1
|
Lindemeier D, Graubner W, Mehner-Breitfeld D, Malešević M, Brüser T. Positive charges promote the recognition of proteins by the chaperone SlyD from Escherichia coli. PLoS One 2024; 19:e0305823. [PMID: 38917203 PMCID: PMC11198818 DOI: 10.1371/journal.pone.0305823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 06/04/2024] [Indexed: 06/27/2024] Open
Abstract
SlyD is a widely-occurring prokaryotic FKBP-family prolyl isomerase with an additional chaperone domain. Often, such as in Escherichia coli, a third domain is found at its C-terminus that binds nickel and provides it for nickel-enzyme biogenesis. SlyD has been found to bind signal peptides of proteins that are translocated by the Tat pathway, a system for the transport of folded proteins across membranes. Using peptide arrays to analyze these signal peptide interactions, we found that SlyD interacted only with positively charged peptides, with a preference for arginines over lysines, and large hydrophobic residues enhanced binding. Especially a twin-arginine motif was recognized, a pair of highly conserved arginines adjacent to a stretch of hydrophobic residues. Using isothermal titration calorimetry (ITC) with purified SlyD and a signal peptide-containing model Tat substrate, we could show that the wild type twin-arginine signal peptide was bound with higher affinity than an RR>KK mutated variant, confirming that positive charges are recognized by SlyD, with a preference of arginines over lysines. The specific role of negative charges of the chaperone domain surface and of hydrophobic residues in the chaperone active site was further analyzed by ITC of mutated SlyD variants. Our data show that the supposed key hydrophobic residues of the active site are indeed crucial for binding, and that binding is influenced by negative charges on the chaperone domain. Recognition of positive charges is likely achieved by a large negatively charged surface region of the chaperone domain, which is highly conserved although individual positions are variable.
Collapse
Affiliation(s)
- Daniel Lindemeier
- Institute of Microbiology, Leibniz Universität Hannover, Hanover, Germany
| | - Wenke Graubner
- Institute of Microbiology, Leibniz Universität Hannover, Hanover, Germany
| | | | - Miroslav Malešević
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Thomas Brüser
- Institute of Microbiology, Leibniz Universität Hannover, Hanover, Germany
| |
Collapse
|
2
|
Hernández-Martínez G, Ares MA, Rosales-Reyes R, Soria-Bustos J, Yañez-Santos JA, Cedillo ML, Girón JA, Martínez-Laguna Y, Leng F, Ibarra JA, De la Cruz MA. The nucleoid protein HU positively regulates the expression of type VI secretion systems in Enterobacter cloacae. mSphere 2024; 9:e0006024. [PMID: 38647313 DOI: 10.1128/msphere.00060-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024] Open
Abstract
Enterobacter cloacae is an emerging pathogen isolated in healthcare-associated infections. A major virulence factor of this bacterium is the type VI secretion system (T6SS). The genome of E. cloacae harbors two T6SS gene clusters (T6SS-1 and T6SS-2), and the functional characterization of both systems showed that these two T6SSs are not expressed under the same conditions. Here, we report that the major histone-like protein HU positively regulates the expression of both T6SSs and, therefore, the function that each T6SS exerts in E. cloacae. Single deletions of the genes encoding the HU subunits (hupA and hupB) decreased mRNA levels of both T6SS. In contrast, the hupA hupB double mutant dramatically affected the T6SS expression, diminishing its transcription. The direct binding of HU to the promoter regions of T6SS-1 and T6SS-2 was confirmed by electrophoretic mobility shift assay. In addition, single and double mutations in the hup genes affected the ability of inter-bacterial killing, biofilm formation, adherence to epithelial cells, and intestinal colonization, but these phenotypes were restored when such mutants were trans-complemented. Our data broaden our understanding of the regulation of HU-mediated T6SS in these pathogenic bacteria. IMPORTANCE T6SS is a nanomachine that functions as a weapon of bacterial destruction crucial for successful colonization in a specific niche. Enterobacter cloacae expresses two T6SSs required for bacterial competition, adherence, biofilm formation, and intestinal colonization. Expression of T6SS genes in pathogenic bacteria is controlled by multiple regulatory systems, including two-component systems, global regulators, and nucleoid proteins. Here, we reported that the HU nucleoid protein directly activates both T6SSs in E. cloacae, affecting the T6SS-related phenotypes. Our data describe HU as a new regulator involved in the transcriptional regulation of T6SS and its impact on E. cloacae pathogenesis.
Collapse
Affiliation(s)
- Gabriela Hernández-Martínez
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Miguel A Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Roberto Rosales-Reyes
- Unidad de Medicina Experimental de la Facultad de Medicina, Universidad Autónoma de México, Mexico City, Mexico
| | - Jorge Soria-Bustos
- Pathogen and Microbiome Division, Translational Genomics Research Institute (TGen) North, Flagstaff, Arizona, USA
- Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Pachuca, Hidalgo, Mexico
| | | | - María L Cedillo
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Jorge A Girón
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Ygnacio Martínez-Laguna
- Centro de Investigación en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Fenfei Leng
- Biomolecular Sciences Institute and Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - J Antonio Ibarra
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Miguel A De la Cruz
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
- Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| |
Collapse
|
3
|
Son A, Smetana JS, Horowitz S, Lennon CW. An intein-based biosensor to measure protein stability in vivo. Protein Sci 2024; 33:e4925. [PMID: 38380775 PMCID: PMC10880411 DOI: 10.1002/pro.4925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/10/2024] [Accepted: 01/29/2024] [Indexed: 02/22/2024]
Abstract
Biosensors to measure protein stability in vivo are valuable tools for a variety of applications. Previous work has demonstrated that a tripartite design, whereby a protein of interest (POI) is inserted within a reporter, can link POI stability to reporter activity. Inteins are translated within other proteins and excised in a self-mediated protein splicing reaction. Here, we developed a novel folding biosensor where a POI is inserted within an intein, which is subsequently translated within an antibiotic resistance marker. We showed that protein splicing is required for antibiotic resistance and that housing a stable POI within the intein, compared to an unstable variant, results in a 100,000-fold difference in survival. Further, using a fluorescent protein that matures slowly as the POI, we developed a reporter with two simultaneous readouts for protein folding. Finally, we showed that co-expression of GroEL can significantly increase the activity of both reporters, further verifying that protein folding factors can act on the POI in the biosensor. As a whole, our work provides a new twist on the traditional tripartite approach to measuring protein stability in vivo.
Collapse
Affiliation(s)
- Ahyun Son
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy AgingUniversity of DenverDenverColoradoUSA
| | - John S. Smetana
- Department of Biological SciencesMurray State UniversityMurrayKentuckyUSA
| | - Scott Horowitz
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy AgingUniversity of DenverDenverColoradoUSA
| | | |
Collapse
|
4
|
Haase A, Arlt C, Sinz A, Sawers RG. Evidence the Isc iron-sulfur cluster biogenesis machinery is the source of iron for [NiFe]-cofactor biosynthesis in Escherichia coli. Sci Rep 2024; 14:3026. [PMID: 38321125 PMCID: PMC10847431 DOI: 10.1038/s41598-024-53745-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/04/2024] [Indexed: 02/08/2024] Open
Abstract
[NiFe]-hydrogenases have a bimetallic NiFe(CN)2CO cofactor in their large, catalytic subunit. The 136 Da Fe(CN)2CO group of this cofactor is preassembled on a distinct HypC-HypD scaffold complex, but the intracellular source of the iron ion is unresolved. Native mass spectrometric analysis of HypCD complexes defined the [4Fe-4S] cluster associated with HypD and identified + 26 to 28 Da and + 136 Da modifications specifically associated with HypC. A HypCC2A variant without the essential conserved N-terminal cysteine residue dissociated from its complex with native HypD lacked all modifications. Native HypC dissociated from HypCD complexes isolated from Escherichia coli strains deleted for the iscS or iscU genes, encoding core components of the Isc iron-sulfur cluster biogenesis machinery, specifically lacked the + 136 Da modification, but this was retained on HypC from suf mutants. The presence or absence of the + 136 Da modification on the HypCD complex correlated with the hydrogenase enzyme activity profiles of the respective mutant strains. Notably, the [4Fe-4S] cluster on HypD was identified in all HypCD complexes analyzed. These results suggest that the iron of the Fe(CN)2CO group on HypCD derives from the Isc machinery, while either the Isc or the Suf machinery can deliver the [4Fe-4S] cluster to HypD.
Collapse
Affiliation(s)
- Alexander Haase
- Institute of Biology/ Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Christian Arlt
- Institute of Pharmacy, Center for Structural Mass Spectrometry, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany
| | - Andrea Sinz
- Institute of Pharmacy, Center for Structural Mass Spectrometry, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany
| | - R Gary Sawers
- Institute of Biology/ Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany.
| |
Collapse
|
5
|
Lee Upton S, Tay JW, Schwartz DK, Sousa MC. Similarly slow diffusion of BAM and SecYEG complexes in live E. coli cells observed with 3D spt-PALM. Biophys J 2023; 122:4382-4394. [PMID: 37853695 PMCID: PMC10698321 DOI: 10.1016/j.bpj.2023.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/05/2023] [Accepted: 10/16/2023] [Indexed: 10/20/2023] Open
Abstract
The β-barrel assembly machinery (BAM) complex is responsible for inserting outer membrane proteins (OMPs) into the Escherichia coli outer membrane. The SecYEG translocon inserts inner membrane proteins into the inner membrane and translocates both soluble proteins and nascent OMPs into the periplasm. Recent reports describe Sec possibly playing a direct role in OMP biogenesis through interactions with the soluble polypeptide transport-associated (POTRA) domains of BamA (the central OMP component of BAM). Here we probe the diffusion behavior of these protein complexes using photoactivatable super-resolution localization microscopy and single-particle tracking in live E. coli cells of BAM and SecYEG components BamA and SecE and compare them to other outer and inner membrane proteins. To accurately measure trajectories on the highly curved cell surface, three-dimensional tracking was performed using double-helix point-spread function microscopy. All proteins tested exhibit two diffusive modes characterized by "slow" and "fast" diffusion coefficients. We implement a diffusion coefficient analysis as a function of the measurement lag time to separate positional uncertainty from true mobility. The resulting true diffusion coefficients of the slow and fast modes showed a complete immobility of full-length BamA constructs in the time frame of the experiment, whereas the OMP OmpLA displayed a slow diffusion consistent with the high viscosity of the outer membrane. The periplasmic POTRA domains of BamA were found to anchor BAM to other cellular structures and render it immobile. However, deletion of individual distal POTRA domains resulted in increased mobility, suggesting that these domains are required for the full set of cellular interactions. SecE diffusion was much slower than that of the inner membrane protein PgpB and was more like OMPs and BamA. Strikingly, SecE diffused faster upon POTRA domain deletion. These results are consistent with the existence of a BAM-SecYEG trans-periplasmic assembly in live E. coli cells.
Collapse
Affiliation(s)
- Stephen Lee Upton
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado
| | - Jian Wei Tay
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Daniel Keith Schwartz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado
| | | |
Collapse
|
6
|
Hubert T, Madec M, Schalk IJ. Experimental and computational methods to highlight behavioural variations in TonB-dependent transporter expression in Pseudomonas aeruginosa versus siderophore concentration. Sci Rep 2023; 13:20015. [PMID: 37974013 PMCID: PMC10654771 DOI: 10.1038/s41598-023-46585-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
Iron is a key nutrient for bacterial growth. The source can be either heme or siderophore-Fe complexes. Siderophores are small molecules synthesized by bacteria to scavenge iron from the bacterial environment. The pathogen Pseudomonas aeruginosa can express at least 15 different iron uptake pathways and all but one involve a TonB-dependent transporter (TBDT) for the uptake of iron across the outer membrane. Little is known about how bacteria modulate and adapt the expression of their different iron import pathways according to their environment. Here, we have developed fluorescent reporters between the promoter region of genes encoding a TBDT and the fluorescent reporter mCherry. With these constructs, we can follow the expression of TBDTs under different growth conditions. Mathematical modelling of the data obtained showed the transcription and expression of the gene encoding the TBDT PfeA to have a sigmoidal shape, whereas it was logarithmic for the TBDT gene foxA. Maximum transcription for pfeA was reached in the presence of 3 µM enterobactin, the siderophore recognized by PfeA, whereas the maximum was not reached for foxA with 100 µM nocardamine, the siderophore of FoxA.
