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Billini M, Hoffmann T, Kühn J, Bremer E, Thanbichler M. The cytoplasmic phosphate level has a central regulatory role in the phosphate starvation response of Caulobacter crescentus. Commun Biol 2024; 7:772. [PMID: 38926609 PMCID: PMC11208175 DOI: 10.1038/s42003-024-06469-y] [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: 10/07/2023] [Accepted: 06/19/2024] [Indexed: 06/28/2024] Open
Abstract
In bacteria, the availability of environmental inorganic phosphate is typically sensed by the conserved PhoR-PhoB two-component signal transduction pathway, which uses the flux through the PstSCAB phosphate transporter as a readout of the extracellular phosphate level to control phosphate-responsive genes. While the sensing of environmental phosphate is well-investigated, the regulatory effects of cytoplasmic phosphate are unclear. Here, we disentangle the physiological and transcriptional responses of Caulobacter crescentus to changes in the environmental and cytoplasmic phosphate levels by uncoupling phosphate uptake from the activity of the PstSCAB system, using an additional, heterologously produced phosphate transporter. This approach reveals a two-pronged response of C. crescentus to phosphate limitation, in which PhoR-PhoB signaling mostly facilitates the utilization of alternative phosphate sources, whereas the cytoplasmic phosphate level controls the morphological and physiological adaptation of cells to growth under global phosphate limitation. These findings open the door to a comprehensive understanding of phosphate signaling in bacteria.
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Affiliation(s)
- Maria Billini
- Department of Biology, University of Marburg, 35043, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Tamara Hoffmann
- Department of Biology, University of Marburg, 35043, Marburg, Germany
- Center for Synthetic Microbiology, 35043, Marburg, Germany
| | - Juliane Kühn
- Department of Biology, University of Marburg, 35043, Marburg, Germany
| | - Erhard Bremer
- Department of Biology, University of Marburg, 35043, Marburg, Germany
- Center for Synthetic Microbiology, 35043, Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, 35043, Marburg, Germany.
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
- Center for Synthetic Microbiology, 35043, Marburg, Germany.
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2
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Zorz J, Paquette AJ, Gillis T, Kouris A, Khot V, Demirkaya C, De La Hoz Siegler H, Strous M, Vadlamani A. Coordinated proteome change precedes cell lysis and death in a mat-forming cyanobacterium. THE ISME JOURNAL 2023; 17:2403-2414. [PMID: 37914776 PMCID: PMC10689466 DOI: 10.1038/s41396-023-01545-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
Cyanobacteria form dense multicellular communities that experience transient conditions in terms of access to light and oxygen. These systems are productive but also undergo substantial biomass turnover through cell death, supplementing heightened heterotrophic respiration. Here we use metagenomics and metaproteomics to survey the molecular response of a mat-forming cyanobacterium undergoing mass cell lysis after exposure to dark and anoxic conditions. A lack of evidence for viral, bacterial, or eukaryotic antagonism contradicts commonly held beliefs on the causative agent for cyanobacterial death during dense growth. Instead, proteogenomics data indicated that lysis likely resulted from a genetically programmed response triggered by a failure to maintain osmotic pressure in the wake of severe energy limitation. Cyanobacterial DNA was rapidly degraded, yet cyanobacterial proteins remained abundant. A subset of proteins, including enzymes involved in amino acid metabolism, peptidases, toxin-antitoxin systems, and a potentially self-targeting CRISPR-Cas system, were upregulated upon lysis, indicating possible involvement in the programmed cell death response. We propose this natural form of cell death could provide new pathways for controlling harmful algal blooms and for sustainable bioproduct production.
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Affiliation(s)
- Jackie Zorz
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada.
| | - Alexandre J Paquette
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Timber Gillis
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Angela Kouris
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
- Synergia Biotech Inc., Calgary, AB, Canada
| | - Varada Khot
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Cigdem Demirkaya
- Department of Chemical and Petroleum Engineering, University of Calgary, Calgary, AB, Canada
| | | | - Marc Strous
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Agasteswar Vadlamani
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
- Synergia Biotech Inc., Calgary, AB, Canada
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3
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Montuori E, Martinez KA, De Luca D, Ianora A, Lauritano C. Transcriptome Sequencing of the Diatom Asterionellopsis thurstonii and In Silico Identification of Enzymes Potentially Involved in the Synthesis of Bioactive Molecules. Mar Drugs 2023; 21:md21020126. [PMID: 36827167 PMCID: PMC9959416 DOI: 10.3390/md21020126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Microalgae produce a plethora of primary and secondary metabolites with possible applications in several market sectors, including cosmetics, human nutrition, aquaculture, biodiesel production and treatment/prevention of human diseases. Diatoms, in particular, are the most diversified microalgal group, many species of which are known to have anti-cancer, anti-oxidant, anti-diabetes, anti-inflammatory and immunomodulatory properties. Compounds responsible for these activities are often still unknown. The aim of this study was to de novo sequence the full transcriptome of two strains of the diatom Asterionellopsis thurstonii, sampled from two different locations and cultured in both control and phosphate starvation conditions. We used an RNA-sequencing approach to in silico identify transcripts potentially involved in the synthesis/degradation of compounds with anti-cancer and immunomodulatory properties. We identified transcript coding for L-asparaginase I, polyketide cyclase/dehydrase, bifunctional polyketide phosphatase/kinase, 1-deoxy-D-xylulose-5-phosphate synthase (fragment), inositol polyphosphate 5-phosphatase INPP5B/F, catechol O-Methyltransferase, digalactosyldiacylglycerol synthase (DGD1), 1,2-diacylglycerol-3-beta-galactosyltransferase and glycerolphosphodiester phosphodiesterase. Differential expression analysis also allowed to identify in which culturing condition these enzymes are more expressed. Overall, these data give new insights on the annotation of diatom genes, enzymatic pathways involved in the generation of bioactive molecules and possible exploitation of Asterionellopsis thurstonii.
