export in bacteria is facilitated by the canonical SecB chaperone, which binds to unfolded precursor proteins, maintains them in a translocation competent state and specifically cooperates with the translocase motor SecA to ensure their proper targeting to the Sec translocon at the cytoplasmic membrane. Besides its key contribution to the Sec pathway, SecB chaperone tasking is critical for the secretion of the Sec-independent heme-binding protein HasA and actively contributes to the cellular network of chaperones that control general proteostasis in Escherichia coli, as judged by the significant interplay found between SecB and the trigger factor, DnaK and GroEL chaperones. Although SecB is mainly a proteobacterial chaperone associated with the presence of an outer membrane and outer membrane proteins, secB-like genes are also found in Gram-positive bacteria as well as in certain phages and plasmids, thus suggesting alternative functions. In addition, a SecB-like protein is also present in the major human pathogen Mycobacterium tuberculosis where it specifically controls a stress-responsive toxin–antitoxin system. This review focuses on such very diverse chaperone functions of SecB, both in E. coli and in other unrelated bacteria.
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Affiliation(s)
- Ambre Sala
- Laboratoire de Microbiologie et Génétique Moléculaire, Centre National de la Recherche Scientifique, Université Paul Sabatier, Toulouse, France
| | - Patricia Bordes
- Laboratoire de Microbiologie et Génétique Moléculaire, Centre National de la Recherche Scientifique, Université Paul Sabatier, Toulouse, France
| | - Pierre Genevaux
- Laboratoire de Microbiologie et Génétique Moléculaire, Centre National de la Recherche Scientifique, Université Paul Sabatier, Toulouse, France
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19
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Overexpression, purification and validation of antigenic Salmonella enterica serovar Typhi proteins identified from LC-MS/MS. Appl Biochem Biotechnol 2014; 174:1897-906. [PMID: 25149461 DOI: 10.1007/s12010-014-1173-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 08/15/2014] [Indexed: 11/25/2022]
Abstract
In our earlier study, an immunoblot analysis using sera from febrile patients revealed that a 50-kDa band from an outer membrane protein fraction of Salmonella enterica serovar Typhi was specifically recognized only by typhoid sera and not sera from other febrile illnesses. Here, we investigated the identities of the proteins contained in the immunogenic 50-kDa band to pinpoint antigens responsible for its immunogenicity. We first used LC-MS/MS for protein identification, then used the online tool ANTIGENpro for antigenicity prediction and produced recombinant proteins of the lead antigens for validation in an enzyme-linked immunosorbent assay (ELISA). We found that proteins TolC, GlpK and SucB were specific to typhoid sera but react to antibodies differently under native and denatured conditions. This difference suggests the presence of linear and conformational epitopes on these proteins.
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20
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Cruz R, Huesgen P, Riley SP, Wlodawer A, Faro C, Overall CM, Martinez JJ, Simões I. RC1339/APRc from Rickettsia conorii is a novel aspartic protease with properties of retropepsin-like enzymes. PLoS Pathog 2014; 10:e1004324. [PMID: 25144529 PMCID: PMC4140852 DOI: 10.1371/journal.ppat.1004324] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 07/09/2014] [Indexed: 11/18/2022] Open
Abstract
Members of the species Rickettsia are obligate intracellular, gram-negative, arthropod-borne pathogens of humans and other mammals. The life-threatening character of diseases caused by many Rickettsia species and the lack of reliable protective vaccine against rickettsioses strengthens the importance of identifying new protein factors for the potential development of innovative therapeutic tools. Herein, we report the identification and characterization of a novel membrane-embedded retropepsin-like homologue, highly conserved in 55 Rickettsia genomes. Using R. conorii gene homologue RC1339 as our working model, we demonstrate that, despite the low overall sequence similarity to retropepsins, the gene product of rc1339 APRc (for Aspartic Protease from Rickettsia conorii) is an active enzyme with features highly reminiscent of this family of aspartic proteases, such as autolytic activity impaired by mutation of the catalytic aspartate, accumulation in the dimeric form, optimal activity at pH 6, and inhibition by specific HIV-1 protease inhibitors. Moreover, specificity preferences determined by a high-throughput profiling approach confirmed common preferences between this novel rickettsial enzyme and other aspartic proteases, both