Collapse
Affiliation(s)
- Thibaut Hubert
- CNRS, UMR7242, ESBS, University of Strasbourg, Bld Sébastien Brant, 67412, Illkirch, Strasbourg, France
- ICube Laboratory, CNRS, UMR 7357, University of Strasbourg, Bld Sébastien Brant, 67412, Illkirch, Strasbourg, France
| | - Morgan Madec
- ICube Laboratory, CNRS, UMR 7357, University of Strasbourg, Bld Sébastien Brant, 67412, Illkirch, Strasbourg, France.
| | - Isabelle J Schalk
- CNRS, UMR7242, ESBS, University of Strasbourg, Bld Sébastien Brant, 67412, Illkirch, Strasbourg, France.
| |
Collapse
|
7
|
Yao Y, Sun H, Wurihan, Gegeheng, Gezi, Skarstad K, Fan L, Morigen. A DnaA-dependent riboswitch for transcription attenuation of the his operon. MLIFE 2023; 2:126-140. [PMID: 38817620 PMCID: PMC10989985 DOI: 10.1002/mlf2.12075] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 06/04/2023] [Indexed: 06/01/2024]
Abstract
Transcription attenuation in response to the availability of a specific amino acid is believed to be controlled by alternative configurations of RNA secondary structures that lead to the arrest of translation or the release of the arrested ribosome from the leader mRNA molecule. In this study, we first report a possible example of the DnaA-dependent riboswitch for transcription attenuation in Escherichia coli. We show that (i) DnaA regulates the transcription of the structural genes but not that of the leader hisL gene; (ii) DnaA might bind to rDnaA boxes present in the HisL-SL RNA, and subsequently attenuate the transcription of the operon; (iii) the HisL-SL RNA and rDnaA boxes are phylogenetically conserved and evolutionarily important; and (iv) the translating ribosome is required for deattenuation of the his operon, whereas tRNAHis strengthens attenuation. This mechanism seems to be phylogenetically conserved in Gram-negative bacteria and evolutionarily important.
Collapse
Affiliation(s)
- Yuan Yao
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Hongwei Sun
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Wurihan
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Gegeheng
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Gezi
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Kirsten Skarstad
- Department of Molecular Cell Biology and Department of MicrobiologyOslo University HospitalOsloNorway
| | - Lifei Fan
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| | - Morigen
- State Key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
| |
Collapse
|
8
|
Kannoly S, Oken G, Shadan J, Musheyev D, Singh K, Singh A, Dennehy JJ. Single-Cell Approach Reveals Intercellular Heterogeneity in Phage-Producing Capacities. Microbiol Spectr 2023; 11:e0266321. [PMID: 36541779 PMCID: PMC9927085 DOI: 10.1128/spectrum.02663-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bacteriophage burst size is the average number of phage virions released from infected bacterial cells, and its magnitude depends on the duration of an intracellular progeny accumulation phase. Burst size is often measured at the population level, not the single-cell level, and consequently, statistical moments are not commonly available. In this study, we estimated the bacteriophage lambda (λ) single-cell burst size mean and variance following different intracellular accumulation period durations by employing Escherichia coli lysogens bearing lysis-deficient λ prophages. Single lysogens can be isolated and chemically lysed at desired times following prophage induction to quantify progeny intracellular accumulation within individual cells. Our data showed that λ phage burst size initially increased exponentially with increased lysis time (i.e., period between induction and chemical lysis) and then saturated at longer lysis times. We also demonstrated that cell-to-cell variation, or "noise," in lysis timing did not contribute significantly to burst size noise. The burst size noise remained constant with increasing mean burst size. The most likely explanation for the experimentally observed constant burst size noise was that cell-to-cell differences in burst size originated from intercellular heterogeneity in cellular capacities to produce phages. The mean burst size measured at different lysis times was positively correlated to cell volume, which may determine the cellular phage production capacity. However, experiments controlling for cell size indicated that there are other factors in addition to cell size that determine this cellular capacity. IMPORTANCE Phages produce offspring by hijacking a cell's replicative machinery. Previously, it was noted that the variation in the number of phages produced by single infected cells far exceeded cell size variation. It was hypothesized that this variation is a consequence of variation in the timing of host cell lysis. Here, we show that cell-to-cell variation in lysis timing does not significantly contribute to the burst size variation. We suggest that the constant burst size variation across different host lysis times results from cell-to-cell differences in capacity to produce phages. We found that the mean burst size measured at different lysis times was positively correlated to cell volume, which may determine the cellular phage production capacity. However, experiments controlling for cell size indicated that there are other factors in addition to cell size that determine this cellular capacity.
Collapse
Affiliation(s)
- Sherin Kannoly
- Biology Department, Queens College of The City University of New York, New York, New York, USA
| | - Gabriella Oken
- Biology Department, Queens College of The City University of New York, New York, New York, USA
| | - Jonathan Shadan
- Biology Department, Queens College of The City University of New York, New York, New York, USA
| | - David Musheyev
- Biology Department, Queens College of The City University of New York, New York, New York, USA
| | - Kevin Singh
- Biology Department, Queens College of The City University of New York, New York, New York, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware, USA
| | - John J. Dennehy
- Biology Department, Queens College of The City University of New York, New York, New York, USA
- The Graduate Center of The City University of New York, New York, New York, USA
| |
Collapse
|
9
|
Haase A, Sawers RG. A redox-active HybG-HypD scaffold complex is required for optimal ATPase activity during [NiFe]-hydrogenase maturation in Escherichia coli. FEBS Open Bio 2023; 13:341-351. [PMID: 36602404 PMCID: PMC9900092 DOI: 10.1002/2211-5463.13546] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/23/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023] Open
Abstract
Four Hyp proteins build a scaffold complex upon which the Fe(CN)2 CO group of the [NiFe]-cofactor of hydrogenases (Hyd) is made. Two of these Hyp proteins, the redox-active, [4Fe-4S]-containing HypD protein and the HypC chaperone, form the basis of this scaffold complex. Two different scaffold complexes exist in Escherichia coli, HypCD, and the paralogous HybG-HypD complex, both of which exhibit ATPase activity. Apart from a Rossmann fold, there is no obvious ATP-binding site in HypD. The aim of this study, therefore, was to identify amino acid motifs in HypD that are required for the ATPase activity of the HybG-HypD scaffold complex. Amino acid-exchange variants in three conserved motifs within HypD were generated. Variants in which individual cysteine residues coordinating the iron-sulfur ([4Fe-4S]) cluster were exchanged abolished Hyd enzyme activity and reduced ATPase activity but also destabilized the complex. Two conserved cysteine residues, C69 and C72, form part of HypD's Rossmann fold and play a role in HypD's thiol-disulfide exchange activity. Substitution of these two residues individually with alanine also abolished hydrogenase activity and strongly reduced ATPase activity, particularly the C72A exchange. Residues in a further conserved GFETT motif were exchanged, but neither hydrogenase enzyme activity nor ATPase activity of the isolated HybG-HypD complexes was significantly affected. Together, our findings identify a strong correlation between the redox activity of HypD, ATPase activity, and the ability of the complex to mature Hyd enzymes. These results further highlight the important role of thiol residues in the HybG-HypD scaffold complex during [NiFe]-cofactor biosynthesis.
Collapse
Affiliation(s)
- Alexander Haase
- Institute for Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergGermany
| | - R. Gary Sawers
- Institute for Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergGermany
| |
Collapse
|
10
|
Hall CP, Jadeja NB, Sebeck N, Agaisse H. Characterization of MxiE- and H-NS-Dependent Expression of ipaH7.8, ospC1, yccE, and yfdF in Shigella flexneri. mSphere 2022; 7:e0048522. [PMID: 36346241 PMCID: PMC9769918 DOI: 10.1128/msphere.00485-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2022] Open
Abstract
Shigella flexneri uses a type 3 secretion system (T3SS) apparatus to inject virulence effector proteins into the host cell cytosol. Upon host cell contact, MxiE, an S. flexneri AraC-like transcriptional regulator, is required for the expression of a subset of T3SS effector genes encoded on the large virulence plasmid. Here, we defined the MxiE regulon using RNA-seq. We identified virulence plasmid- and chromosome-encoded genes that are activated in response to type 3 secretion in a MxiE-dependent manner. Bioinformatic analysis revealed that similar to previously known MxiE-dependent genes, chromosome-encoded genes yccE and yfdF contain a regulatory element known as the MxiE box, which is required for their MxiE-dependent expression. The significant AT enrichment of MxiE-dependent genes suggested the involvement of H-NS. Using a dominant negative H-NS system, we demonstrate that H-NS silences the expression of MxiE-dependent genes located on the virulence plasmid (ipaH7.8 and ospC1) and the chromosome (yccE and yfdF). Furthermore, we show that MxiE is no longer required for the expression of ipaH7.8, ospC1, yccE, and yfdF when H-NS silencing is relieved. Finally, we show that the H-NS anti-silencer VirB is not required for ipaH7.8 and yccE expression upon MxiE/IpgC overexpression. Based on these genetic studies, we propose a model of MxiE-dependent gene regulation in which MxiE counteracts H-NS-mediated silencing. IMPORTANCE The expression of horizontally acquired genes, including virulence genes, is subject to complex regulation involving xenogeneic silencing proteins, and counter-silencing mechanisms. The pathogenic properties of Shigella flexneri mainly rely on the acquisition of the type 3 secretion system (T3SS) and cognate effector proteins, whose expression is repressed by the xenogeneic silencing protein H-NS. Based on previous studies, releasing H-NS-mediated silencing mainly relies on two mechanisms involving (i) a temperature shift leading to the release of H-NS at the virF promoter, and (ii) the virulence factor VirB, which dislodges H-NS upon binding to specific motifs upstream of virulence genes, including those encoding the T3SS. In this study, we provide genetic evidence supporting the notion that, in addition to VirB, the AraC family member MxiE also contributes to releasing H-NS-mediated silencing in S. flexneri.
Collapse
Affiliation(s)
- Chelsea P. Hall
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Niti B. Jadeja
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Natalie Sebeck
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Hervé Agaisse
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| |
Collapse
|
11
|
Eismann L, Fijalkowski I, Galmozzi CV, Koubek J, Tippmann F, Van Damme P, Kramer G. Selective ribosome profiling reveals a role for SecB in the co-translational inner membrane protein biogenesis. Cell Rep 2022; 41:111776. [PMID: 36476862 DOI: 10.1016/j.celrep.2022.111776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 10/04/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
The chaperone SecB has been implicated in de novo protein folding and translocation across the membrane, but it remains unclear which nascent polypeptides SecB binds, when during translation SecB acts, how SecB function is coordinated with other chaperones and targeting factors, and how polypeptide engagement contributes to protein biogenesis. Using selective ribosome profiling, we show that SecB binds many nascent cytoplasmic and translocated proteins generally late during translation and controlled by the chaperone trigger factor. Revealing an uncharted role in co-translational translocation, inner membrane proteins (IMPs) are the most prominent nascent SecB interactors. Unlike other substrates, IMPs are bound early during translation, following the membrane targeting by the signal recognition particle. SecB remains bound until translation is terminated, and contributes to membrane insertion. Our study establishes a role of SecB in the co-translational maturation of proteins from all cellular compartments and functionally implicates cytosolic chaperones in membrane protein biogenesis.
Collapse
Affiliation(s)
- Lena Eismann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Igor Fijalkowski
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Carla Verónica Galmozzi
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain; Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/ Universidad de Sevilla, 41013 Seville, Spain
| | - Jiří Koubek
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Frank Tippmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.
| |
Collapse
|
12
|
Smets D, Tsirigotaki A, Smit JH, Krishnamurthy S, Portaliou AG, Vorobieva A, Vranken W, Karamanou S, Economou A. Evolutionary adaptation of the protein folding pathway for secretability. EMBO J 2022; 41:e111344. [PMID: 36031863 PMCID: PMC9713715 DOI: 10.15252/embj.2022111344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/14/2022] [Accepted: 08/02/2022] [Indexed: 01/15/2023] Open
Abstract
Secretory preproteins of the Sec pathway are targeted post-translationally and cross cellular membranes through translocases. During cytoplasmic transit, mature domains remain non-folded for translocase recognition/translocation. After translocation and signal peptide cleavage, mature domains fold to native states in the bacterial periplasm or traffic further. We sought the structural basis for delayed mature domain folding and how signal peptides regulate it. We compared how evolution diversified a periplasmic peptidyl-prolyl isomerase PpiA mature domain from its structural cytoplasmic PpiB twin. Global and local hydrogen-deuterium exchange mass spectrometry showed that PpiA is a slower folder. We defined at near-residue resolution hierarchical folding initiated by similar foldons in the twins, at different order and rates. PpiA folding is delayed by less hydrophobic native contacts, frustrated residues and a β-turn in the earliest foldon and by signal peptide-mediated disruption of foldon hierarchy. When selected PpiA residues and/or its signal peptide were grafted onto PpiB, they converted it into a slow folder with enhanced in vivo secretion. These structural adaptations in a secretory protein facilitate trafficking.