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Affiliation(s)
- Eleonora Montuori
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
- Ecosustainable Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Via Acton 55, 80133 Naples, Italy
| | - Kevin A. Martinez
- Ecosustainable Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Via Acton 55, 80133 Naples, Italy
| | - Daniele De Luca
- Department of Biology, University of Naples Federico II, Via Foria 223, 80139 Naples, Italy
| | - Adrianna Ianora
- Ecosustainable Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Via Acton 55, 80133 Naples, Italy
| | - Chiara Lauritano
- Ecosustainable Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Via Acton 55, 80133 Naples, Italy
- Correspondence: author:
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4
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The Bacterial MtrAB Two-Component System Regulates the Cell Wall Homeostasis Responding to Environmental Alkaline Stress. Microbiol Spectr 2022; 10:e0231122. [PMID: 36073914 PMCID: PMC9602371 DOI: 10.1128/spectrum.02311-22] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Throughout the course of evolution, bacteria have developed signal transduction tools such as two-component systems (TCSs) to meet their demands to thrive even under the most challenging environmental conditions. One TCS called MtrAB is commonly found in Actinobacteria and is implicated in cell wall metabolism, osmoprotection, cell proliferation, antigen secretion, and biosynthesis of secondary metabolites. However, precisely how the MtrAB TCS regulates the bacterial responses to external environments remains unclear. Here, we report that the MtrAB TCS regulates the cell envelope response of alkali-tolerant bacterium Dietzia sp. strain DQ12-45-1b to extreme alkaline stimuli. We found that under alkaline conditions, an mtrAB mutant exhibited both reduced growth and abnormal morphology compared to the wild-type strain. Electrophoretic mobility shift assay analysis showed that MtrA binds the promoter of the mraZ gene critical for cell wall homeostasis, suggesting that MtrA directly controls transcription of this regulator. In conclusion, our findings demonstrate that MtrAB TCS is involved in controlling the bacterial response to alkaline stimuli by regulating the expression of the cell wall homeostasis regulator MraZ in Dietzia sp. DQ12-45-1b, providing novel details critical for a mechanistic understanding of how cell wall homeostasis is controlled. IMPORTANCE Microorganisms can be found in most extreme environments, and they have to adapt to a wide range of environmental stresses. The two-component systems (TCSs) found in bacteria detect environmental stimuli and regulate physiological pathways for survival. The MtrAB TCS conserved in Corynebacterineae is critical for maintaining the metabolism of the cell wall components that protects bacteria from diverse environmental stresses. However, how the MtrAB TCS regulates cell wall homeostasis and adaptation under stress conditions is unclear. Here, we report that the MtrAB TCS in Dietzia sp. DQ12-45-1b plays a critical role in alkaline resistance by modulating the cell wall homeostasis through the MtrAB-MraZ pathway. Thus, our work provides a novel regulatory pathway used by bacteria for adaptation and survival under extreme alkaline stresses.
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5
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Ferrarini MG, Dell’Aglio E, Vallier A, Balmand S, Vincent-Monégat C, Hughes S, Gillet B, Parisot N, Zaidman-Rémy A, Vieira C, Heddi A, Rebollo R. Efficient compartmentalization in insect bacteriomes protects symbiotic bacteria from host immune system. MICROBIOME 2022; 10:156. [PMID: 36163269 PMCID: PMC9513942 DOI: 10.1186/s40168-022-01334-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 07/25/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Many insects house symbiotic intracellular bacteria (endosymbionts) that provide them with essential nutrients, thus promoting the usage of nutrient-poor habitats. Endosymbiont seclusion within host specialized cells, called bacteriocytes, often organized in a dedicated organ, the bacteriome, is crucial in protecting them from host immune defenses while avoiding chronic host immune activation. Previous evidence obtained in the cereal weevil Sitophilus oryzae has shown that bacteriome immunity is activated against invading pathogens, suggesting endosymbionts might be targeted and impacted by immune effectors during an immune challenge. To pinpoint any molecular determinants associated with such challenges, we conducted a dual transcriptomic analysis of S. oryzae's bacteriome subjected to immunogenic peptidoglycan fragments. RESULTS We show that upon immune challenge, the bacteriome actively participates in the innate immune response via induction of antimicrobial peptides (AMPs). Surprisingly, endosymbionts do not undergo any transcriptomic changes, indicating that this potential threat goes unnoticed. Immunohistochemistry showed that TCT-induced AMPs are located outside the bacteriome, excluding direct contact with the endosymbionts. CONCLUSIONS This work demonstrates that endosymbiont protection during an immune challenge is mainly achieved by efficient confinement within bacteriomes, which provides physical separation between host systemic response and endosymbionts. Video Abstract.