retropepsins and pepsin-like. This is the first report on a retropepsin-like protease in gram-negative intracellular bacteria such as Rickettsia, contributing to the analysis of the evolutionary relationships between the two types of aspartic proteases. Additionally, we have also shown that APRc is transcribed and translated in R. conorii and R. rickettsii and is integrated into the outer membrane of both species. Finally, we demonstrated that APRc is sufficient to catalyze the in vitro processing of two conserved high molecular weight autotransporter adhesin/invasion proteins, Sca5/OmpB and Sca0/OmpA, thereby suggesting the participation of this enzyme in a relevant proteolytic pathway in rickettsial life-cycle. As a novel bona fide member of the retropepsin family of aspartic proteases, APRc emerges as an intriguing target for therapeutic intervention against fatal rickettsioses. Several rickettsiae are pathogenic to humans by causing severe infections, including epidemic typhus (Rickettsia prowazekii), Rocky Mountain spotted fever (Rickettsia rickettsii), and Mediterranean spotted fever (Rickettsia conorii). Progress in correlating rickettsial genes and gene functions has been greatly hampered by the intrinsic difficulty in working with these obligate intracellular bacteria, despite the increasing insights into the mechanisms of pathogenesis of and the immune response to rickettsioses. Therefore, comparison of the multiple available genomes of Rickettsia is proving to be the most practical method to identify new factors that may play a role in pathogenicity. Here, we identified and characterized a novel retropepsin-like enzyme, APRc, that is expressed by at least two pathogenic rickettsial species, R. conorii and R. rickettsii. We have also established that APRc acts to process two major surface antigen/virulence determinants (OmpB/Sca5, OmpA/Sca0) in vitro and we suggest that this processing event is important for protein function. We demonstrate that APRc is specifically inhibited by drugs clinically used to treat HIV infections, providing the exciting possibility of targeting this enzyme for therapeutic intervention. With this work, we demonstrate that retropepsin-type aspartic proteases are indeed present in prokaryotes, suggesting that these enzymes may represent an ancestral form of these proteases.
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Affiliation(s)
- Rui Cruz
- The Center for Neuroscience and Cell Biology (CNC), Coimbra, Portugal
- Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - Pitter Huesgen
- Centre for Blood Research and Department of Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean P. Riley
- Vector-Borne Diseases Laboratories, Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Carlos Faro
- The Center for Neuroscience and Cell Biology (CNC), Coimbra, Portugal
- Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - Christopher M. Overall
- Centre for Blood Research and Department of Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Juan J. Martinez
- Vector-Borne Diseases Laboratories, Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail: (JJM); (IS)
| | - Isaura Simões
- The Center for Neuroscience and Cell Biology (CNC), Coimbra, Portugal
- Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
- * E-mail: (JJM); (IS)
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21
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Browning DF, Matthews SA, Rossiter AE, Sevastsyanovich YR, Jeeves M, Mason JL, Wells TJ, Wardius CA, Knowles TJ, Cunningham AF, Bavro VN, Overduin M, Henderson IR. Mutational and topological analysis of the Escherichia coli BamA protein. PLoS One 2013; 8:e84512. [PMID: 24376817 PMCID: PMC3871556 DOI: 10.1371/journal.pone.0084512] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 11/15/2013] [Indexed: 11/18/2022] Open
Abstract
The multi-protein β-barrel assembly machine (BAM) of Escherichia coli is responsible for the folding and insertion of β-barrel containing integral outer membrane proteins (OMPs) into the bacterial outer membrane. An essential component of this complex is the BamA protein, which binds unfolded β-barrel precursors via the five polypeptide transport-associated (POTRA) domains in its N-terminus. The C-terminus of BamA contains a β-barrel domain, which tethers BamA to the outer membrane and is also thought to be involved in OMP insertion. Here we mutagenize BamA using linker scanning mutagenesis and demonstrate that all five POTRA domains are essential for BamA protein function in our experimental system. Furthermore, we generate a homology based model of the BamA β-barrel and test our model using insertion mutagenesis, deletion analysis and immunofluorescence to identify β-strands, periplasmic turns and extracellular loops. We show that the surface-exposed loops of the BamA β-barrel are essential.