Collapse
Affiliation(s)
- Dries Smets
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular BacteriologyKU LeuvenLeuvenBelgium
| | - Alexandra Tsirigotaki
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular BacteriologyKU LeuvenLeuvenBelgium
| | - Jochem H Smit
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular BacteriologyKU LeuvenLeuvenBelgium
| | - Srinath Krishnamurthy
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular BacteriologyKU LeuvenLeuvenBelgium
| | - Athina G Portaliou
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular BacteriologyKU LeuvenLeuvenBelgium
| | - Anastassia Vorobieva
- Structural Biology BrusselsVrije Universiteit Brussel and Center for Structural BiologyBrusselsBelgium
- VIB‐VUB Center for Structural Biology, VIBBrusselsBelgium
| | - Wim Vranken
- Structural Biology BrusselsVrije Universiteit Brussel and Center for Structural BiologyBrusselsBelgium
- VIB‐VUB Center for Structural Biology, VIBBrusselsBelgium
- Interuniversity Institute of Bioinformatics in BrusselsFree University of BrusselsBrusselsBelgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular BacteriologyKU LeuvenLeuvenBelgium
| | - Anastassios Economou
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular BacteriologyKU LeuvenLeuvenBelgium
| |
Collapse
|
13
|
Sanz D, Díaz E. Genetic characterization of the cyclohexane carboxylate degradation pathway in the denitrifying bacterium Aromatoleum sp. CIB. Environ Microbiol 2022; 24:4987-5004. [PMID: 35768954 PMCID: PMC9795900 DOI: 10.1111/1462-2920.16093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/01/2022] [Indexed: 12/30/2022]
Abstract
The alicyclic compound cyclohexane carboxylate (CHC) is anaerobically degraded through a peripheral pathway that converges with the central benzoyl-CoA degradation pathway of aromatic compounds in Rhodopseudomonas palustris (bad pathway) and some strictly anaerobic bacteria. Here we show that in denitrifying bacteria, e.g. Aromatoleum sp. CIB strain, CHC is degraded through a bad-ali pathway similar to that reported in R. palustris but that does not share common intermediates with the benzoyl-CoA degradation pathway (bzd pathway) of this bacterium. The bad-ali genes are also involved in the aerobic degradation of CHC in strain CIB, and orthologous bad-ali clusters have been identified in the genomes of a wide variety of bacteria. Expression of bad-ali genes in strain CIB is under control of the BadR transcriptional repressor, which was shown to recognize CHC-CoA, the first intermediate of the pathway, as effector, and whose operator region (CAAN4 TTG) was conserved in bad-ali clusters from Gram-negative bacteria. The bad-ali and bzd pathways generate pimelyl-CoA and 3-hydroxypimelyl-CoA, respectively, that are metabolized through a common aab pathway whose genetic determinants form a supraoperonic clustering with the bad-ali genes. A synthetic bad-ali-aab catabolic module was engineered and it was shown to confer CHC degradation abilities to different bacterial hosts.
Collapse
Affiliation(s)
- David Sanz
- Department of Microbial and Plant BiotechnologyCentro de Investigaciones Biológicas Margarita Salas‐CSICMadridSpain
| | - Eduardo Díaz
- Department of Microbial and Plant BiotechnologyCentro de Investigaciones Biológicas Margarita Salas‐CSICMadridSpain
| |
Collapse
|
14
|
Soto-Aceves MP, González-Valdez A, Cocotl-Yañez M, Soberón-Chávez G. Pseudomonas aeruginosa LasR overexpression leads to a RsaL-independent pyocyanin production inhibition in a low phosphate condition. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36301076 DOI: 10.1099/mic.0.001262] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Several Pseudomonas aeruginosa virulence-related traits like pyocyanin are regulated by an intricate regulatory network called quorum sensing (QS) that relies on transcriptional regulators that are activated through binding to a self-produced molecule called an autoinducer (AI). QS is composed of three systems, Las, Rhl and Pqs. In the Las system, the regulatory protein LasR interacts with its AI to activate the other two QS systems. In turn, the Rhl and Pqs systems regulate the expression of multiple virulence-related genes, such as the genes of the reiterated operons phzA1B1C1D1E1F1G1 and phzA2B2C2D2E2F2G2 involved in pyocyanin production. The Las system also regulates the negative regulator RsaL, which provides negative feedback to the QS-response, including repression of pyocyanin synthesis genes. In this work, we describe that LasR can act as a negative regulator of phzA1 transcription and hence of pyocyanin production and that this regulation is independent of RsaL activity. This work contributes to the understanding of QS-dependent pyocyanin production and demonstrates a previously uncharacterized role of LasR as a repressor.
Collapse
Affiliation(s)
- Martín Paolo Soto-Aceves
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Present address: Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Miguel Cocotl-Yañez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Gloria Soberón-Chávez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
15
|
Kammel M, Sawers RG. Distinguishing functional from structural roles of conserved pore residues during formate translocation by the FocA anion channel. Microbiologyopen 2022; 11:e1312. [PMID: 36031960 PMCID: PMC9380403 DOI: 10.1002/mbo3.1312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 11/10/2022] Open
Abstract
The formate‐specific anion channel FocA of Escherichia coli belongs to the superfamily of homopentameric formate‐nitrite transporters (FNT). Minimally nine amino acid residues are conserved in the formate translocation pore of each protomer of the pentamer, including a histidine (H209) and a threonine (T91), both of which are crucial for bidirectional formate translocation through the pore. Information regarding in vivo functional or structural roles for the other seven conserved residues is limited, or nonexistent. Here, we conducted an amino acid‐exchange analysis of these seven conserved residues. Using an established formate‐responsive lacZ‐based assay to monitor changes in intracellular formate levels and anaerobic growth rate due to the inhibitory formate analog hypophosphite, we identified five of the seven residues analyzed to be important for the structural integrity of the pentamer, in particular, two highly conserved asparagine residues, N213 and N262. The remaining two conserved residues, K156 and N172, were essential for formate/hypophosphite translocation. K156 is located on the periplasmic fringe of the pore and aids the attraction of formate to the channel. Here, we show that this residue is also important for formate efflux from the cytoplasm to the periplasm, suggesting a role in formate release from the pore. N172 could be replaced by alanine with retention of low‐level bidirectional anion translocation function; however, exchange for threonine abolished anion translocation. N172 is, therefore, crucial for bidirectional formate translocation, possibly through its interaction with the conserved pore residue, T91.
Collapse
Affiliation(s)
- Michelle Kammel
- Institute for Biology/Microbiology, Martin Luther University Halle-Wittenberg, Halle, Saale, Germany
| | - R Gary Sawers
- Institute for Biology/Microbiology, Martin Luther University Halle-Wittenberg, Halle, Saale, Germany
| |
Collapse
|
16
|
Soboh B, Adrian L, Stripp ST. An in vitro reconstitution system to monitor iron transfer to the active site during the maturation of [NiFe]-hydrogenase. J Biol Chem 2022; 298:102291. [PMID: 35868564 PMCID: PMC9418501 DOI: 10.1016/j.jbc.2022.102291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/13/2022] [Accepted: 07/16/2022] [Indexed: 11/29/2022] Open
Abstract
[NiFe]-hydrogenases comprise a small and a large subunit. The latter harbors the biologically unique [NiFe](CN)2CO active site cofactor. The maturation process includes the assembly of the [Fe](CN)2CO cofactor precursor, nickel binding, endoproteolytic cleavage of the large subunit, and dimerization with the small subunit to yield active enzyme. The biosynthesis of the [Fe](CN)2CO moiety of [NiFe]-Hydrogenase 1 (Hyd-1) and Hyd-2 occurs on the scaffold complex HybG-HypD (GD), whereas the HypC-HypD complex (CD) is specific for the assembly of Hyd-3. The metabolic source and the route for delivering iron to the active site remain unclear. To investigate the maturation process of O2-tolerant Hyd-1 from Escherichia coli, we developed an enzymatic in vitro reconstitution system that allows for the synthesis of Hyd-1 using only purified components. Together with this in vitro reconstitution system, we employed biochemical analyses, infrared spectroscopy (ATR FTIR), mass spectrometry, and microscale thermophoresis (MST) to monitor the iron transfer during the maturation process and to understand how the [Fe](CN)2CO cofactor precursor is ultimately incorporated into the large subunit. We demonstrate the direct transfer of iron from 57Fe-labeled GD complex to the large subunit of Hyd-1. Our data reveal that the GD complex exclusively interacts with the large subunit of Hyd-1 and Hyd-2 but not with the large subunit of Hyd-3. Furthermore, we show that the presence of iron in the active site is a prerequisite for nickel insertion. Taken together, these findings reveal how the [Fe](CN)2CO cofactor precursor is transferred and incorporated into the active site of [NiFe]-hydrogenase.
Collapse
Affiliation(s)
- Basem Soboh
- Genetic Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany.
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany; Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
| | - Sven T Stripp
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| |
Collapse
|
17
|
Mehner-Breitfeld D, Ringel MT, Tichy DA, Endter LJ, Stroh KS, Lünsdorf H, Risselada HJ, Brüser T. TatA and TatB generate a hydrophobic mismatch important for the function and assembly of the Tat translocon in Escherichia coli. J Biol Chem 2022; 298:102236. [PMID: 35809643 PMCID: PMC9424591 DOI: 10.1016/j.jbc.2022.102236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 11/10/2022] Open
Abstract
The twin-arginine translocation (Tat) system serves to translocate folded proteins across energy-transducing membranes in bacteria, archaea, plastids, and some mitochondria. In Escherichia coli, TatA, TatB, and TatC constitute functional translocons. TatA and TatB both possess an N-terminal transmembrane helix (TMH) followed by an amphipathic helix. The TMHs of TatA and TatB generate a hydrophobic mismatch with the membrane, as the helices comprise only 12 consecutive hydrophobic residues; however, the purpose of this mismatch is unclear. Here, we shortened or extended this stretch of hydrophobic residues in either TatA, TatB, or both and analyzed effects on translocon function and assembly. We found the WT length helices functioned best, but some variation was clearly tolerated. Defects in function were exacerbated by simultaneous mutations in TatA and TatB, indicating partial compensation of mutations in each by the other. Furthermore, length variation in TatB destabilized TatBC-containing complexes, revealing that the 12-residue-length is important but not essential for this interaction and translocon assembly. To also address potential effects of helix length on TatA interactions, we characterized these interactions by molecular dynamics simulations, after having characterized the TatA assemblies by metal-tagging transmission electron microscopy. In these simulations, we found that interacting short TMHs of larger TatA assemblies were thinning the membrane and—together with laterally-aligned tilted amphipathic helices—generated a deep V-shaped membrane groove. We propose the 12 consecutive hydrophobic residues may thus serve to destabilize the membrane during Tat transport, and their conservation could represent a delicate compromise between functionality and minimization of proton leakage.
Collapse
Affiliation(s)
| | - Michael T Ringel
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Daniel Alexander Tichy
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany; Institute for Theoretical Physics, Georg August University Göttingen, Göttingen, Germany
| | - Laura J Endter
- Institute for Theoretical Physics, Georg August University Göttingen, Göttingen, Germany
| | - Kai Steffen Stroh
- Institute for Theoretical Physics, Georg August University Göttingen, Göttingen, Germany
| | | | - Herre Jelger Risselada
- Institute for Theoretical Physics, Georg August University Göttingen, Göttingen, Germany
| | - Thomas Brüser
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany.
| |
Collapse
|
18
|
Abstract
Bacteriophage Mu is a paradigm coliphage studied mainly because of its use of transposition for genome replication. However, in extensive nonsense mutant screens, only one lysis gene has been identified, the endolysin gp22. This is surprising because in Gram-negative hosts, lysis by Caudovirales phages has been shown to require proteins which disrupt all three layers of the cell envelope. Usually this involves a holin, an endolysin, and a spanin targeting the cytoplasmic membrane, peptidoglycan (PG), and outer membrane (OM), respectively, with the holin determining the timing of lysis initiation. Here, we demonstrate that gp22 is a signal-anchor-release (SAR) endolysin and identify gp23 and gp23.1 as two-component spanin subunits. However, we find that Mu lacks a holin and instead encodes a membrane-tethered cytoplasmic protein, gp25, which is required for the release of the SAR endolysin. Mutational analysis showed that this dependence on gp25 is conferred by lysine residues at positions 6 and 7 of the short cytoplasmic domain of gp22. gp25, which we designate as a releasin, also facilitates the release of SAR endolysins from other phages. Moreover, the entire length of gp25, including its N-terminal transmembrane domain, belongs to a protein family, DUF2730, found in many Mu-like phages, including those with cytoplasmic endolysins. These results are discussed in terms of models for the evolution and mechanism of releasin function and a rationale for Mu lysis without holin control. IMPORTANCE Host cell lysis is the terminal event of the bacteriophage infection cycle. In Gram-negative hosts, lysis requires proteins that disrupt each of the three cell envelope components, only one of which has been identified in Mu: the endolysin gp22. We show that gp22 can be characterized as a SAR endolysin, a muralytic enzyme that activates upon release from the membrane to degrade the cell wall. Furthermore, we identify genes 23 and 23.1 as spanin subunits used for outer membrane disruption. Significantly, we demonstrate that Mu is the first known Caudovirales phage to lack a holin, a protein that disrupts the inner membrane and is traditionally known to release endolysins. In its stead, we report the discovery of a lysis protein, termed the releasin, which Mu uses for SAR endolysin release. This is an example of a system where the dynamic membrane localization of one protein is controlled by a secondary protein.