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Affiliation(s)
- Mariana Galvão Ferrarini
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, 69621 Villeurbanne, France
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
| | - Elisa Dell’Aglio
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Agnès Vallier
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Séverine Balmand
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, 69621 Villeurbanne, France
| | | | - Sandrine Hughes
- UMR5242, Institut de Génomique Fonctionnelle de Lyon (IGFL), Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon (Univ Lyon), F-69007 Lyon, France
| | - Benjamin Gillet
- UMR5242, Institut de Génomique Fonctionnelle de Lyon (IGFL), Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon (Univ Lyon), F-69007 Lyon, France
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Anna Zaidman-Rémy
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
| | - Abdelaziz Heddi
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Rita Rebollo
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, 69621 Villeurbanne, France
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6
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MraZ Transcriptionally Controls the Critical Level of FtsL Required for Focusing Z-Rings and Kickstarting Septation in Bacillus subtilis. J Bacteriol 2022; 204:e0024322. [PMID: 35943250 PMCID: PMC9487581 DOI: 10.1128/jb.00243-22] [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: 11/20/2022] Open
Abstract
The bacterial division and cell wall (dcw) cluster is a highly conserved region of the genome which encodes several essential cell division factors, including the central divisome protein FtsZ. Understanding the regulation of this region is key to our overall understanding of the division process. mraZ is found at the 5' end of the dcw cluster, and previous studies have described MraZ as a sequence-specific DNA binding protein. In this article, we investigate MraZ to elucidate its role in Bacillus subtilis. Through our investigation, we demonstrate that increased levels of MraZ result in lethal filamentation due to repression of its own operon (mraZ-mraW-ftsL-pbpB). We observed rescue of filamentation upon decoupling ftsL expression, but not other genes in the operon, from MraZ control. Our data suggest that regulation of the mra operon may be an alternative way for cells to quickly arrest cytokinesis, potentially during entry into the stationary phase and in the event of DNA replication arrest. Furthermore, through time-lapse microscopy, we were able to identify that overexpression of mraZ or depletion of FtsL results in decondensation of the FtsZ ring (Z-ring). Using fluorescent d-amino acid labeling, we also observed that coordinated peptidoglycan insertion at the division site is dysregulated in the absence of FtsL. Thus, we reveal that the precise role of FtsL is in Z-ring maturation and focusing septal peptidoglycan synthesis. IMPORTANCE MraZ is a highly conserved protein found in a diverse range of bacteria, including genome-reduced Mycoplasma. We investigated the role of MraZ in Bacillus subtilis and found that overproduction of MraZ is toxic due to cell division inhibition. Upon further analysis, we observed that MraZ is a repressor of its own operon, which includes genes that encode the essential cell division factors FtsL and PBP2B. We noted that decoupling of ftsL alone was sufficient to abolish MraZ-mediated cell division inhibition. Using time-lapse microscopy, we showed that under conditions where the FtsL level is depleted, the cell division machinery is unable to initiate cytokinesis. Thus, our results pinpoint that the precise role of FtsL is in concentrating septal cell wall synthesis to facilitate cell division.
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7
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Bianchi D, Pelletier JF, Hutchison CA, Glass JI, Luthey-Schulten Z. Toward the Complete Functional Characterization of a Minimal Bacterial Proteome. J Phys Chem B 2022; 126:6820-6834. [PMID: 36048731 PMCID: PMC9483919 DOI: 10.1021/acs.jpcb.2c04188] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/10/2022] [Indexed: 11/29/2022]
Abstract
Recently, we presented a whole-cell kinetic model of the genetically minimal bacterium JCVI-syn3A that described the coupled metabolic and genetic information processes and predicted behaviors emerging from the interactions among these networks. JCVI-syn3A is a genetically reduced bacterial cell that has the fewest number and smallest fraction of genes of unclear function, with approximately 90 of its 452 protein-coding genes (that is less than 20%) unannotated. Further characterization of unclear JCVI-syn3A genes strengthens the robustness and predictive power of cell modeling efforts and can lead to a deeper understanding of biophysical processes and pathways at the cell scale. Here, we apply computational analyses to elucidate the functions of the products of several essential but previously uncharacterized genes involved in integral cellular processes, particularly those directly affecting cell growth, division, and morphology. We also suggest directed wet-lab experiments informed by our analyses to further understand these "missing puzzle pieces" that are an essential part of the mosaic of biological interactions present in JCVI-syn3A. Our workflow leverages evolutionary sequence analysis, protein structure prediction, interactomics, and genome architecture to determine upgraded annotations. Additionally, we apply the structure prediction analysis component of our work to all 452 protein coding genes in JCVI-syn3A to expedite future functional annotation studies as well as the inverse mapping of the cell state to more physical models requiring all-atom or coarse-grained representations for all JCVI-syn3A proteins.
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Affiliation(s)
- David
M. Bianchi
- Department
of Chemistry, University of Illinois Urbana−Champaign, 600 S Mathews Ave, Urbana, Illinois 61801, United States
| | - James F. Pelletier
- Centro
Nacional de Biotecnologia, Calle Darwin no. 3, 28049 Madrid, Spain
| | - Clyde A. Hutchison
- J.
Craig Venter Institute, 4120 Capricorn Ln. La Jolla, California 92037, United States
| | - John I. Glass
- J.