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Affiliation(s)
- Douglas F. Browning
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- * E-mail: (DFB); (IRH)
| | - Sophie A. Matthews
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Amanda E. Rossiter
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Yanina R. Sevastsyanovich
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Mark Jeeves
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Jessica L. Mason
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Timothy J. Wells
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Catherine A. Wardius
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Timothy J. Knowles
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Adam F. Cunningham
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Vassiliy N. Bavro
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Michael Overduin
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Ian R. Henderson
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- * E-mail: (DFB); (IRH)
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22
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Sala A, Calderon V, Bordes P, Genevaux P. TAC from Mycobacterium tuberculosis: a paradigm for stress-responsive toxin-antitoxin systems controlled by SecB-like chaperones. Cell Stress Chaperones 2013; 18:129-35. [PMID: 23264229 PMCID: PMC3581621 DOI: 10.1007/s12192-012-0396-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 12/05/2012] [Accepted: 12/06/2012] [Indexed: 01/27/2023] Open
Abstract
Bacterial type II toxin-antitoxins (TAs) are two-component systems that modulate growth in response to specific stress conditions, thus promoting adaptation and persistence. The major human pathogen Mycobacterium tuberculosis potentially encodes 75 TAs and it has been proposed that persistence induced by active toxins might be relevant for its pathogenesis. In this work, we focus on the newly discovered toxin-antitoxin-chaperone (TAC) system of M. tuberculosis, an atypical stress-responsive TA system tightly controlled by a molecular chaperone that shows similarity to the canonical SecB chaperone involved in Sec-dependent protein export in Gram-negative bacteria. We performed a large-scale genome screening to reconstruct the evolutionary history of TAC systems and found that TAC is not restricted to mycobacteria and seems to have disseminated in diverse taxonomic groups by horizontal gene transfer. Our results suggest that TAC chaperones are evolutionary related to the solitary chaperone SecB and have diverged to become specialized toward their cognate antitoxins.
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Affiliation(s)
- Ambre Sala
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de la Recherche Scientifique and Université Paul Sabatier, 31000 Toulouse, France
| | - Virginie Calderon
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de la Recherche Scientifique and Université Paul Sabatier, 31000 Toulouse, France
| | - Patricia Bordes
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de la Recherche Scientifique and Université Paul Sabatier, 31000 Toulouse, France
| | - Pierre Genevaux
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de la Recherche Scientifique and Université Paul Sabatier, 31000 Toulouse, France
- Laboratoire de Microbiologie et Génétique Moléculaires, IBCG, CNRS, Université Paul Sabatier, 118, route de Narbonne, 31062 Toulouse cedex 09, France
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23
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Ko HJ, Park E, Song J, Yang TH, Lee HJ, Kim KH, Choi IG. Functional cell surface display and controlled secretion of diverse Agarolytic enzymes by Escherichia coli with a novel ligation-independent cloning vector based on the autotransporter YfaL. Appl Environ Microbiol 2012; 78:3051-8. [PMID: 22344647 PMCID: PMC3346495 DOI: 10.1128/aem.07004-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Accepted: 02/08/2012] [Indexed: 11/20/2022] Open
Abstract
Autotransporters have been employed as the anchoring scaffold for cell surface display by replacing their passenger domains with heterologous proteins to be displayed. We adopted an autotransporter (YfaL) of Escherichia coli for the cell surface display system. The critical regions in YfaL for surface display were identified for the construction of a ligation-independent cloning (LIC)-based display system. The designed system showed no detrimental effect on either the growth of the host cell or overexpressing heterologous proteins on the cell surface. We functionally displayed monomeric red fluorescent protein (mRFP1) as a reporter protein and diverse agarolytic enzymes from Saccharophagus degradans 2-40, including Aga86C and Aga86E, which previously had failed to be functional expressed. The system could display different sizes of proteins ranging from 25.3 to 143 kDa. We also attempted controlled release of the displayed proteins by incorporating a tobacco etch virus protease cleavage site into the C termini of the displayed proteins. The maximum level of the displayed protein was 6.1 × 10(4) molecules per a single cell, which corresponds to 5.6% of the entire cell surface of actively growing E. coli.