Collapse
|
19
|
An Optimal Lysis Time Maximizes Bacteriophage Fitness in Quasi-Continuous Culture. mBio 2022; 13:e0359321. [PMID: 35467417 PMCID: PMC9239172 DOI: 10.1128/mbio.03593-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Optimality models have a checkered history in evolutionary biology. While optimality models have been successful in providing valuable insight into the evolution of a wide variety of biological traits, a common objection is that optimality models are overly simplistic and ignore organismal genetics. We revisit evolutionary optimization in the context of a major bacteriophage life history trait, lysis time. Lysis time refers to the period spanning phage infection of a host cell and its lysis, whereupon phage progenies are released. Lysis time, therefore, directly determines phage fecundity assuming progeny assembly does not exhaust host resources prior to lysis. Noting that previous tests of lysis time optimality rely on batch culture, we implemented a quasi-continuous culture system to observe productivity of a panel of isogenic phage λ genotypes differing in lysis time. We report that under our experimental conditions, λ phage productivity is maximized around optimal lysis times ranging from 60 to 100 min, and λ wildtype strain falls within this range. It would appear that natural selection on phage λ lysis time uncovered a set of genetic solutions that optimized progeny production in its ecological milieu relative to alternative genotypes. We discuss this finding in light of recent results that lysis time variation is also minimized in the strains with lysis times closer to the λ wild-type strain. IMPORTANCE Optimality theory presents the idea that natural selection acts on organismal traits to produce genotypes that maximize organismal survival and reproduction. As such, optimality theory is a valuable tool in guiding our understanding of the genetic constraints and tradeoffs organisms experience as their genotypes are selected to produce optimal solutions to biological problems. However, optimality theory is often critiqued as being overly simplistic and ignoring the roles of chance and history in the evolution of organismal traits. We show here that the wild-type genotype of a popular laboratory model organism, the bacteriophage λ, produces a phenotype for a major life history trait, lysis time, that maximizes the reproductive success of bearers of that genotype relative to other possible genotypes. This result demonstrates, as is rarely shown experimentally, that natural selection can achieve optimal solutions to ecological challenges.
Collapse
|
20
|
Haase A, Sawers RG. Exchange of a Single Amino Acid Residue in the HybG Chaperone Allows Maturation of All H 2-Activating [NiFe]-Hydrogenases in Escherichia coli. Front Microbiol 2022; 13:872581. [PMID: 35422773 PMCID: PMC9002611 DOI: 10.3389/fmicb.2022.872581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/01/2022] [Indexed: 11/18/2022] Open
Abstract
The biosynthesis of the NiFe(CN)2CO organometallic cofactor of [NiFe]-hydrogenase (Hyd) involves several discreet steps, including the synthesis of the Fe(CN)2CO group on a HypD-HypC scaffold complex. HypC has an additional function in transferring the Fe(CN)2CO group to the apo-precursor of the Hyd catalytic subunit. Bacteria that synthesize more than one Hyd enzyme often have additional HypC-type chaperones specific for each precursor. The specificity determinants of this large chaperone family are not understood. Escherichia coli synthesizes two HypC paralogs, HypC and HybG. HypC delivers the Fe(CN)2CO group to pre-HycE, the precursor of the H2-evolving Hyd-3 enzyme, while HybG transfers the group to the pre-HybC of the H2-oxidizing Hyd-2 enzyme. We could show that a conserved histidine residue around the amino acid position 50 in both HypC and HybG, when exchanged for an alanine, resulted in a severe reduction in the activity of its cognate Hyd enzyme. This reduction in enzyme activity proved to be due to the impaired ability of the chaperones to interact with HypD. Surprisingly, and only in the case of the HybGH52A variant, its co-synthesis with HypD improved its interaction with pre-HycE, resulting in the maturation of Hyd-3. This study demonstrates that the conserved histidine residue helps enhance the interaction of the chaperone with HypD, but additionally, and in E. coli only for HybG, acts as a determinant to prevent the inadvertent maturation of the wrong large-subunit precursor. This study identifies a new level of control exerted by a bacterium synthesizing multiple [NiFe]-Hyd to ensure the correct enzyme is matured only under the appropriate physiological conditions.
Collapse
Affiliation(s)
- Alexander Haase
- Institute of Microbiology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - R Gary Sawers
- Institute of Microbiology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| |
Collapse
|
21
|
Protection of bacteriophage-sensitive Escherichia coli by lysogens. Proc Natl Acad Sci U S A 2022; 119:e2106005119. [PMID: 35344423 PMCID: PMC9168506 DOI: 10.1073/pnas.2106005119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Some viruses that infect bacteria, temperate bacteriophages, can confer immunity to infection by the same virus. Here we report λ-immune bacteria could protect λ-sensitive bacteria from killing by phage λ in mixed culture. The protection depended on the extent to which the immune bacteria were able to adsorb the phage. Reconciling modeling with experiment led to identifying a decline in protection as bacteria stopped growing. Adsorption of λ was compromised by inhibition of bacterial energy metabolism, explaining the loss of protection as bacterial growth ceased. Bacteriophage λ is a temperate virus infecting the bacterium Escherichia coli. Temperate phages have the ability to form lysogens where the prophage is maintained in the infected bacterium in a largely quiescent state. The lysogen becomes immune to superinfection by λ by blocking the development of the superinfecting phage. Here we report the λ lysogen not only protected itself from killing by λ phages but also protected λ-sensitive bacteria in mixed culture. This protection required that the lysogen was able to adsorb the superinfecting λ phages. The protection was also sensitive to the growth state of the mixed culture, and the λ lysogen lost efficiency in protecting λ-sensitive bacteria as it stopped growing. A mutant of the λ tail protein, λJ, was not subject to this loss of protection. Adsorption of λ having the wild-type J protein but not the mutant λJ protein to E. coli was inhibited by interference with bacterial energy metabolism. The last observation suggests wild-type λ preferentially infects bacteria with competent energy metabolism.
Collapse
|
22
|
Kammel M, Sawers RG. The FocA channel functions to maintain intracellular formate homeostasis during Escherichia coli fermentation. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35377837 DOI: 10.1099/mic.0.001168] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
FocA translocates formate/formic acid bi-directionally across the cytoplasmic membrane when Escherichia coli grows by fermentation. It remains unclear, however, what physiological benefit is imparted by FocA, because formic acid (pK a=3.75) can diffuse passively across the membrane, especially at low pH. Here, we monitored changes in intra- and extracellular formate levels during batch-culture fermentation, comparing a parental E. coli K-12 strain with its isogenic focA mutant. Our results show that, regardless of the initial pH in the culture, FocA functions to maintain relatively constant intracellular formate levels during growth. Analysis of a strain synthesizing a FocAT91A variant with an exchange in a conserved threonine residue within the translocation pore revealed the strain accumulated formate intracellularly and imported formate poorly, but in a pH-dependent manner, which was different to uptake by native FocA. We conclude that FocA maintains formate homeostasis, using different mechanisms for efflux and uptake of the anion.
Collapse
Affiliation(s)
- Michelle Kammel
- Institute for Biology/Microbiology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3 06120 Halle (Saale), Germany
| | - R Gary Sawers
- Institute for Biology/Microbiology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3 06120 Halle (Saale), Germany
| |
Collapse
|
23
|
The Autonomous Glycyl Radical Protein GrcA Restores Activity to Inactive Full-Length Pyruvate Formate-Lyase In Vivo. J Bacteriol 2022; 204:e0007022. [PMID: 35377165 DOI: 10.1128/jb.00070-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During glucose fermentation, Escherichia coli and many other microorganisms employ the glycyl radical enzyme (GRE) pyruvate formate-lyase (PflB) to catalyze the coenzyme A-dependent cleavage of pyruvate to formate and acetyl-coenzyme A (CoA). Due to its extreme reactivity, the radical in PflB must be controlled carefully and, once generated, is particularly susceptible to dioxygen. Exposure to oxygen of the radical on glycine residue 734 of PflB results in cleavage of the polypeptide chain and consequent inactivation of the enzyme. Two decades ago, a small 14-kDa protein called YfiD (now called autonomous glycyl radical cofactor [GrcA]) was shown to be capable of restoring activity to O2-inactivated PflB in vitro; however, GrcA has never been shown to have this function in vivo. By constructing a strain with a chromosomally encoded PflB enzyme variant with a G734A residue exchange, we could show that cells retained near-wild type fermentative growth, as well as formate and H2 production; H2 is derived by enzymatic disproportionation of formate. Introducing a grcA deletion mutation into this strain completely prevented formate and H2 generation and reduced anaerobic growth. We could show that the conserved glycine at position 102 on GrcA was necessary for GrcA to restore PflB activity and that this recovered activity depended on the essential cysteine residues 418 and 419 in the active site of PflB. Together, our findings demonstrate that GrcA is capable of restoring in vivo activity to inactive full-length PflB and support a model whereby GrcA displaces the C-terminal glycyl radical domain to rescue the catalytic function of PflB. IMPORTANCE Many facultative anaerobic microorganisms use glycyl radical enzymes (GREs) to catalyze chemically challenging reactions under anaerobic conditions. Pyruvate formate-lyase (PflB) is a GRE that catalyzes cleavage of the carbon-carbon bond of pyruvate during glucose fermentation. The problem is that glycyl radicals are destroyed readily, especially by oxygen. To protect and restore activity to inactivated PflB, bacteria like Escherichia coli have a small autonomous glycyl radical cofactor protein called GrcA, which functions to rescue inactivated PflB. To date, this proposed function of GrcA has only been demonstrated in vitro. Our data reveal that GrcA rescues and restores enzyme activity to an inactive full-length form of PflB in vivo. These results have important implications for the evolution of radical-based enzyme mechanisms.
Collapse
|
24
|
Li W, Yin F, Bu Z, Liu Y, Zhang Y, Chen X, Li S, Li L, Zhou R, Huang Q. An Engineered Outer Membrane-Defective Escherichia coli Secreting Protective Antigens against Streptococcus suis via the Twin-Arginine Translocation Pathway as a Vaccine. J Microbiol Biotechnol 2022; 32:278-286. [PMID: 35283432 PMCID: PMC9628857 DOI: 10.4014/jmb.2107.07052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/20/2022] [Accepted: 02/09/2022] [Indexed: 12/15/2022]
Abstract
Live bacterial vector vaccines are one of the most promising vaccine types and have the advantages of low cost, flexibility, and good safety. Meanwhile, protein secretion systems have been reported as useful tools to facilitate the release of heterologous antigen proteins from bacterial vectors. The twin-arginine translocation (Tat) system is an important protein export system that transports fully folded proteins in a signal peptide-dependent manner. In this study, we constructed a live vector vaccine using an engineered commensal Escherichia coli strain in which amiA and amiC genes were deleted, resulting in a leaky outer membrane that allows the release of periplasmic proteins to the extracellular environment. The protective antigen proteins SLY, enolase, and Sbp against Streptococcus suis were targeted to the Tat pathway by fusing a Tat signal peptide. Our results showed that by exploiting the Tat pathway and the outer membrane-defective E. coli strain, the antigen proteins were successfully secreted. The strains secreting the antigen proteins were used to vaccinate mice. After S. suis challenge, the vaccinated group showed significantly higher survival and milder clinical symptoms compared with the vector group. Further analysis showed that the mice in the vaccinated group had lower burdens of bacteria load and slighter pathological changes. Our study reports a novel live bacterial vector vaccine that uses the Tat system and provides a new alternative for developing S. suis vaccine.