Craig Venter Institute, 4120 Capricorn Ln. La Jolla, California 92037, United States
| | - Zaida Luthey-Schulten
- Department
of Chemistry, University of Illinois Urbana−Champaign, 600 S Mathews Ave, Urbana, Illinois 61801, United States
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8
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Effect of a Stannous Fluoride Dentifrice on Biofilm Composition, Gene Expression and Biomechanical Properties. Microorganisms 2022; 10:microorganisms10091691. [PMID: 36144293 PMCID: PMC9506307 DOI: 10.3390/microorganisms10091691] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
An in situ study was conducted to examine the mode of action of a 0.454% stannous fluoride (SnF2)-containing dentifrice in controlling the composition and properties of oral biofilm. Thirteen generally healthy individuals participated in the study. Each participant wore an intra-oral appliance over a 48-h period to measure differences in the resulting biofilm’s architecture, mechanical properties, and bacterial composition after using two different toothpaste products. In addition, metatranscriptomics analysis of supragingival plaque was conducted to identify the gene pathways influenced. The thickness and volume of the microcolonies formed when brushing with the SnF2 dentifrice were dramatically reduced compared to the control 0.76% sodium monofluorophosphate (MFP)-containing toothpaste. Similarly, the biophysical and nanomechanical properties measured by atomic force microscopy (AFM) demonstrated a significant reduction in biofilm adhesive properties. Metatranscriptomic analysis identified pathways associated with biofilm formation, cell adhesion, quorum sensing, and N-glycosylation that are significantly downregulated with SnF2. This study provides a clinically relevant snapshot of how the use of a stabilized, SnF2 toothpaste formulation can change the spatial organization, nanomechanical, and gene expression properties of bacterial communities.
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9
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Nyongesa S, Weber PM, Bernet È, Pulido F, Nieves C, Nieckarz M, Delaby M, Viehboeck T, Krause N, Rivera-Millot A, Nakamura A, Vischer NOE, vanNieuwenhze M, Brun YV, Cava F, Bulgheresi S, Veyrier FJ. Evolution of longitudinal division in multicellular bacteria of the Neisseriaceae family. Nat Commun 2022; 13:4853. [PMID: 35995772 PMCID: PMC9395523 DOI: 10.1038/s41467-022-32260-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Rod-shaped bacteria typically elongate and divide by transverse fission. However, several bacterial species can form rod-shaped cells that divide longitudinally. Here, we study the evolution of cell shape and division mode within the family Neisseriaceae, which includes Gram-negative coccoid and rod-shaped species. In particular, bacteria of the genera Alysiella, Simonsiella and Conchiformibius, which can be found in the oral cavity of mammals, are multicellular and divide longitudinally. We use comparative genomics and ultrastructural microscopy to infer that longitudinal division within Neisseriaceae evolved from a rod-shaped ancestor. In multicellular longitudinally-dividing species, neighbouring cells within multicellular filaments are attached by their lateral peptidoglycan. In these bacteria, peptidoglycan insertion does not appear concentric, i.e. from the cell periphery to its centre, but as a medial sheet guillotining each cell. Finally, we identify genes and alleles associated with multicellularity and longitudinal division, including the acquisition of amidase-encoding gene amiC2, and amino acid changes in proteins including MreB and FtsA. Introduction of amiC2 and allelic substitution of mreB in a rod-shaped species that divides by transverse fission results in shorter cells with longer septa. Our work sheds light on the evolution of multicellularity and longitudinal division in bacteria, and suggests that members of the Neisseriaceae family may be good models to study these processes due to their morphological plasticity and genetic tractability. Rod-shaped bacteria typically elongate and divide by transverse fission, but a few species are known to divide longitudinally. Here, the authors use genomic, phylogenetic and microscopy techniques to shed light on the evolution of cell shape, multicellularity and division mode within the family Neisseriaceae.
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Affiliation(s)
- Sammy Nyongesa
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, QC, H7V 1B7, Canada
| | - Philipp M Weber
- Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, University of Vienna, Vienna, Djerassiplatz 1, 1030, Vienna, Austria.,University of Vienna, Vienna Doctoral School of Ecology and Evolution, Vienna, Austria
| | - Ève Bernet
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, QC, H7V 1B7, Canada
| | - Francisco Pulido
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, QC, H7V 1B7, Canada
| | - Cecilia Nieves
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, QC, H7V 1B7, Canada
| | - Marta Nieckarz
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, SE-90187, Sweden
| | - Marie Delaby
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC, Canada
| | - Tobias Viehboeck
- Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, University of Vienna, Vienna, Djerassiplatz 1, 1030, Vienna, Austria.,University of Vienna, Vienna Doctoral School of Ecology and Evolution, Vienna, Austria.,Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, , University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Nicole Krause
- Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, University of Vienna, Vienna, Djerassiplatz 1, 1030, Vienna, Austria.,University of Vienna, Vienna Doctoral School of Ecology and Evolution, Vienna, Austria
| | - Alex Rivera-Millot
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, QC, H7V 1B7, Canada
| | - Arnaldo Nakamura
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, QC, H7V 1B7, Canada
| | - Norbert O E Vischer
- Bacterial Cell Biology & Physiology, Swammerdam Institute of Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098, Amsterdam, the Netherlands
| | | | - Yves V Brun
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC, Canada
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, SE-90187, Sweden
| | - Silvia Bulgheresi
- Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, University of Vienna, Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Frédéric J Veyrier
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, QC, H7V 1B7, Canada.