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Affiliation(s)
- Hyeok-Jin Ko
- Computational and Synthetic Biology Laboratory, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Eunhye Park
- Computational and Synthetic Biology Laboratory, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Joseph Song
- Computational and Synthetic Biology Laboratory, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Taek Ho Yang
- Chemical and Polymer Laboratory, R&D Center, GS Caltex Corporation, Daejeon, South Korea
| | - Hee Jong Lee
- Chemical and Polymer Laboratory, R&D Center, GS Caltex Corporation, Daejeon, South Korea
| | - Kyoung Heon Kim
- Computational and Synthetic Biology Laboratory, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - In-Geol Choi
- Computational and Synthetic Biology Laboratory, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
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24
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Klepsch MM, Persson JO, de Gier JWL. Consequences of the overexpression of a eukaryotic membrane protein, the human KDEL receptor, in Escherichia coli. J Mol Biol 2011; 407:532-42. [PMID: 21316372 PMCID: PMC3069486 DOI: 10.1016/j.jmb.2011.02.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2010] [Revised: 02/02/2011] [Accepted: 02/02/2011] [Indexed: 02/04/2023]
Abstract
Escherichia coli is the most widely used host for producing membrane proteins. Thus far, to study the consequences of membrane protein overexpression in E. coli, we have focussed on prokaryotic membrane proteins as overexpression targets. Their overexpression results in the saturation of the Sec translocon, which is a protein-conducting channel in the cytoplasmic membrane that mediates both protein translocation and insertion. Saturation of the Sec translocon leads to (i) protein misfolding/aggregation in the cytoplasm, (ii) impaired respiration, and (iii) activation of the Arc response, which leads to inefficient ATP production and the formation of acetate. The overexpression yields of eukaryotic membrane proteins in E. coli are usually much lower than those of prokaryotic ones. This may be due to differences between the consequences of the overexpression of prokaryotic and eukaryotic membrane proteins in E. coli. Therefore, we have now also studied in detail how the overexpression of a eukaryotic membrane protein, the human KDEL receptor, affects E. coli. Surprisingly, the consequences of the overexpression of a prokaryotic and a eukaryotic membrane protein are very similar. Strain engineering and likely also protein engineering can be used to remedy the saturation of the Sec translocon upon overexpression of both prokaryotic and eukaryotic membrane proteins in E. coli.
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Affiliation(s)
- Mirjam M. Klepsch
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jan O. Persson
- Department of Mathematics & Statistics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jan-Willem L. de Gier
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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25
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Outer membrane protein X (Ail) contributes to Yersinia pestis virulence in pneumonic plague and its activity is dependent on the lipopolysaccharide core length. Infect Immun 2010; 78:5233-43. [PMID: 20837715 DOI: 10.1128/iai.00783-10] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yersinia pestis, the causative agent of plague, is one of the most virulent microorganisms known. The outer membrane protein X (OmpX) in Y. pestis KIM is required for efficient bacterial adherence to and internalization by cultured HEp-2 cells and confers resistance to human serum. Here, we tested the contribution of OmpX to disease progression in the fully virulent Y. pestis CO92 strain by engineering a deletion mutant and comparing its ability in mediating pneumonic plague to that of the wild type in two animal models. The deletion of OmpX delayed the time to death up to 48 h in a mouse model and completely attenuated virulence in a rat model of disease. All rats challenged with 1 × 10(8) CFU of the ompX mutant survived, compared to the 50% lethal dose (LD50) of 1.2 × 10(3) CFU for the wild-type strain. Because murine serum is not bactericidal for the ompX mutant, the mechanism underlying the delay in time to death in mice was attributed to loss of adhesion/internalization properties but not serum resistance. The rat model, which is most similar to humans, highlighted the critical role of serum resistance in disease. To resolve conflicting evidence for the role of Y. pestis lipopolysaccharide (LPS) and OmpX in serum resistance, ompX was cloned into Escherichia coli D21 and three isogenic derivatives engineered to have progressively truncated LPS core saccharides. OmpX-mediated serum resistance, adhesiveness, and invasiveness, although dependent on LPS core length, displayed these functions in E. coli, independently of other Yersinia proteins and/or LPS. Also, autoaggregation was required for efficient OmpX-mediated adhesiveness and internalization but not serum resistance.
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Evolution of the RpoS regulon: origin of RpoS and the conservation of RpoS-dependent regulation in bacteria. J Mol Evol 2010; 70:557-71. [PMID: 20506020 DOI: 10.1007/s00239-010-9352-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Accepted: 05/03/2010] [Indexed: 10/19/2022]
Abstract
The RpoS sigma factor in proteobacteria regulates genes in stationary phase and in response to stress. Although of conserved function, the RpoS regulon may have different gene composition across species due to high genomic diversity and to known environmental conditions that select for RpoS mutants. In this study, the distribution of RpoS homologs in prokaryotes and the differential dependence of regulon members on RpoS for expression in two gamma-proteobacteria (Escherichia coli and Pseudomonas aeruginosa) were examined. Using a maximum-likelihood phylogeny and reciprocal best hits analysis, we show that the RpoS sigma factor is conserved within gamma-, beta-, and delta-proteobacteria. Annotated RpoS of Borrelia and the enteric RpoS are postulated to have separate evolutionary origins. To determine the conservation of RpoS-dependent gene expression across species, reciprocal best hits analysis was used to identify orthologs of the E. coli RpoS regulon in the RpoS regulon of P. aeruginosa. Of the 186 RpoS-dependent genes of E. coli, 50 proteins have an ortholog within the P. aeruginosa genome. Twelve genes of the 50 orthologs are RpoS-dependent in both species, and at least four genes are regulated by RpoS in other gamma-proteobacteria. Despite RpoS conservation in gamma-, beta-, and delta-proteobacteria, RpoS regulon composition is subject to modification between species. Environmental selection for RpoS mutants likely contributes to the evolutionary divergence and specialization of the RpoS regulon within different bacterial genomes.