Collapse
Affiliation(s)
- Wenyu Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China,Shandong Vocational Animal Science and Veterinary College, Weifang, P.R. China
| | - Fan Yin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Zixuan Bu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Yuying Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Yongqing Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Xiabing Chen
- Institute of Animal Husbandry and Veterinary Science, Wuhan Academy of Agricultural Science and Technology, Wuhan 430070, P.R. China
| | - Shaowen Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Lu Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China,Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, P.R. China,International Research Center for Animal Disease, Ministry of Science and Technology, Wuhan 430070, P.R. China,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of China, Wuhan 430070, P.R. China
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China,Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, P.R. China,International Research Center for Animal Disease, Ministry of Science and Technology, Wuhan 430070, P.R. China,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of China, Wuhan 430070, P.R. China
| | - Qi Huang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China,Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, P.R. China,International Research Center for Animal Disease, Ministry of Science and Technology, Wuhan 430070, P.R. China,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of China, Wuhan 430070, P.R. China,Corresponding author Phone: +86-27-87281878 Fax: + 86-27-8728 2608 E-mail:
| |
Collapse
|
25
|
Lv B, Bian M, Huang X, Sun F, Gao Y, Wang Y, Fu Y, Yang B, Fu X. n-Butanol Potentiates Subinhibitory Aminoglycosides against Bacterial Persisters and Multidrug-Resistant MRSA by Rapidly Enhancing Antibiotic Uptake. ACS Infect Dis 2022; 8:373-386. [PMID: 35100802 DOI: 10.1021/acsinfecdis.1c00559] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Potentiation of traditional antibiotics is of significance for combating antibiotic-resistant bacteria that have become a severe threat to human and animal health. Here, we report that 1 min co-treatment with n-butanol greatly and specifically enhances the bactericidal action of aminoglycosides by 5 orders of magnitude against stationary-phase Staphylococcus aureus cells, with n-propanol and isobutanol showing less potency. This combined treatment also rapidly kills various S. aureus persisters, methicillin-resistant S. aureus (MRSA) cells, and numerous Gram-positive and -negative pathogens including some clinically isolated multidrug-resistant pathogens (e.g., S. aureus, Staphylococcus epidermidis, and Enterococcus faecalis) in vitro, as well as S. aureus in mice. Mechanistically, the potentiation results from the actions of aminoglycosides on their conventional target ribosome rather than the antiseptic effect of n-butanol and is achieved by rapidly enhancing the bacterial uptake of aminoglycosides, while salts and inhibitors of proton motive force (e.g., CCCP) can diminish this uptake. Importantly, such n-butanol-enhanced antibiotic uptake even enables subinhibitory concentrations of aminoglycosides to rapidly kill both MRSA and conventional S. aureus cells. Given n-butanol is a non-metabolite in the pathogens we tested, our work may open avenues to develop a metabolite-independent strategy for aminoglycoside potentiation to rapidly eliminate antibiotic-resistant/tolerant pathogens, as well as for reducing the toxicity associated with aminoglycoside use.
Collapse
Affiliation(s)
- Boyan Lv
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou City, Fujian Province 350117, China
| | - Mengmeng Bian
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou City, Fujian Province 350117, China
| | - Xuebing Huang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou City, Fujian Province 350117, China
| | - Fengqi Sun
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou City, Fujian Province 350117, China
| | - Yuanyuan Gao
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou City, Fujian Province 350117, China
| | - Yan Wang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou City, Fujian Province 350117, China
| | - Yajuan Fu
- Biomedical Research Center of South China, Fujian Normal University, Fuzhou, Fujian Province 350117, China
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province 350117, China
| | - Xinmiao Fu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou City, Fujian Province 350117, China
| |
Collapse
|
26
|
Tan WB, Chng SS. Genetic interaction mapping highlights key roles of the Tol-Pal complex. Mol Microbiol 2022; 117:921-936. [PMID: 35066953 DOI: 10.1111/mmi.14882] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/30/2022]
Abstract
The conserved Tol-Pal trans-envelope complex is important for outer membrane (OM) stability and cell division in Gram-negative bacteria. It is proposed to mediate OM constriction during cell division via cell wall tethering. Yet, recent studies suggest the complex has additional roles in OM lipid homeostasis and septal wall separation. How Tol-Pal facilitates all these processes is unclear. To gain insights into its function(s), we applied transposon-insertion sequencing, and report here a detailed network of genetic interactions with the tol-pal locus in Escherichia coli. We found one positive and >20 negative strong interactions based on fitness. Disruption osmoregulated-periplasmic glucan biosynthesis restores fitness and OM barrier function, but not proper division, in tol-pal mutants. In contrast, deleting genes involved in OM homeostasis and cell wall remodeling cause synthetic growth defects in strains lacking Tol-Pal, especially exacerbating OM barrier and/or division phenotypes. Notably, the ΔtolA mutant having additional defects in OM protein assembly (ΔbamB) exhibited severe division phenotypes, even when single mutants divided normally; this highlights the possibility for OM phenotypes to indirectly impact cell division. Overall, our work underscores the intricate nature of Tol-Pal function, and reinforces its key roles in cell wall-OM tethering, cell wall remodeling, and in particular, OM homeostasis.
Collapse
Affiliation(s)
- Wee Boon Tan
- Department of Chemistry, National University of Singapore, Singapore.,Singapore Center for Environmental Life Sciences Engineering, National University of Singapore (SCELSE-NUS), Singapore
| | - Shu-Sin Chng
- Department of Chemistry, National University of Singapore, Singapore.,Singapore Center for Environmental Life Sciences Engineering, National University of Singapore (SCELSE-NUS), Singapore
| |
Collapse
|
27
|
Wilson A, Iniguez C, Ruiz N. Use of Mutagenesis and Functional Screens to Characterize Essential Genes Involved in Lipopolysaccharide Transport. Methods Mol Biol 2022; 2548:3-19. [PMID: 36151488 PMCID: PMC9630823 DOI: 10.1007/978-1-0716-2581-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Structure-function analysis is a powerful strategy to characterize the contribution of specific residues to the biogenesis and function of a protein. This approach requires the characterization of strains that express mutant alleles in the absence of the wild-type protein. When studying nonessential bacterial genes, collections of mutants can be easily constructed by introducing plasmid-encoded alleles of interest into a strain that already lacks the wild-type gene. However, this high-throughput approach is not applicable to studying essential genes since their respective null strains are not viable. While there are several tools currently available to modify essential genes, they can be greatly limited by the amount of effort it takes to build and analyze each mutant strain. Here, we describe a high-throughput system for the rapid structure-function analysis of essential genes involved in lipopolysaccharide transport in Escherichia coli. This method, which can be applied to study any essential gene, relies on the initial construction of a single bacterial strain that can be used to generate and functionally characterize multiple plasmid-encoded alleles in under 24 h. We will discuss the advantages and possible shortcomings of our protocol in comparison to other commonly used methods.
Collapse
|
28
|
Machado LFM, Dixon N. Directed Evolution of Transcription Factor-Based Biosensors for Altered Effector Specificity. Methods Mol Biol 2022; 2461:175-193. [PMID: 35727451 DOI: 10.1007/978-1-0716-2152-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Transcription factor-based biosensors are important tools in Synthetic Biology for the sensing of industrially valuable molecules and clinically important metabolites, therefore presenting applications in the bioremediation, industrial biotechnology, and biomedical fields. The directed evolution of allosteric transcription factors (aTFs) with the aim of altering effector specificity has the potential for the development of new biosensors to detect natural and nonnatural molecules, expanding the scope of available aTF-based biosensors. In this chapter, we delineate a general method for the directed evolution of aTFs. The theory of library design is discussed, along with the detailed methodology for an improved transformation of combined libraries, and the experimental search space by counterselection using fluorescence-activated cell sorting (FACS) is presented.
Collapse
|
29
|
Arlt C, Nutschan K, Haase A, Ihling C, Tänzler D, Sinz A, Sawers RG. Native mass spectrometry identifies the HybG chaperone as carrier of the Fe(CN) 2CO group during maturation of E. coli [NiFe]-hydrogenase 2. Sci Rep 2021; 11:24362. [PMID: 34934150 PMCID: PMC8692609 DOI: 10.1038/s41598-021-03900-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/06/2021] [Indexed: 01/27/2023] Open
Abstract
[NiFe]-hydrogenases activate dihydrogen. Like all [NiFe]-hydrogenases, hydrogenase 2 of Escherichia coli has a bimetallic NiFe(CN)2CO cofactor in its catalytic subunit. Biosynthesis of the Fe(CN)2CO group of the [NiFe]-cofactor occurs on a distinct scaffold complex comprising the HybG and HypD accessory proteins. HybG is a member of the HypC-family of chaperones that confers specificity towards immature hydrogenase catalytic subunits during transfer of the Fe(CN)2CO group. Using native mass spectrometry of an anaerobically isolated HybG-HypD complex we show that HybG carries the Fe(CN)2CO group. Our results also reveal that only HybG, but not HypD, interacts with the apo-form of the catalytic subunit. Finally, HybG was shown to have two distinct, and apparently CO2-related, covalent modifications that depended on the presence of the N-terminal cysteine residue on the protein, possibly representing intermediates during Fe(CN)2CO group biosynthesis. Together, these findings suggest that the HybG chaperone is involved in both biosynthesis and delivery of the Fe(CN)2CO group to its target protein. HybG is thus suggested to shuttle between the assembly complex and the apo-catalytic subunit. This study provides new insights into our understanding of how organometallic cofactor components are assembled on a scaffold complex and transferred to their client proteins.
Collapse
Affiliation(s)
- Christian Arlt
- Institute of Pharmacy, Center for Structural Mass Spectrometry, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany
| | - Kerstin Nutschan
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Alexander Haase
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Christian Ihling
- Institute of Pharmacy, Center for Structural Mass Spectrometry, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany
| | - Dirk Tänzler
- Institute of Pharmacy, Center for Structural Mass Spectrometry, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany
| | - Andrea Sinz
- Institute of Pharmacy, Center for Structural Mass Spectrometry, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany.
| | - R Gary Sawers
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany.
| |
Collapse
|
30
|
Midgett CR, Talbot KM, Day JL, Munson GP, Kull FJ. Structure of the master regulator Rns reveals an inhibitor of enterotoxigenic Escherichia coli virulence regulons. Sci Rep 2021; 11:15663. [PMID: 34341412 PMCID: PMC8329261 DOI: 10.1038/s41598-021-95123-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 07/14/2021] [Indexed: 02/07/2023] Open
Abstract
Enteric infections caused by the gram-negative bacteria enterotoxigenic Escherichia coli (ETEC), Vibrio cholerae, Shigella flexneri, and Salmonella enterica are among the most common and affect billions of people each year. These bacteria control expression of virulence factors using a network of transcriptional regulators, some of which are modulated by small molecules as has been shown for ToxT, an AraC family member from V. cholerae. In ETEC the expression of many types of adhesive pili is dependent upon the AraC family member Rns. We present here the 3 Å crystal structure of Rns and show it closely resembles ToxT. Rns crystallized as a dimer via an interface similar to that observed in other dimeric AraC's. Furthermore, the structure of Rns revealed the presence of a ligand, decanoic acid, that inhibits its activity in a manner similar to the fatty acid mediated inhibition observed for ToxT and the S. enterica homologue HilD. Together, these results support our hypothesis that fatty acids regulate virulence controlling AraC family members in a common manner across a number of enteric pathogens. Furthermore, for the first time this work identifies a small molecule capable of inhibiting the ETEC Rns regulon, providing a basis for development of therapeutics against this deadly human pathogen.
Collapse
Affiliation(s)
| | - Kacey Marie Talbot
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jessica L Day
- Department of Chemistry, Dartmouth College, Hanover, NH, USA
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - George P Munson
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - F Jon Kull
- Department of Chemistry, Dartmouth College, Hanover, NH, USA.
| |
Collapse
|
31
|
Grass LM, Wollenhaupt J, Barthel T, Parfentev I, Urlaub H, Loll B, Klauck E, Antelmann H, Wahl MC. Large-scale ratcheting in a bacterial DEAH/RHA-type RNA helicase that modulates antibiotics susceptibility. Proc Natl Acad Sci U S A 2021; 118:e2100370118. [PMID: 34290142 PMCID: PMC8325345 DOI: 10.1073/pnas.2100370118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Many bacteria harbor RNA-dependent nucleoside-triphosphatases of the DEAH/RHA family, whose molecular mechanisms and cellular functions are poorly understood. Here, we show that the Escherichia coli DEAH/RHA protein, HrpA, is an ATP-dependent 3 to 5' RNA helicase and that the RNA helicase activity of HrpA influences bacterial survival under antibiotics treatment. Limited proteolysis, crystal structure analysis, and functional assays showed that HrpA contains an N-terminal DEAH/RHA helicase cassette preceded by a unique N-terminal domain and followed by a large C-terminal region that modulates the helicase activity. Structures of an expanded HrpA helicase cassette in the apo and RNA-bound states in combination with cross-linking/mass spectrometry revealed ratchet-like domain movements upon RNA engagement, much more pronounced than hitherto observed in related eukaryotic DEAH/RHA enzymes. Structure-based functional analyses delineated transient interdomain contact sites that support substrate loading and unwinding, suggesting that similar conformational changes support RNA translocation. Consistently, modeling studies showed that analogous dynamic intramolecular contacts are not possible in the related but helicase-inactive RNA-dependent nucleoside-triphosphatase, HrpB. Our results indicate that HrpA may be an interesting target to interfere with bacterial tolerance toward certain antibiotics and suggest possible interfering strategies.