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10
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Ge Z, Yuan P, Chen L, Chen J, Shen D, She Z, Lu Y. New Global Insights on the Regulation of the Biphasic Life Cycle and Virulence Via ClpP-Dependent Proteolysis in Legionella pneumophila. Mol Cell Proteomics 2022; 21:100233. [PMID: 35427813 PMCID: PMC9112007 DOI: 10.1016/j.mcpro.2022.100233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 02/17/2022] [Accepted: 04/07/2022] [Indexed: 01/11/2023] Open
Abstract
Legionella pneumophila, an environmental bacterium that parasitizes protozoa, causes Legionnaires’ disease in humans that is characterized by severe pneumonia. This bacterium adopts a distinct biphasic life cycle consisting of a nonvirulent replicative phase and a virulent transmissive phase in response to different environmental conditions. Hence, the timely and fine-tuned expression of growth and virulence factors in a life cycle–dependent manner is crucial for survival and replication. Here, we report that the completion of the biphasic life cycle and bacterial pathogenesis is greatly dependent on the protein homeostasis regulated by caseinolytic protease P (ClpP)-dependent proteolysis. We characterized the ClpP-dependent dynamic profiles of the regulatory and substrate proteins during the biphasic life cycle of L. pneumophila using proteomic approaches and discovered that ClpP-dependent proteolysis specifically and conditionally degraded the substrate proteins, thereby directly playing a regulatory role or indirectly controlling cellular events via the regulatory proteins. We further observed that ClpP-dependent proteolysis is required to monitor the abundance of fatty acid biosynthesis–related protein Lpg0102/Lpg0361/Lpg0362 and SpoT for the normal regulation of L. pneumophila differentiation. We also found that the control of the biphasic life cycle and bacterial virulence is independent. Furthermore, the ClpP-dependent proteolysis of Dot/Icm (defect in organelle trafficking/intracellular multiplication) type IVB secretion system and effector proteins at a specific phase of the life cycle is essential for bacterial pathogenesis. Therefore, our findings provide novel insights on ClpP-dependent proteolysis, which spans a broad physiological spectrum involving key metabolic pathways that regulate the transition of the biphasic life cycle and bacterial virulence of L. pneumophila, facilitating adaptation to aquatic and intracellular niches. ClpP is the major determinant of biphasic life cycle–dependent protein turnover. ClpP-dependent proteolysis monitors SpoT abundance for cellular differentiation. ClpP-dependent regulation of life cycle and bacterial virulence is independent. ClpP-dependent proteolysis of T4BSS and effector proteins is vital for virulence.
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Affiliation(s)
- Zhenhuang Ge
- School of Chemistry, Sun Yat-sen University, Guangzhou, China; School of Life Sciences, Sun Yat-sen University, Guangzhou, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou, China
| | - Peibo Yuan
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Lingming Chen
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Junyi Chen
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou, China
| | - Dong Shen
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhigang She
- School of Chemistry, Sun Yat-sen University, Guangzhou, China
| | - Yongjun Lu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou, China.
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11
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Beroual W, Prévost K, Lalaouna D, Ben Zaina N, Valette O, Denis Y, Djendli M, Brasseur G, Brilli M, Robledo Garrido M, Jimenez-Zurdo JI, Massé E, Biondi EG. The noncoding RNA CcnA modulates the master cell cycle regulators CtrA and GcrA in Caulobacter crescentus. PLoS Biol 2022; 20:e3001528. [PMID: 35192605 PMCID: PMC8959179 DOI: 10.1371/journal.pbio.3001528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 03/28/2022] [Accepted: 01/05/2022] [Indexed: 12/01/2022] Open
Abstract
Bacteria are powerful models for understanding how cells divide and accomplish global regulatory programs. In Caulobacter crescentus, a cascade of essential master regulators supervises the correct and sequential activation of DNA replication, cell division, and development of different cell types. Among them, the response regulator CtrA plays a crucial role coordinating all those functions. Here, for the first time, we describe the role of a novel factor named CcnA (cell cycle noncoding RNA A), a cell cycle–regulated noncoding RNA (ncRNA) located at the origin of replication, presumably activated by CtrA, and responsible for the accumulation of CtrA itself. In addition, CcnA may be also involved in the inhibition of translation of the S-phase regulator, GcrA, by interacting with its 5′ untranslated region (5′ UTR). Performing in vitro experiments and mutagenesis, we propose a mechanism of action of CcnA based on liberation (ctrA) or sequestration (gcrA) of their ribosome-binding site (RBS). Finally, its role may be conserved in other alphaproteobacterial species, such as Sinorhizobium meliloti, representing indeed a potentially conserved process modulating cell cycle in Caulobacterales and Rhizobiales. During cell cycle progression in the bacterium Caulobacter crescentus, the master cell cycle regulator CtrA is controlled by CcnA, a cell cycle-regulated non-coding RNA transcribed from a gene located at the origin of replication.