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Korea CG, Badouraly R, Prevost MC, Ghigo JM, Beloin C. Escherichia coli K-12 possesses multiple cryptic but functional chaperone-usher fimbriae with distinct surface specificities. Environ Microbiol 2010; 12:1957-77. [PMID: 20345943 DOI: 10.1111/j.1462-2920.2010.02202.x] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Commensal and pathogenic Escherichia coli adherence to host and environmental surfaces is mediated by a variety of adhesins. Although extensively studied as a model bacterium, 34% of the genes in the E. coli K-12 genome have no known function. We hypothesized that some of them may correspond to functional adhesins. We characterized E. coli K-12 ycb, ybg, yfc, yad, yra, sfm and yeh operons, which display sequence and organizational homologies to type 1 fimbriae exported by the chaperone/usher pathway. We showed that, although these operons are poorly expressed under laboratory conditions, six of them are nevertheless functional when expressed, and promote adhesion to abiotic and/or epithelial cell surfaces. While the studied fimbriae display different binding specificities, we obtained evidence of synergy/interference with other adhesins such as Ag43 or type 1 fimbriae. We showed that their expression is under the negative control of H-NS and, except for yad, subjected to cAMP receptor protein-mediated activation and carbon catabolite repression. These results therefore demonstrate that ycb, yfc, yad, yra, sfm and yeh operons encode cryptic but functional fimbriae adhesins whose expression following environmental modifications could contribute to E. coli's ability to adhere to and colonize a wide diversity of surfaces in its various ecological niches.
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Affiliation(s)
- Charalampia-Georgia Korea
- Institut Pasteur, Unité de Génétique des Biofilms, CNRS URA 2172, 25-28 rue du Dr Roux, 750724 Paris Cedex 15, France
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Predicting weakly stable regions, oligomerization state, and protein-protein interfaces in transmembrane domains of outer membrane proteins. Proc Natl Acad Sci U S A 2009; 106:12735-40. [PMID: 19622743 DOI: 10.1073/pnas.0902169106] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Although the structures of many beta-barrel membrane proteins are available, our knowledge of the principles that govern their energetics and oligomerization states is incomplete. Here we describe a computational method to study the transmembrane (TM) domains of beta-barrel membrane proteins. Our method is based on a physical interaction model, a simplified conformational space for efficient enumeration, and an empirical potential function from a detailed combinatorial analysis. Using this method, we can identify weakly stable regions in the TM domain, which are found to be important structural determinants for beta-barrel membrane proteins. By calculating the melting temperatures of the TM strands, our method can also assess the stability of beta-barrel membrane proteins. Predictions on membrane enzyme PagP are consistent with recent experimental NMR and mutant studies. We have also discovered that out-clamps, in-plugs, and oligomerization are 3 general mechanisms for stabilizing weakly stable TM regions. In addition, we have found that extended and contiguous weakly stable regions often signal the existence of an oligomer and that strands located in the interfaces of protein-protein interactions are considerably less stable. Based on these observations, we can predict oligomerization states and can identify the interfaces of protein-protein interactions for beta-barrel membrane proteins by using either structure or sequence information. In a set of 25 nonhomologous proteins with known structures, our method successfully predicted whether a protein forms a monomer or an oligomer with 91% accuracy; in addition, our method identified with 82% accuracy the protein-protein interaction interfaces by using sequence information only when correct strands are given.
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29
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Localized and efficient curli nucleation requires the chaperone-like amyloid assembly protein CsgF. Proc Natl Acad Sci U S A 2009; 106:900-5. [PMID: 19131513 DOI: 10.1073/pnas.0812143106] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Elucidation of the early events in amyloidogenesis is key to understanding the pathology of, and developing therapies for, amyloid diseases. Critical informants about these early events are amyloid assembly proteins that facilitate the transition from monomer to amyloid fiber. Curli are a functional amyloid whose in vivo polymerization requires a dedicated nucleator protein, CsgB, and an assembly protein, CsgF. Here we demonstrate that without CsgF, curli subunits are released from the cell into the media and are inefficiently polymerized, resulting in fewer and mislocalized curli fibers. CsgF is secreted to the cell surface, where it mediates the cell-association and protease-resistance of the CsgB nucleator, suggesting that CsgF is required for specific localization and/or chaperoning of CsgB for full nucleator activity. CsgF is thus critical to achieve localized and efficient nucleation of fiber subunits into functional, cell-associated amyloid.