Collapse
Affiliation(s)
- Lena M Grass
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, D-12489 Berlin, Germany
| | - Tatjana Barthel
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, D-14195 Berlin, Germany
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, D-12489 Berlin, Germany
| | - Iwan Parfentev
- Bioanalytical Mass Spectrometry, Max-Planck-Institut für biophysikalische Chemie, D-37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max-Planck-Institut für biophysikalische Chemie, D-37077 Göttingen, Germany
- Bioanalytics, Institute of Clinical Chemistry, Universitätsmedizin Göttingen, D-37075 Göttingen, Germany
| | - Bernhard Loll
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Eberhard Klauck
- Microbiology, Institute of Biology, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Haike Antelmann
- Microbiology, Institute of Biology, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Markus C Wahl
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, D-14195 Berlin, Germany;
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, D-12489 Berlin, Germany
| |
Collapse
|
32
|
Lara-Ochoa C, González-Lara F, Romero-González LE, Jaramillo-Rodríguez JB, Vázquez-Arellano SI, Medrano-López A, Cedillo-Ramírez L, Martínez-Laguna Y, Girón JA, Pérez-Rueda E, Puente JL, Ibarra JA. The transcriptional activator of the bfp operon in EPEC (PerA) interacts with the RNA polymerase alpha subunit. Sci Rep 2021; 11:8541. [PMID: 33879812 PMCID: PMC8058060 DOI: 10.1038/s41598-021-87586-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/30/2021] [Indexed: 11/09/2022] Open
Abstract
Enteropathogenic E. coli virulence genes are under the control of various regulators, one of which is PerA, an AraC/XylS-like regulator. PerA directly promotes its own expression and that of the bfp operon encoding the genes involved in the biogenesis of the bundle-forming pilus (BFP); it also activates PerC expression, which in turn stimulates locus of enterocyte effacement (LEE) activation through the LEE-encoded regulator Ler. Monomeric PerA directly binds to the per and bfp regulatory regions; however, it is not known whether interactions between PerA and the RNA polymerase (RNAP) are needed to activate gene transcription as has been observed for other AraC-like regulators. Results showed that PerA interacts with the alpha subunit of the RNAP polymerase and that it is necessary for the genetic and phenotypic expression of bfpA. Furthermore, an in silico analysis shows that PerA might be interacting with specific alpha subunit amino acids residues highlighting the direction of future experiments.
Collapse
Affiliation(s)
- Cristina Lara-Ochoa
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico.
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
| | - Fabiola González-Lara
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Luis E Romero-González
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Juan B Jaramillo-Rodríguez
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | - Abraham Medrano-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Lilia Cedillo-Ramírez
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Ygnacio Martínez-Laguna
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
- Vicerrectoría de Investigación y Estudios de Posgrado, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Jorge A Girón
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Mexico
| | - José Luis Puente
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - J Antonio Ibarra
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico.
| |
Collapse
|
33
|
Carroll CJ, Hocking DM, Azzopardi KI, Praszkier J, Bennett-Wood V, Almeida K, Ingle DJ, Baines SL, Tauschek M, Robins-Browne RM. Re-evaluation of a Neonatal Mouse Model of Infection With Enterotoxigenic Escherichia coli. Front Microbiol 2021; 12:651488. [PMID: 33815340 PMCID: PMC8013722 DOI: 10.3389/fmicb.2021.651488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 02/17/2021] [Indexed: 12/03/2022] Open
Abstract
Enterotoxigenic E. coli (ETEC) is a common cause of diarrhea in children in low- and middle-income countries, and in travelers to these countries. ETEC is also an important cause of morbidity and premature mortality in piglets, calves, goat kids and lambs. The major virulence determinants of ETEC are enterotoxins and colonization factors, which enable the pathogen to colonize the small intestine and deliver enterotoxins, such as the heat-stable enterotoxins, STp and STh, to epithelial cells. Because most ETEC strains are host-specific, there are few convenient animal models to investigate the pathogenesis of ETEC infections or to evaluate specific anti-ETEC interventions, such as drugs and vaccines. An exception is ETEC strains bearing F41 pili, which mediate intestinal colonization of various young animals, including neonatal mice, to cause disease and in some cases death. In this study, we used the archetypal F41-producing bovine ETEC strain, B41 (O101:NM; K99, F41, STp) to validate and further explore the contribution of F41 and STp to bacterial virulence. By using targeted gene deletion and trans-complementation studies, augmented by whole genome sequencing, and in vitro and animal studies of virulence, we established that F41 mediates colonization of the mouse intestine and is essential for bacterial virulence. In addition, we showed for the first time that STp is as important as F41 for virulence. Together, these findings validate the use of neonatal mice to study the pathogenesis of F41-bearing ETEC and to investigate possible specific anti-ETEC interventions including vaccines that target heat-stable enterotoxins.
Collapse
Affiliation(s)
- Carla J Carroll
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Dianna M Hocking
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Kristy I Azzopardi
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Judyta Praszkier
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Vicki Bennett-Wood
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Kaylani Almeida
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Danielle J Ingle
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Marija Tauschek
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Roy M Robins-Browne
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| |
Collapse
|
34
|
Tuttle AR, Trahan ND, Son MS. Growth and Maintenance of Escherichia coli Laboratory Strains. Curr Protoc 2021; 1:e20. [PMID: 33484484 DOI: 10.1002/cpz1.20] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Escherichia coli is a Gram-negative bacterium, commonly used in both teaching and research laboratories. This article includes protocols for the growth and maintenance of E. coli in any teaching- or research-associated laboratory. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Growth of E. coli from frozen stocks Basic Protocol 2: Growth of E. coli in liquid media Basic Protocol 3: Enumeration of E. coli on solid media Basic Protocol 4: Storage of E. coli frozen stocks in glycerol Basic Protocol 5: Storage of E. coli in agar stabs Basic Protocol 6: Growth curve of E. coli liquid culture.
Collapse
Affiliation(s)
| | | | - Mike S Son
- Plymouth State University, Plymouth, New Hampshire
| |
Collapse
|
35
|
The Auxiliary NADH Dehydrogenase Plays a Crucial Role in Redox Homeostasis of Nicotinamide Cofactors in the Absence of the Periplasmic Oxidation System in Gluconobacter oxydans NBRC3293. Appl Environ Microbiol 2021; 87:AEM.02155-20. [PMID: 33127815 DOI: 10.1128/aem.02155-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/22/2020] [Indexed: 02/04/2023] Open
Abstract
Gluconobacter oxydans has the unique property of a glucose oxidation system in the periplasmic space, where glucose is oxidized incompletely to ketogluconic acids in a nicotinamide cofactor-independent manner. Elimination of the gdhM gene for membrane-bound glucose dehydrogenase, the first enzyme for the periplasmic glucose oxidation system, induces a metabolic change whereby glucose is oxidized in the cytoplasm to acetic acid. G. oxydans strain NBRC3293 possesses two molecular species of type II NADH dehydrogenase (NDH), the primary and auxiliary NDHs that oxidize NAD(P)H by reducing ubiquinone in the cell membrane. The substrate specificities of the two NDHs are different from each other: primary NDH (p-NDH) oxidizes NADH specifically but auxiliary NDH (a-NDH) oxidizes both NADH and NADPH. We constructed G. oxydans NBRC3293 derivatives defective in the ndhA gene for a-NDH, in the gdhM gene, and in both. Our ΔgdhM derivative yielded higher cell biomass on glucose, as reported previously, but grew at a lower rate than the wild-type strain. The ΔndhA derivative showed growth behavior on glucose similar to that of the wild type. The ΔgdhM ΔndhA double mutant showed greatly delayed growth on glucose, but its cell biomass was similar to that of the ΔgdhM strain. The double mutant accumulated intracellular levels of NAD(P)H and thus shifted the redox balance to reduction. Accumulated NAD(P)H levels might repress growth on glucose by limiting oxidative metabolisms in the cytoplasm. We suggest that a-NDH plays a crucial role in redox homeostasis of nicotinamide cofactors in the absence of the periplasmic oxidation system in G. oxydans IMPORTANCE Nicotinamide cofactors NAD+ and NADP+ mediate redox reactions in metabolism. Gluconobacter oxydans, a member of the acetic acid bacteria, oxidizes glucose incompletely in the periplasmic space-outside the cell. This incomplete oxidation of glucose is independent of nicotinamide cofactors. However, if the periplasmic oxidation of glucose is abolished, the cells oxidize glucose in the cytoplasm by reducing nicotinamide cofactors. Reduced forms of nicotinamide cofactors are reoxidized by NADH dehydrogenase (NDH) on the cell membrane. We found that two kinds of NDH in G. oxydans have different substrate specificities: the primary enzyme is NADH specific, and the auxiliary one oxidizes both NADH and NADPH. Inactivation of the latter enzyme in G. oxydans cells in which we had induced cytoplasmic glucose oxidation resulted in elevated intracellular levels of NAD(P)H, limiting cell growth on glucose. We suggest that the auxiliary enzyme is important if G. oxydans grows independently of the periplasmic oxidation system.
Collapse
|
36
|
Koga N, Hosomi T, Zwama M, Jirayupat C, Yanagida T, Nishino K, Yamasaki S. Identification of Genetic Variants via Bacterial Respiration Gas Analysis. Front Microbiol 2020; 11:581571. [PMID: 33304330 PMCID: PMC7701088 DOI: 10.3389/fmicb.2020.581571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/27/2020] [Indexed: 11/13/2022] Open
Abstract
Indole is a signal molecule derived from the conversion of tryptophan, and it is present in bacterial respiratory gas. Besides influencing bacterial growth, indole exhibits effects on human health, including a positive effect on inflammation and protection against pathogens. However, a high fecal indole concentration (FIC) can suggest an unbalanced gut flora or the presence of certain pathogens. To analyze the indole produced by bacteria, its collection and detection is required. Traditional methods usually require centrifugation of liquid bacterial culture medium and subsequent extraction of indole from the medium or partial purification of indole from fecal samples (e.g., by distillation or extraction). In this study, we demonstrate the possibility of identifying gas contents directly from bacteria, and we distinguish the difference in species and their genetics without the need to centrifuge or extract. Using an absorbent sheet placed above a liquid culture, we were able to collect gas content directly from bacteria. Gas chromatography-mass spectrometry (GC-MS) was used for the analysis. The GC-MS results showed a clear peak attributed to indole for wild-type Escherichia coli cells (MG1655 and MC4100 strains), whereas the indole peak was absent in the chromatograms of cells where proteins, part of the indole production pathway from tryptophan (TnaA and TnaB), were not expressed (by using tnaAB-deleted cells). The indole observed was measured to be present in a low nmol-range. This method can distinguish whether the bacterial genome contains the tnaAB gene or not and can be used to collect gas compounds from bacterial cultures quickly and easily. This method is useful for other goals and future research, such as for measurements in restrooms, for food-handling facilities, and for various applications in medical settings.
Collapse
Affiliation(s)
- Naoki Koga
- School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Takuro Hosomi
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Martijn Zwama
- Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | | | - Takeshi Yanagida
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.,Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka, Japan
| | - Kunihiko Nishino
- School of Pharmaceutical Sciences, Osaka University, Osaka, Japan.,Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Seiji Yamasaki
- School of Pharmaceutical Sciences, Osaka University, Osaka, Japan.,Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan.,Institute for Advanced Co-Creation Studies, Osaka University, Osaka, Japan
| |
Collapse
|
37
|
Two Signal Recognition Particle Sequences Are Present in the Amino-Terminal Domain of the C-Tailed Protein SciP. J Bacteriol 2020; 203:JB.00312-20. [PMID: 33020223 DOI: 10.1128/jb.00312-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/01/2020] [Indexed: 01/22/2023] Open
Abstract
During their synthesis, the C-tailed membrane proteins expose the membrane-spanning segment late from the ribosome and consequently can insert into the membrane only posttranslationally. However, the C-tailed type 6 secretion system (T6SS) component SciP uses the bacterial signal recognition particle (SRP) system for membrane targeting, which operates cotranslationally. Analysis of possible sequence regions in the amino-terminal part of the protein revealed two candidates that were then tested for whether they function as SRP signal peptides. Both sequences were tested positive as synthetic peptides for binding to SRP. In addition, purified ribosomes with stalled nascent chains exposing either sequence were capable of binding to SRP and SRP-FtsY complexes with high affinity. Together, the data suggest that both peptides can serve as an SRP signal sequence promoting an early membrane targeting of SciP during its synthesis. Like observed for multispanning membrane proteins, the two cytoplasmic SRP signal sequences of SciP may also facilitate a retargeting event, making the targeting more efficient.IMPORTANCE C-tail proteins are anchored in the inner membrane with a transmembrane segment at the C terminus in an N-in/C-out topology. Due to this topology, membrane insertion occurs only posttranslationally. Nevertheless, the C-tail-anchored protein SciP is targeted cotranslationally by SRP. We report here that two amino-terminal hydrophobic stretches in SciP are individually recognized by SRP and target the nascent protein to FtsY. The presence of two signal sequences may enable a retargeting mechanism, as already observed for multispanning membrane proteins, to make the posttranslational insertion of SciP by YidC more efficient.