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Affiliation(s)
- Wanassa Beroual
- Aix-Marseille Université, CNRS, LCB, IMM, Turing Center for Living Systems, Marseille, France
| | - Karine Prévost
- Département de biochimie et de génomique fonctionnelle, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - David Lalaouna
- Département de biochimie et de génomique fonctionnelle, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Nadia Ben Zaina
- Aix-Marseille Université, CNRS, LCB, IMM, Turing Center for Living Systems, Marseille, France
| | - Odile Valette
- Aix-Marseille Université, CNRS, LCB, IMM, Turing Center for Living Systems, Marseille, France
| | - Yann Denis
- Aix-Marseille Univ, CNRS, Plate-forme Transcriptome, IMM, Marseille, France
| | - Meriem Djendli
- Aix-Marseille Université, CNRS, LCB, IMM, Turing Center for Living Systems, Marseille, France
| | - Gaël Brasseur
- Aix-Marseille Université, CNRS, LCB, IMM, Turing Center for Living Systems, Marseille, France
| | - Matteo Brilli
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biosciences, University of Milan, Milan, Italy
| | - Marta Robledo Garrido
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Jose-Ignacio Jimenez-Zurdo
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Eric Massé
- Département de biochimie et de génomique fonctionnelle, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Emanuele G. Biondi
- Aix-Marseille Université, CNRS, LCB, IMM, Turing Center for Living Systems, Marseille, France
- * E-mail:
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12
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Was the Last Bacterial Common Ancestor a Monoderm after All? Genes (Basel) 2022; 13:genes13020376. [PMID: 35205421 PMCID: PMC8871954 DOI: 10.3390/genes13020376] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022] Open
Abstract
The very nature of the last bacterial common ancestor (LBCA), in particular the characteristics of its cell wall, is a critical issue to understand the evolution of life on earth. Although knowledge of the relationships between bacterial phyla has made progress with the advent of phylogenomics, many questions remain, including on the appearance or disappearance of the outer membrane of diderm bacteria (also called Gram-negative bacteria). The phylogenetic transition between monoderm (Gram-positive bacteria) and diderm bacteria, and the associated peptidoglycan expansion or reduction, requires clarification. Herein, using a phylogenomic tree of cultivated and characterized bacteria as an evolutionary framework and a literature review of their cell-wall characteristics, we used Bayesian ancestral state reconstruction to infer the cell-wall architecture of the LBCA. With the same phylogenomic tree, we further revisited the evolution of the division and cell-wall synthesis (dcw) gene cluster using homology- and model-based methods. Finally, extensive similarity searches were carried out to determine the phylogenetic distribution of the genes involved with the biosynthesis of the outer membrane in diderm bacteria. Quite unexpectedly, our analyses suggest that all cultivated and characterized bacteria might have evolved from a common ancestor with a monoderm cell-wall architecture. If true, this would indicate that the appearance of the outer membrane was not a unique event and that selective forces have led to the repeated adoption of such an architecture. Due to the lack of phenotypic information, our methodology cannot be applied to all extant bacteria. Consequently, our conclusion might change once enough information is made available to allow the use of an even more diverse organism selection.
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13
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Bai J, Wu Y, Bu Q, Zhong K, Gao H. Comparative study on antibacterial mechanism of shikimic acid and quinic acid against Staphylococcus aureus through transcriptomic and metabolomic approaches. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112441] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC. Persistence and plasticity in bacterial gene regulation. Nat Methods 2021; 18:1499-1505. [PMID: 34824476 DOI: 10.1038/s41592-021-01312-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/24/2021] [Indexed: 11/09/2022]
Abstract
Organisms orchestrate cellular functions through transcription factor (TF) interactions with their target genes, although these regulatory relationships are largely unknown in most species. Here we report a high-throughput approach for characterizing TF-target gene interactions across species and its application to 354 TFs across 48 bacteria, generating 17,000 genome-wide binding maps. This dataset revealed themes of ancient conservation and rapid evolution of regulatory modules. We observed rewiring, where the TF sensing and regulatory role is maintained while the arrangement and identity of target genes diverges, in some cases encoding entirely new functions. We further integrated phenotypic information to define new functional regulatory modules and pathways. Finally, we identified 242 new TF DNA binding motifs, including a 70% increase of known Escherichia coli motifs and the first annotation in Pseudomonas simiae, revealing deep conservation in bacterial promoter architecture. Our method provides a versatile tool for functional characterization of genetic pathways in prokaryotes and eukaryotes.
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Affiliation(s)
- Leo A Baumgart
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ji Eun Lee
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Asaf Salamov
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David J Dilworth
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hyunsoo Na
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew Mingay
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew J Blow
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yu Zhang
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yuko Yoshinaga
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris G Daum
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ronan C O'Malley
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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15
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Wang B, Duan J, Jin Y, Zhan Q, Xu Y, Zhao H, Wang X, Rao L, Guo Y, Yu F. Functional Insights of MraZ on the Pathogenicity of Staphylococcus aureus. Infect Drug Resist 2021; 14:4539-4551. [PMID: 34754202 PMCID: PMC8572050 DOI: 10.2147/idr.s332777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/08/2021] [Indexed: 01/08/2023] Open
Abstract
Introduction In recent years, multidrug-resistant methicillin-resistant Staphylococcus aureus has become increasingly prevalent, which raised a huge challenge to antibiotic treatment of infectious diseases. The anti-virulence strategy targeting virulent factors is a promising novel therapy for S. aureus infection. The virulence mechanism of S. aureus was needed to explore deeply to develop more targets and improve the effectiveness of anti-virulence strategies. Results In this study, we found mraZ was highly conserved in S. aureus, and its production is homologous with the MraZ of Escherichia coli, a transcriptional regulator involved in the growth and cell division of E. coli. To investigate the function of mraZ in S. aureus, we constructed a MW2 mraZ deletion mutant and its complementary mutant for virulence comparison. Although no remarkable influence on the growth, the mraZ deletion mutant led to significantly reduced resistance to human neutrophils and decreased virulence in Galleria mellonella model as well as mouse skin and soft tissue infection models, indicating its essential contribution to virulence and immune evasion to support the pathogenicity of S. aureus infection. RNA-Seq and quantitative RT-qPCR revealed that MraZ is a multi-functional regulator; it involves in diverse biological processes and can up-regulate the expression of various virulence genes by agr and sarA. Conclusion mraZ plays vital roles in the pathyogenicity of S. aureus via regulating many virulence genes. It may be an attractive target for anti-virulence therapy of S. aureus.