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30
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Outer and inner membrane proteins compose an arginine-agmatine exchange system in Chlamydophila pneumoniae. J Bacteriol 2008; 190:7431-40. [PMID: 18790867 DOI: 10.1128/jb.00652-08] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Most chlamydial strains have a pyruvoyl-dependent decarboxylase protein that converts L-arginine to agmatine. However, chlamydiae do not produce arginine, so they must import it from their host. Chlamydophila pneumoniae has a gene cluster encoding a putative outer membrane porin (CPn1033 or aaxA), an arginine decarboxylase (CPn1032 or aaxB), and a putative cytoplasmic membrane transporter (CPn1031 or aaxC). The aaxC gene was expressed in Escherichia coli producing an integral cytoplasmic membrane protein that catalyzed the exchange of L-arginine for agmatine. Expression of the aaxA gene produced an outer membrane protein that enhanced the arginine uptake and decarboxylation activity of cells coexpressing aaxB and aaxC. This chlamydial arginine/agmatine exchange system complemented an E. coli mutant missing the native arginine-dependent acid resistance system. These cells survived extreme acid shock in the presence of L-arginine. Biochemical and evolutionary analysis showed the aaxABC genes evolved convergently with the enteric arginine degradation system, and they could have a different physiological role in chlamydial cells. The chlamydial system uniquely includes an outer membrane porin, and it is most active at a higher pH from 3 to 5. The chlamydial AaxC transporter was resistant to cadaverine, L-lysine and L-ornithine, which inhibit the E. coli AdiC antiporter.
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31
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Weiner JH, Li L. Proteome of the Escherichia coli envelope and technological challenges in membrane proteome analysis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:1698-713. [PMID: 17904518 DOI: 10.1016/j.bbamem.2007.07.020] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Revised: 07/19/2007] [Accepted: 07/23/2007] [Indexed: 11/28/2022]
Abstract
The envelope of Escherichia coli is a complex organelle composed of the outer membrane, periplasm-peptidoglycan layer and cytoplasmic membrane. Each compartment has a unique complement of proteins, the proteome. Determining the proteome of the envelope is essential for developing an in silico bacterial model, for determining cellular responses to environmental alterations, for determining the function of proteins encoded by genes of unknown function and for development and testing of new experimental technologies such as mass spectrometric methods for identifying and quantifying hydrophobic proteins. The availability of complete genomic information has led several groups to develop computer algorithms to predict the proteome of each part of the envelope by searching the genome for leader sequences, beta-sheet motifs and stretches of alpha-helical hydrophobic amino acids. In addition, published experimental data has been mined directly and by machine learning approaches. In this review we examine the somewhat confusing available literature and relate published experimental data to the most recent gene annotation of E. coli to describe the predicted and experimental proteome of each compartment. The problem of characterizing integral versus membrane-associated proteins is discussed. The E. coli envelope proteome provides an excellent test bed for developing mass spectrometric techniques for identifying hydrophobic proteins that have generally been refractory to analysis. We describe the gel based and solution based proteome analysis approaches along with protein cleavage and proteolysis methods that investigators are taking to tackle this difficult problem.
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Affiliation(s)
- Joel H Weiner
- Membrane Protein Research Group and The Institute for Biomolecular Design, University of Alberta, Canada.
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32
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Role of the Helicobacter hepaticus flagellar sigma factor FliA in gene regulation and murine colonization. J Bacteriol 2008; 190:6398-408. [PMID: 18689480 DOI: 10.1128/jb.00626-08] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The enterohepatic Helicobacter species Helicobacter hepaticus colonizes the murine intestinal and hepatobiliary tract and is associated with chronic intestinal inflammation, gall stone formation, hepatitis, and hepatocellular carcinoma. Thus far, the role of H. hepaticus motility and flagella in intestinal colonization is unknown. In other, closely related bacteria, late flagellar genes are mainly regulated by the sigma factor FliA (sigma(28)). We investigated the function of the H. hepaticus FliA in gene regulation, flagellar biosynthesis, motility, and murine colonization. Competitive microarray analysis of the wild type versus an isogenic fliA mutant revealed that 11 genes were significantly more highly expressed in wild-type bacteria and 2 genes were significantly more highly expressed in the fliA mutant. Most of these were flagellar genes, but four novel FliA-regulated genes of unknown function were identified. H. hepaticus possesses two identical copies of the gene encoding the FliA-dependent major flagellin subunit FlaA (open reading frames HH1364 and HH1653). We characterized the phenotypes of mutants in which fliA or one or both copies of the flaA gene were knocked out. flaA_1 flaA_2 double mutants and fliA mutants did not synthesize detectable amounts of FlaA and possessed severely truncated flagella. Also, both mutants were nonmotile and unable to colonize mice. Mutants with either flaA gene knocked out produced flagella morphologically similar to those of wild-type bacteria and expressed FlaA and FlaB. flaA_1 mutants which had flagella but displayed reduced motility did not colonize mice, indicating that motility is required for intestinal colonization by H. hepaticus and that the presence of flagella alone is not sufficient.