Collapse
|
38
|
Kammel M, Hunger D, Sawers RG. The soluble cytoplasmic N-terminal domain of the FocA channel gates bidirectional formate translocation. Mol Microbiol 2020; 115:758-773. [PMID: 33169422 DOI: 10.1111/mmi.14641] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/05/2020] [Indexed: 11/28/2022]
Abstract
FocA belongs to the pentameric FNT (formate-nitrite transporter) superfamily of anion channels, translocating formate bidirectionally across the cytoplasmic membrane of Escherichia coli and other microorganisms. While the membrane-integral core of FocA shares considerable amino acid sequence conservation with other FNT family members, the soluble cytoplasmic N-terminal domain does not. To analyze the potential biochemical function of FocA's N-terminal domain in vivo, we constructed truncation derivatives and amino acid-exchange variants, and determined their ability to translocate formate across the membrane of E. coli cells by monitoring intracellular formate levels using a formate-sensitive reporter system. Analysis of strains synthesizing these FocA variants provided insights into formate efflux. Strains lacking the ability to generate formate intracellularly allowed us to determine whether these variants could import formate or its toxic chemical analog hypophosphite. Our findings reveal that the N-terminal domain of FocA is crucial for bidirectional FocA-dependent permeation of formate across the membrane. Moreover, we show that an amino acid sequence motif and secondary structural features of the flexible N-terminal domain are important for formate translocation, and efflux/influx is influenced by pyruvate formate-lyase. The soluble N-terminal domain is, therefore, essential for bidirectional formate translocation by FocA, suggesting a "gate-keeper" function controlling anion accessibility.
Collapse
Affiliation(s)
- Michelle Kammel
- Institute of Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Doreen Hunger
- Institute of Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Robert Gary Sawers
- Institute of Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| |
Collapse
|
39
|
Romero-González LE, Pérez-Morales D, Cortés-Avalos D, Vázquez-Guerrero E, Paredes-Hernández DA, Estrada-de los Santos P, Villa-Tanaca L, De la Cruz MA, Bustamante VH, Ibarra JA. The Salmonella Typhimurium InvF-SicA complex is necessary for the transcription of sopB in the absence of the repressor H-NS. PLoS One 2020; 15:e0240617. [PMID: 33119619 PMCID: PMC7595419 DOI: 10.1371/journal.pone.0240617] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/21/2020] [Indexed: 12/25/2022] Open
Abstract
Expression of virulence factors in non-typhoidal Salmonella enterica depends on a wide variety of general and specific transcriptional factors that act in response to multiple environmental signals. Expression of genes for cellular invasion located in the Salmonella pathogenicity island 1 (SPI-1) is tightly regulated by several transcriptional regulators arrayed in a cascade, while repression of this system is exerted mainly by H-NS. In SPI-1, H-NS represses the expression mainly by binding to the regulatory region of hilA and derepression is exercised mainly by HilD. However, the possible regulatory role of H-NS in genes downstream from HilD and HilA, such as those regulated by InvF, has not been fully explored. Here the role of H-NS on the expression of sopB, an InvF dependent gene encoded in SPI-5, was evaluated. Our data show that InvF is required for the expression of sopB even in the absence of H-NS. Furthermore, in agreement with previous results on other InvF-regulated genes, we found that the expression of sopB requires the InvF/SicA complex. Our results support that SicA is not required for DNA binding nor for increasing affinity of InvF to DNA in vitro. Moreover, by using a bacterial two-hybrid system we were able to identify interactions between SicA and InvF. Lastly, protein-protein interaction assays suggest that InvF functions as a monomer. Derived from these results we postulate that the InvF/SicA complex does not act on sopB as an anti-H-NS factor; instead, it seems to induce the expression of sopB by acting as a classical transcriptional regulator.
Collapse
Affiliation(s)
- Luis E. Romero-González
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Deyanira Pérez-Morales
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Daniel Cortés-Avalos
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Edwin Vázquez-Guerrero
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Denisse A. Paredes-Hernández
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Paulina Estrada-de los Santos
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Lourdes Villa-Tanaca
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Miguel A. De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarías, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Víctor H. Bustamante
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - J. Antonio Ibarra
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
- * E-mail: ,
| |
Collapse
|
40
|
SecY-mediated quality control prevents the translocation of non-gated porins. Sci Rep 2020; 10:16347. [PMID: 33004891 PMCID: PMC7530735 DOI: 10.1038/s41598-020-73185-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 09/09/2020] [Indexed: 01/24/2023] Open
Abstract
OmpC and OmpF are among the most abundant outer membrane proteins in E. coli and serve as hydrophilic channels to mediate uptake of small molecules including antibiotics. Influx selectivity is controlled by the so-called constriction zone or eyelet of the channel. Mutations in the loop domain forming the eyelet can disrupt transport selectivity and thereby interfere with bacterial viability. In this study we show that a highly conserved motif of five negatively charged amino acids in the eyelet, which is critical to regulate pore selectivity, is also required for SecY-mediated transport of OmpC and OmpF into the periplasm. Variants with a deleted or mutated motif were expressed in the cytosol and translocation was initiated. However, after signal peptide cleavage, import into the periplasm was aborted and the mutated proteins were redirected to the cytosol. Strikingly, reducing the proof-reading capacity of SecY by introducing the PrlA4 substitutions restored transport of OmpC with a mutated channel domain into the periplasm. Our study identified a SecY-mediated quality control pathway to restrict transport of outer membrane porin proteins with a deregulated channel activity into the periplasm.
Collapse
|
41
|
Fricke PM, Link T, Gätgens J, Sonntag C, Otto M, Bott M, Polen T. A tunable L-arabinose-inducible expression plasmid for the acetic acid bacterium Gluconobacter oxydans. Appl Microbiol Biotechnol 2020; 104:9267-9282. [PMID: 32974745 PMCID: PMC7567684 DOI: 10.1007/s00253-020-10905-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/04/2020] [Accepted: 09/10/2020] [Indexed: 01/21/2023]
Abstract
Abstract The acetic acid bacterium (AAB) Gluconobacter oxydans incompletely oxidizes a wide variety of carbohydrates and is therefore used industrially for oxidative biotransformations. For G. oxydans, no system was available that allows regulatable plasmid-based expression. We found that the l-arabinose-inducible PBAD promoter and the transcriptional regulator AraC from Escherichia coli MC4100 performed very well in G. oxydans. The respective pBBR1-based plasmids showed very low basal expression of the reporters β-glucuronidase and mNeonGreen, up to 480-fold induction with 1% l-arabinose, and tunability from 0.1 to 1% l-arabinose. In G. oxydans 621H, l-arabinose was oxidized by the membrane-bound glucose dehydrogenase, which is absent in the multi-deletion strain BP.6. Nevertheless, AraC-PBAD performed similar in both strains in the exponential phase, indicating that a gene knockout is not required for application of AraC-PBAD in wild-type G. oxydans strains. However, the oxidation product arabinonic acid strongly contributed to the acidification of the growth medium in 621H cultures during the stationary phase, which resulted in drastically decreased reporter activities in 621H (pH 3.3) but not in BP.6 cultures (pH 4.4). These activities could be strongly increased quickly solely by incubating stationary cells in d-mannitol-free medium adjusted to pH 6, indicating that the reporters were hardly degraded yet rather became inactive. In a pH-controlled bioreactor, these reporter activities remained high in the stationary phase (pH 6). Finally, we created a multiple cloning vector with araC-PBAD based on pBBR1MCS-5. Together, we demonstrated superior functionality and good tunability of an AraC-PBAD system in G. oxydans that could possibly also be used in other AAB. Key points • We found the AraC-PBADsystem from E. coli MC4100 was well tunable in G. oxydans. • In the absence of AraC orl-arabinose, expression from PBADwas extremely low. • This araC-PBADsystem could also be fully functional in other acetic acid bacteria. Electronic supplementary material The online version of this article (10.1007/s00253-020-10905-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Philipp Moritz Fricke
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Tobias Link
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Jochem Gätgens
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Christiane Sonntag
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Maike Otto
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Tino Polen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
| |
Collapse
|
42
|
Begeman A, Son A, Litberg TJ, Wroblewski TH, Gehring T, Huizar Cabral V, Bourne J, Xuan Z, Horowitz S. G-Quadruplexes act as sequence-dependent protein chaperones. EMBO Rep 2020; 21:e49735. [PMID: 32945124 PMCID: PMC7534610 DOI: 10.15252/embr.201949735] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 01/06/2023] Open
Abstract
Maintaining proteome health is important for cell survival. Nucleic acids possess the ability to prevent protein aggregation more efficiently than traditional chaperone proteins. In this study, we explore the sequence specificity of the chaperone activity of nucleic acids. Evaluating over 500 nucleic acid sequences' effects on protein aggregation, we show that the holdase chaperone effect of nucleic acids is sequence-dependent. G-Quadruplexes prevent protein aggregation via quadruplex:protein oligomerization. They also increase the folded protein level of a biosensor in E. coli. These observations contextualize recent reports of quadruplexes playing important roles in aggregation-related diseases, such as fragile X and amyotrophic lateral sclerosis (ALS), and provide evidence that nucleic acids have the ability to modulate the folding environment of E. coli.
Collapse
Affiliation(s)
- Adam Begeman
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Ahyun Son
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Theodore J Litberg
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Tadeusz H Wroblewski
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Thane Gehring
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Veronica Huizar Cabral
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Jennifer Bourne
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Zhenyu Xuan
- Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX, USA
| | - Scott Horowitz
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| |
Collapse
|
43
|
Wood TE, Howard SA, Förster A, Nolan LM, Manoli E, Bullen NP, Yau HCL, Hachani A, Hayward RD, Whitney JC, Vollmer W, Freemont PS, Filloux A. The Pseudomonas aeruginosa T6SS Delivers a Periplasmic Toxin that Disrupts Bacterial Cell Morphology. Cell Rep 2020; 29:187-201.e7. [PMID: 31577948 PMCID: PMC6899460 DOI: 10.1016/j.celrep.2019.08.094] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 07/02/2019] [Accepted: 08/27/2019] [Indexed: 01/10/2023] Open
Abstract
The type VI secretion system (T6SS) is crucial in interbacterial competition and is a virulence determinant of many Gram-negative bacteria. Several T6SS effectors are covalently fused to secreted T6SS structural components such as the VgrG spike for delivery into target cells. In Pseudomonas aeruginosa, the VgrG2b effector was previously proposed to mediate bacterial internalization into eukaryotic cells. In this work, we find that the VgrG2b C-terminal domain (VgrG2bC-ter) elicits toxicity in the bacterial periplasm, counteracted by a cognate immunity protein. We resolve the structure of VgrG2bC-ter and confirm it is a member of the zinc-metallopeptidase family of enzymes. We show that this effector causes membrane blebbing at midcell, which suggests a distinct type of T6SS-mediated growth inhibition through interference with cell division, mimicking the impact of β-lactam antibiotics. Our study introduces a further effector family to the T6SS arsenal and demonstrates that VgrG2b can target both prokaryotic and eukaryotic cells. The structure of the VgrG2b C-terminal domain presents a metallopeptidase fold VgrG2b exerts antibacterial activity in the periplasmic space Toxicity of VgrG2b is counteracted by a cognate periplasmic immunity protein VgrG2bC-ter-intoxicated prey cells bleb at the midcell and lyse
Collapse
Affiliation(s)
- Thomas E Wood
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Sophie A Howard
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Andreas Förster
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Laura M Nolan
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Eleni Manoli
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Nathan P Bullen
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Hamish C L Yau
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Abderrahman Hachani
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Richard D Hayward
- Division of Microbiology and Parasitology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - John C Whitney
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Paul S Freemont
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
| |
Collapse
|
44
|
Jeffries J, Thongsomboon W, Visser JA, Enriquez K, Yager D, Cegelski L. Variation in the ratio of curli and phosphoethanolamine cellulose associated with biofilm architecture and properties. Biopolymers 2020; 112:e23395. [PMID: 32894594 DOI: 10.1002/bip.23395] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 11/11/2022]
Abstract
Bacterial biofilms are communities of bacteria entangled in a self-produced extracellular matrix (ECM). Escherichia coli direct the assembly of two insoluble biopolymers, curli amyloid fibers, and phosphoethanolamine (pEtN) cellulose, to build remarkable biofilm architectures. Intense curiosity surrounds how bacteria harness these amyloid-polysaccharide composites to build biofilms, and how these biopolymers function to benefit bacterial communities. Defining ECM composition involving insoluble polymeric assemblies poses unique challenges to analysis and, thus, to comparing strains with quantitative ECM molecular correlates. In this work, we present results from a sum-of-the-parts 13 C solid-state nuclear magnetic resonance (NMR) analysis to define the curli-to-pEtN cellulose ratio in the isolated ECM of the E. coli laboratory K12 strain, AR3110. We compare and contrast the compositional analysis and comprehensive biofilm phenotypes for AR3110 and a well-studied clinical isolate, UTI89. The ECM isolated from AR3110 contains approximately twice the amount of pEtN cellulose relative to curli content as UTI89, revealing plasticity in matrix assembly principles among strains. The two parent strains and a panel of relevant gene mutants were investigated in three biofilm models, examining: (a) macrocolonies on agar, (b) pellicles at the liquid-air interface, and (c) biomass accumulation on plastic. We describe the influence of curli, cellulose, and the pEtN modification on biofilm phenotypes with power in the direct comparison of these strains. The results suggest that curli more strongly influence adhesion, while pEtN cellulose drives cohesion. Their individual and combined influence depends on both the biofilm modality (agar, pellicle, or plastic-associated) and the strain itself.