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Affiliation(s)
- Bingjie Wang
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Jingjing Duan
- Department of Clinical Laboratory, Renmin Hospital, Hubei University of Medicine, Hubei, People's Republic of China
| | - Ye Jin
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Qing Zhan
- Jiangxi Provincial Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang, People's Republic of China
| | - Yanlei Xu
- Jiangxi Provincial Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang, People's Republic of China
| | - Huilin Zhao
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Xinyi Wang
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Lulin Rao
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Yinjuan Guo
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Fangyou Yu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
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16
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Merker Breyer G, Malvessi Cattani A, Silveira Schrank I, Maboni Siqueira F. The influence of regulatory elements on Mycoplasma hyopneumoniae 7448 transcriptional response during oxidative stress and heat shock. Mol Biol Rep 2021; 49:139-147. [PMID: 34676505 DOI: 10.1007/s11033-021-06851-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/15/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND The comprehension of genome organization and gene modulation is essential for understanding pathogens' infection mechanisms. Mycoplasma hyopneumoniae 7448 genome is organized in transcriptional units (TUs), which are flanked by regulatory elements such as putative promoters, terminators and repetitive sequences. Yet the relationship between the presence of these elements and bacterial responses during stress conditions remains unclear. Thus, in this study, in silico and RT-qPCR analyses were associated to determine the effect of regulatory elements in gene expression regulation upon heat shock and oxidative stress conditions. METHODS AND RESULTS Thirteen TU's organizational profiles were found based on promoters and terminators distribution. Differential expression in genes sharing the same TUs was observed, suggesting the activity of internal regulatory elements. Moreover, 88.8% of tested genes were differentially expressed under oxidative stress in comparison to the control condition, being 81.3% of them surrounded by their own regulatory elements. Similarly, under heat shock, 44.4% of the genes showed regulation when compared to control condition, being 75.0% of them surrounded by their own regulatory elements. CONCLUSIONS Altogether, this data suggests the activity of internal regulatory elements in gene modulation of M. hyopneumoniae 7448 transcription.
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Affiliation(s)
- Gabriela Merker Breyer
- Laboratory of Veterinary Bacteriology, Veterinary Pathology Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Amanda Malvessi Cattani
- Graduate Program in Cell and Molecular Biology, Biotechnology Center, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Irene Silveira Schrank
- Graduate Program in Cell and Molecular Biology, Biotechnology Center, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Franciele Maboni Siqueira
- Laboratory of Veterinary Bacteriology, Veterinary Pathology Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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17
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Martínez-Torró C, Torres-Puig S, Marcos-Silva M, Huguet-Ramón M, Muñoz-Navarro C, Lluch-Senar M, Serrano L, Querol E, Piñol J, Pich OQ. Functional Characterization of the Cell Division Gene Cluster of the Wall-less Bacterium Mycoplasma genitalium. Front Microbiol 2021; 12:695572. [PMID: 34589065 PMCID: PMC8475190 DOI: 10.3389/fmicb.2021.695572] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/10/2021] [Indexed: 12/03/2022] Open
Abstract
It is well-established that FtsZ drives peptidoglycan synthesis at the division site in walled bacteria. However, the function and conservation of FtsZ in wall-less prokaryotes such as mycoplasmas are less clear. In the genome-reduced bacterium Mycoplasma genitalium, the cell division gene cluster is limited to four genes: mraZ, mraW, MG_223, and ftsZ. In a previous study, we demonstrated that ftsZ was dispensable for growth of M. genitalium under laboratory culture conditions. Herein, we show that the entire cell division gene cluster of M. genitalium is non-essential for growth in vitro. Our analyses indicate that loss of the mraZ gene alone is more detrimental for growth of M. genitalium than deletion of ftsZ or the entire cell division gene cluster. Transcriptional analysis revealed a marked upregulation of ftsZ in the mraZ mutant. Stable isotope labeling by amino acids in cell culture (SILAC)-based proteomics confirmed the overexpression of FtsZ in MraZ-deprived cells. Of note, we found that ftsZ expression was upregulated in non-adherent cells of M. genitalium, which arise spontaneously at relatively high rates. Single cell analysis using fluorescent markers showed that FtsZ localization varied throughout the cell cycle of M. genitalium in a coordinated manner with the chromosome and the terminal organelle (TMO). In addition, our results indicate a possible role for the RNA methyltransferase MraW in the regulation of FtsZ expression at the post-transcriptional level. Altogether, this study provides an extensive characterization of the cell division gene cluster of M. genitalium and demonstrates the existence of regulatory elements controlling FtsZ expression at the temporal and spatial level in mycoplasmas.