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Effects of SecE depletion on the inner and outer membrane proteomes of Escherichia coli. J Bacteriol 2008; 190:3505-25. [PMID: 18296516 DOI: 10.1128/jb.01631-07] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Sec translocon is a protein-conducting channel that allows polypeptides to be transferred across or integrated into a membrane. Although protein translocation and insertion in Escherichia coli have been studied using only a small set of specific model substrates, it is generally assumed that most secretory proteins and inner membrane proteins use the Sec translocon. Therefore, we have studied the role of the Sec translocon using subproteome analysis of cells depleted of the essential translocon component SecE. The steady-state proteomes and the proteome dynamics were evaluated using one- and two-dimensional gel analysis, followed by mass spectrometry-based protein identification and extensive immunoblotting. The analysis showed that upon SecE depletion (i) secretory proteins aggregated in the cytoplasm and the cytoplasmic sigma(32) stress response was induced, (ii) the accumulation of outer membrane proteins was reduced, with the exception of OmpA, Pal, and FadL, and (iii) the accumulation of a surprisingly large number of inner membrane proteins appeared to be unaffected or increased. These proteins lacked large translocated domains and/or consisted of only one or two transmembrane segments. Our study suggests that several secretory and inner membrane proteins can use Sec translocon-independent pathways or have superior access to the remaining Sec translocons present in SecE-depleted cells.
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34
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Gromiha MM, Yabuki Y, Suwa M. TMB finding pipeline: novel approach for detecting beta-barrel membrane proteins in genomic sequences. J Chem Inf Model 2007; 47:2456-61. [PMID: 17958348 DOI: 10.1021/ci700222s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have developed a novel approach for dissecting transmembrane beta-barrel proteins (TMBs) in genomic sequences. The features include (i) the identification of TMBs using the preference of residue pairs in globular, transmembrane helical (TMH) and TMBs, (ii) elimination of globular/TMH proteins that show sequence identity of more than 70% for the coverage of 80% residues with known structures, (iii) elimination of globular/TMH proteins that have sequence identity of more than 60% with known sequences in SWISS-PROT, and (iv) exclusion of TMH proteins using SOSUI, a prediction system for TMH proteins. Our approach picked up 7% TMBs in all the considered genomes. The comparison between the identified TMBs in E. coli genome and available experimental data demonstrated that the new approach could correctly identify all the 11 known TMBs, whose crystal structures are available. Further, it revealed the presence of 19 TMBs, homology with known structures, 60 TMBs similar to well annotated sequences, and 54 TMBs that have high sequence similarity with Escherichia coli beta-barrel proteins deposited in Transport Classification Database (TCDB). Interestingly, the present approach identified TMBs from all 15 families in TCDB. In human genome, the occurrence of TMBs varies from 0 to 3% in different chromosomes. We suggest that our approach could lead to a step forward in the advancement of structural and functional genomics.
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Affiliation(s)
- M Michael Gromiha
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), AIST Tokyo Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan.
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35
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Garrow AG, Westhead DR. A consensus algorithm to screen genomes for novel families of transmembrane beta barrel proteins. Proteins 2007; 69:8-18. [PMID: 17557332 DOI: 10.1002/prot.21439] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The ability to search sequence datasets for membrane spanning proteins is an important requirement for genome annotation. However, the development of algorithms to identify novel types of transmembrane beta-barrel (TMB) protein has proven substantially harder than for transmembrane helical proteins, owing to a shorter TM domain in which only alternate residues are hydrophobic. Although recent reports have described important improvements in the development of such algorithms, there is still concern over their ability to confidently screen genomes. Here we describe a new algorithm combining composition and hidden Markov model topology based classifiers (called TMB-Hunt2), which achieves a crossvalidation accuracy of >95%, with 96.7% precision and 94.2% recall. An overview is given of the algorithm design, with a thorough assessment of performance and application to a number of genomes. Of particular note is that TMB/extracellular protein discrimination is significantly more difficult than TMB/cytoplasmic protein discrimination, with the predictor correctly rejecting just 74% of extracellular proteins, in comparison to 98% of cytoplasmic proteins. Focus is given to directions for further improvements in TMB/non-TMB protein discrimination, with a call for the development of standardized tests and assessments of such algorithms. Tools and datasets are made available through a website called TMB-Web (http://www.bioinformatics.leeds.ac.uk/TMB-Web/TMB-Hunt2).