Collapse
Affiliation(s)
- Jamie Jeffries
- Department of Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, California, USA
| | | | | | - Kyle Enriquez
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - Deborah Yager
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - Lynette Cegelski
- Department of Chemistry, Stanford University, Stanford, California, USA
| |
Collapse
|
45
|
Jiang X, Tan WB, Shrivastava R, Seow DCS, Chen SL, Guan XL, Chng SS. Mutations in enterobacterial common antigen biosynthesis restore outer membrane barrier function in Escherichia coli tol-pal mutants. Mol Microbiol 2020; 114:991-1005. [PMID: 32808719 DOI: 10.1111/mmi.14590] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/12/2020] [Indexed: 12/27/2022]
Abstract
The outer membrane (OM) is an essential component of the Gram-negative bacterial envelope that protects the cells against external threats. To maintain a functional OM, cells require distinct mechanisms to ensure balance of proteins and lipids in the membrane. Mutations in OM biogenesis and/or homeostasis pathways often result in permeability defects, but how molecular changes in the OM affect barrier function is unclear. Here, we seek potential mechanism(s) that can alleviate permeability defects in Escherichia coli cells lacking the Tol-Pal complex, which accumulate excess PLs in the OM. We identify mutations in enterobacterial common antigen (ECA) biosynthesis that re-establish OM barrier function against large hydrophilic molecules, yet did not restore lipid homeostasis. Furthermore, we demonstrate that build-up of biosynthetic intermediates, but not loss of ECA itself, contributes to the rescue. This suppression of OM phenotypes is unrelated to known effects that accumulation of ECA intermediates have on the cell wall. Finally, we reveal that an unusual diacylglycerol pyrophosphoryl-linked lipid species also accumulates in ECA mutants, and might play a role in the rescue phenotype. Our work provides insights into how OM barrier function can be restored independent of lipid homeostasis, and highlights previously unappreciated effects of ECA-related species in OM biology.
Collapse
Affiliation(s)
- Xiang'Er Jiang
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Wee Boon Tan
- Singapore Center for Environmental Life Sciences Engineering, National University of Singapore (SCELSE-NUS), Singapore, Singapore
| | - Rahul Shrivastava
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Deborah Chwee San Seow
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Swaine Lin Chen
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Xue Li Guan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Shu-Sin Chng
- Department of Chemistry, National University of Singapore, Singapore, Singapore.,Singapore Center for Environmental Life Sciences Engineering, National University of Singapore (SCELSE-NUS), Singapore, Singapore
| |
Collapse
|
46
|
A dual-constriction biological nanopore resolves homonucleotide sequences with high fidelity. Nat Biotechnol 2020; 38:1415-1420. [PMID: 32632300 PMCID: PMC7610451 DOI: 10.1038/s41587-020-0570-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 05/14/2020] [Accepted: 05/19/2020] [Indexed: 02/04/2023]
Abstract
Single-molecule long-read DNA sequencing with biological nanopores is fast and high-throughput but suffers reduced accuracy in homonucleotide stretches. We now combine the CsgG nanopore with the 35-residue N-terminal region of its extracellular interaction partner CsgF to produce a dual-constriction pore with improved signal and basecalling accuracy for homopolymer regions. The electron cryo-microscopy structure of CsgG in complex with full-length CsgF shows that the 33 N-terminal residues of CsgF bind inside the β-barrel of the pore, forming a defined second constriction. In complexes of CsgG bound to a 35-residue CsgF constriction peptide, the second constriction is separated from the primary constriction by ~25 Å. We find that both constrictions contribute to electrical signal modulation upon ssDNA translocation. DNA sequencing using a prototype CsgG:CsgF protein pore with two constrictions improved single-read accuracy by 25 to 70 % in homopolymers up to 9 nucleotides long.
Collapse
|
47
|
Mais CN, Hermann L, Altegoer F, Seubert A, Richter AA, Wernersbach I, Czech L, Bremer E, Bange G. Degradation of the microbial stress protectants and chemical chaperones ectoine and hydroxyectoine by a bacterial hydrolase-deacetylase complex. J Biol Chem 2020; 295:9087-9104. [PMID: 32404365 PMCID: PMC7335791 DOI: 10.1074/jbc.ra120.012722] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 05/06/2020] [Indexed: 12/12/2022] Open
Abstract
When faced with increased osmolarity in the environment, many bacterial cells accumulate the compatible solute ectoine and its derivative 5-hydroxyectoine. Both compounds are not only potent osmostress protectants, but also serve as effective chemical chaperones stabilizing protein functionality. Ectoines are energy-rich nitrogen and carbon sources that have an ecological impact that shapes microbial communities. Although the biochemistry of ectoine and 5-hydroxyectoine biosynthesis is well understood, our understanding of their catabolism is only rudimentary. Here, we combined biochemical and structural approaches to unravel the core of ectoine and 5-hydroxy-ectoine catabolisms. We show that a conserved enzyme bimodule consisting of the EutD ectoine/5-hydroxyectoine hydrolase and the EutE deacetylase degrades both ectoines. We determined the high-resolution crystal structures of both enzymes, derived from the salt-tolerant bacteria Ruegeria pomeroyi and Halomonas elongata These structures, either in their apo-forms or in forms capturing substrates or intermediates, provided detailed insights into the catalytic cores of the EutD and EutE enzymes. The combined biochemical and structural results indicate that the EutD homodimer opens the pyrimidine ring of ectoine through an unusual covalent intermediate, N-α-2 acetyl-l-2,4-diaminobutyrate (α-ADABA). We found that α-ADABA is then deacetylated by the zinc-dependent EutE monomer into diaminobutyric acid (DABA), which is further catabolized to l-aspartate. We observed that the EutD-EutE bimodule synthesizes exclusively the α-, but not the γ-isomers of ADABA or hydroxy-ADABA. Of note, α-ADABA is known to induce the MocR/GabR-type repressor EnuR, which controls the expression of many ectoine catabolic genes clusters. We conclude that hydroxy-α-ADABA might serve a similar function.
Collapse
Affiliation(s)
- Christopher-Nils Mais
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany
| | - Lucas Hermann
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Biology, Marburg, Germany
| | - Florian Altegoer
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany
| | - Andreas Seubert
- Philipps-University Marburg, Faculty of Chemistry, Marburg, Germany
| | - Alexandra A Richter
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Biology, Marburg, Germany
| | - Isa Wernersbach
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany
| | - Laura Czech
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Biology, Marburg, Germany
| | - Erhard Bremer
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Biology, Marburg, Germany.
| | - Gert Bange
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany.
| |
Collapse
|
48
|
Gerken H, Vuong P, Soparkar K, Misra R. Roles of the EnvZ/OmpR Two-Component System and Porins in Iron Acquisition in Escherichia coli. mBio 2020; 11:e01192-20. [PMID: 32576675 PMCID: PMC7315122 DOI: 10.1128/mbio.01192-20] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 05/19/2020] [Indexed: 12/31/2022] Open
Abstract
Escherichia coli secretes high-affinity Fe3+ chelators to solubilize and transport chelated Fe3+ via specific outer membrane receptors. In microaerobic and anaerobic growth environments, where the reduced Fe2+ form is predominant, ferrous transport systems fulfill the bacterial need for iron. Expression of genes coding for iron metabolism is controlled by Fur, which when bound to Fe2+ acts as a repressor. Work carried out here shows that the constitutively activated EnvZ/OmpR two-component system, which normally controls expression of the ompC and ompF porin genes, dramatically increases the intracellular pool of accessible iron, as determined by whole-cell electron paramagnetic resonance spectroscopy, by inducing the OmpC/FeoB-mediated ferrous transport pathway. Elevated levels of intracellular iron in turn activated Fur, which inhibited the ferric transport pathway but not the ferrous transport pathway. The data show that the positive effect of constitutively activated EnvZ/OmpR on feoB expression is sufficient to overcome the negative effect of activated Fur on feoB In a tonB mutant, which lacks functional ferric transport systems, deletion of ompR severely impairs growth on rich medium not supplemented with iron, while the simultaneous deletion of ompC and ompF is not viable. These data, together with the observation of derepression of the Fur regulon in an OmpC mutant, show that the porins play an important role in iron homeostasis. The work presented here also resolves a long-standing paradoxical observation of the effect of certain mutant envZ alleles on iron regulon.IMPORTANCE The work presented here solved a long-standing paradox of the negative effects of certain missense alleles of envZ, which codes for kinase of the EnvZ/OmpR two-component system, on the expression of ferric uptake genes. The data revealed that the constitutive envZ alleles activate the Feo- and OmpC-mediated ferrous uptake pathway to flood the cytoplasm with accessible ferrous iron. This activates the ferric uptake regulator, Fur, which inhibits ferric uptake system but cannot inhibit the feo operon due to the positive effect of activated EnvZ/OmpR. The data also revealed the importance of porins in iron homeostasis.
Collapse
Affiliation(s)
- Henri Gerken
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Phu Vuong
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Ketaki Soparkar
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Rajeev Misra
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| |
Collapse
|
49
|
Tomasek D, Rawson S, Lee J, Wzorek JS, Harrison SC, Li Z, Kahne D. Structure of a nascent membrane protein as it folds on the BAM complex. Nature 2020; 583:473-478. [PMID: 32528179 PMCID: PMC7367713 DOI: 10.1038/s41586-020-2370-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/25/2020] [Indexed: 11/09/2022]
Abstract
Mitochondria, chloroplasts, and Gram-negative bacteria are encased in a double layer of membranes. The outer membrane contains proteins with a β-barrel structure1,2. β-barrels are sheets of β-strands wrapped into a cylinder with the first strand hydrogen-bonded to the last strand. Conserved multi-subunit molecular machines fold and insert these proteins into the outer membrane3–5. One subunit of the machines is itself a β-barrel protein that plays a central role in folding other β-barrels. In Gram-negative bacteria, the β-barrel assembly machine (Bam) consists of the β-barrel protein BamA and four lipoproteins5–8. To understand how the Bam complex accelerates folding without using exogenous energy (e.g., ATP)9, we trapped folding intermediates on the machine. We report here the structure of the Bam complex folding BamA itself. The BamA catalyst (BamAM, for BamAmachine) forms an asymmetric hybrid β-barrel with the BamA substrate (BamAS). The N-terminal edge of BamAM has an antiparallel hydrogen-bonded interface with the C-terminal edge of BamAS, consistent with previous crosslinking studies10–12; the other edges of BamAM and BamAS are close to each other but curl inward and do not pair. Six hydrogen bonds in a membrane environment make the interface between the two proteins very stable. This stability allows folding but creates a high kinetic barrier to substrate release once folding has finished. Features at each end of the substrate overcome the barrier and promote release by stepwise exchange of hydrogen bonds. This mechanism of substrate-assisted product release explains how the Bam complex can stably associate with the substrate during folding and then turn over rapidly when folding is complete.
Collapse
Affiliation(s)
- David Tomasek
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - James Lee
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, NY, USA
| | - Joseph S Wzorek
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. .,Howard Hughes Medical Institute, Boston, MA, USA.
| | - Zongli Li
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. .,Howard Hughes Medical Institute, Boston, MA, USA.
| | - Daniel Kahne
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA. .,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. .,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
50
|
Susceptibility of the Formate Hydrogenlyase Reaction to the Protonophore CCCP Depends on the Total Hydrogenase Composition. INORGANICS 2020. [DOI: 10.3390/inorganics8060038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Fermentative hydrogen production by enterobacteria derives from the activity of the formate hydrogenlyase (FHL) complex, which couples formate oxidation to H2 production. The molybdenum-containing formate dehydrogenase and type-4 [NiFe]-hydrogenase together with three iron-sulfur proteins form the soluble domain, which is attached to the membrane by two integral membrane subunits. The FHL complex is phylogenetically related to respiratory complex I, and it is suspected that it has a role in energy conservation similar to the proton-pumping activity of complex I. We monitored the H2-producing activity of FHL in the presence of different concentrations of the protonophore CCCP. We found an inhibition with an apparent EC50 of 31 µM CCCP in the presence of glucose, a higher tolerance towards CCCP when only the oxidizing hydrogenase Hyd-1 was present, but a higher sensitivity when only Hyd-2 was present. The presence of 200 mM monovalent cations reduced the FHL activity by more than 20%. The Na+/H+ antiporter inhibitor 5-(N-ethyl-N-isopropyl)-amiloride (EIPA) combined with CCCP completely inhibited H2 production. These results indicate a coupling not only between Na+ transport activity and H2 production activity, but also between the FHL reaction, proton import and cation export.
Collapse
|