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Affiliation(s)
- Andrew G Garrow
- Institute of Cellular and Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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36
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Wagner S, Baars L, Ytterberg AJ, Klussmeier A, Wagner CS, Nord O, Nygren PA, van Wijk KJ, de Gier JW. Consequences of membrane protein overexpression in Escherichia coli. Mol Cell Proteomics 2007; 6:1527-50. [PMID: 17446557 DOI: 10.1074/mcp.m600431-mcp200] [Citation(s) in RCA: 268] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Overexpression of membrane proteins is often essential for structural and functional studies, but yields are frequently too low. An understanding of the physiological response to overexpression is needed to improve such yields. Therefore, we analyzed the consequences of overexpression of three different membrane proteins (YidC, YedZ, and LepI) fused to green fluorescent protein (GFP) in the bacterium Escherichia coli and compared this with overexpression of a soluble protein, GST-GFP. Proteomes of total lysates, purified aggregates, and cytoplasmic membranes were analyzed by one- and two-dimensional gel electrophoresis and mass spectrometry complemented with flow cytometry, microscopy, Western blotting, and pulse labeling experiments. Composition and accumulation levels of protein complexes in the cytoplasmic membrane were analyzed with improved two-dimensional blue native PAGE. Overexpression of the three membrane proteins, but not soluble GST-GFP, resulted in accumulation of cytoplasmic aggregates containing the overexpressed proteins, chaperones (DnaK/J and GroEL/S), and soluble proteases (HslUV and ClpXP) as well as many precursors of periplasmic and outer membrane proteins. This was consistent with lowered accumulation levels of secreted proteins in the three membrane protein overexpressors and is likely to be a direct consequence of saturation of the cytoplasmic membrane protein translocation machinery. Importantly accumulation levels of respiratory chain complexes in the cytoplasmic membrane were strongly reduced. Induction of the acetate-phosphotransacetylase pathway for ATP production and a down-regulated tricarboxylic acid cycle indicated the activation of the Arc two-component system, which mediates adaptive responses to changing respiratory states. This study provides a basis for designing rational strategies to improve yields of membrane protein overexpression in E. coli.
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Affiliation(s)
- Samuel Wagner
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91, Stockholm, Sweden
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37
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Hancock V, Klemm P. Global gene expression profiling of asymptomatic bacteriuria Escherichia coli during biofilm growth in human urine. Infect Immun 2007; 75:966-76. [PMID: 17145952 PMCID: PMC1828481 DOI: 10.1128/iai.01748-06] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Accepted: 11/17/2006] [Indexed: 11/20/2022] Open
Abstract
Urinary tract infection (UTI) is an important health problem worldwide, with many millions of cases each year, and Escherichia coli is the most common organism causing UTI in humans. Also, E. coli is responsible for most infections in patients with chronic indwelling bladder catheter. The two asymptomatic bacteriuria (ABU) E. coli strains 83972 and VR50 are significantly better biofilm formers in their natural growth medium, human urine, than the two uropathogenic E. coli isolates CFT073 and 536. We used DNA microarrays to monitor the expression profile during biofilm growth in urine of the two ABU strains 83972 and VR50. Significant differences in expression levels were seen between the biofilm expression profiles of the two strains with the corresponding planktonic expression profiles in morpholinepropanesulfonic acid minimal laboratory medium and human urine; 417 and 355 genes were up- and down-regulated, respectively, during biofilm growth in urine of 83972 and VR50. Many genes involved in transcription and stress were up-regulated in biofilm-grown cells. The role in biofilm formation of four of the up-regulated genes, i.e., yceP, yqgA, ygiD, and aaeX, was investigated by creating single-knockout mutant versions of 83972 and VR50; all mutants showed reduced biofilm formation in urine by 18 to 43% compared with the wild type (P < 0.05). Also, the expression profile of strain 83972 in the human urinary tract partially overlaps with the biofilm expression profile.
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Affiliation(s)
- Viktoria Hancock
- Microbial Adhesion Group, Center for Biomedical Microbiology, BioCentrum-DTU, Building 301, Technical University of Denmark, DK-2800 Lyngby, Denmark
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