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Affiliation(s)
- Carlos Martínez-Torró
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sergi Torres-Puig
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marina Marcos-Silva
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marta Huguet-Ramón
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Carmen Muñoz-Navarro
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Enrique Querol
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jaume Piñol
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Oscar Q. Pich
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Institut d’Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, Sabadell, Spain
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18
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Garcia PS, Duchemin W, Flandrois JP, Gribaldo S, Grangeasse C, Brochier-Armanet C. A Comprehensive Evolutionary Scenario of Cell Division and Associated Processes in the Firmicutes. Mol Biol Evol 2021; 38:2396-2412. [PMID: 33533884 PMCID: PMC8136486 DOI: 10.1093/molbev/msab034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The cell cycle is a fundamental process that has been extensively studied in bacteria. However, many of its components and their interactions with machineries involved in other cellular processes are poorly understood. Furthermore, most knowledge relies on the study of a few models, but the real diversity of the cell division apparatus and its evolution are largely unknown. Here, we present a massive in-silico analysis of cell division and associated processes in around 1,000 genomes of the Firmicutes, a major bacterial phylum encompassing models (i.e. Bacillus subtilis, Streptococcus pneumoniae, and Staphylococcus aureus), as well as many important pathogens. We analyzed over 160 proteins by using an original approach combining phylogenetic reconciliation, phylogenetic profiles, and gene cluster survey. Our results reveal the presence of substantial differences among clades and pinpoints a number of evolutionary hotspots. In particular, the emergence of Bacilli coincides with an expansion of the gene repertoires involved in cell wall synthesis and remodeling. We also highlight major genomic rearrangements at the emergence of Streptococcaceae. We establish a functional network in Firmicutes that allows identifying new functional links inside one same process such as between FtsW (peptidoglycan polymerase) and a previously undescribed Penicilin-Binding Protein or between different processes, such as replication and cell wall synthesis. Finally, we identify new candidates involved in sporulation and cell wall synthesis. Our results provide a previously undescribed view on the diversity of the bacterial cell cycle, testable hypotheses for further experimental studies, and a methodological framework for the analysis of any other biological system.
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Affiliation(s)
- Pierre S Garcia
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918 Villeurbanne F-69622, France.,Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, CNRS, Lyon, France.,Department of Microbiology, Unit "Evolutionary Biology of the Microbial Cell", Institut Pasteur, Paris, France
| | - Wandrille Duchemin
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918 Villeurbanne F-69622, France
| | - Jean-Pierre Flandrois
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918 Villeurbanne F-69622, France
| | - Simonetta Gribaldo
- Department of Microbiology, Unit "Evolutionary Biology of the Microbial Cell", Institut Pasteur, Paris, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918 Villeurbanne F-69622, France
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19
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Parise MTD, Parise D, Aburjaile FF, Pinto Gomide AC, Kato RB, Raden M, Backofen R, Azevedo VADC, Baumbach J. An Integrated Database of Small RNAs and Their Interplay With Transcriptional Gene Regulatory Networks in Corynebacteria. Front Microbiol 2021; 12:656435. [PMID: 34220744 PMCID: PMC8247434 DOI: 10.3389/fmicb.2021.656435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/19/2021] [Indexed: 12/02/2022] Open
Abstract
Small RNAs (sRNAs) are one of the key players in the post-transcriptional regulation of bacterial gene expression. These molecules, together with transcription factors, form regulatory networks and greatly influence the bacterial regulatory landscape. Little is known concerning sRNAs and their influence on the regulatory machinery in the genus Corynebacterium, despite its medical, veterinary and biotechnological importance. Here, we expand corynebacterial regulatory knowledge by integrating sRNAs and their regulatory interactions into the transcriptional regulatory networks of six corynebacterial species, covering four human and animal pathogens, and integrate this data into the CoryneRegNet database. To this end, we predicted sRNAs to regulate 754 genes, including 206 transcription factors, in corynebacterial gene regulatory networks. Amongst them, the sRNA Cd-NCTC13129-sRNA-2 is predicted to directly regulate ydfH, which indirectly regulates 66 genes, including the global regulator glxR in C. diphtheriae. All of the sRNA-enriched regulatory networks of the genus Corynebacterium have been made publicly available in the newest release of CoryneRegNet(www.exbio.wzw.tum.de/coryneregnet/) to aid in providing valuable insights and to guide future experiments.
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Affiliation(s)
- Mariana Teixeira Dornelles Parise
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany.,Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Doglas Parise
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany.,Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Rodrigo Bentes Kato
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Martin Raden
- Bioinformatics, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | | | - Jan Baumbach
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany.,Computational Biomedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark.,Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany
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20
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Pelletier JF, Sun L, Wise KS, Assad-Garcia N, Karas BJ, Deerinck TJ, Ellisman MH, Mershin A, Gershenfeld N, Chuang RY, Glass JI, Strychalski EA. Genetic requirements for cell division in a genomically minimal cell. Cell 2021; 184:2430-2440.e16. [PMID: 33784496 DOI: 10.1016/j.cell.2021.03.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 01/27/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022]
Abstract
Genomically minimal cells, such as JCVI-syn3.0, offer a platform to clarify genes underlying core physiological processes. Although this minimal cell includes genes essential for population growth, the physiology of its single cells remained uncharacterized. To investigate striking morphological variation in JCVI-syn3.0 cells, we present an approach to characterize cell propagation and determine genes affecting cell morphology. Microfluidic chemostats allowed observation of intrinsic cell dynamics that result in irregular morphologies. A genome with 19 genes not retained in JCVI-syn3.0 generated JCVI-syn3A, which presents morphology similar to that of JCVI-syn1.0. We further identified seven of these 19 genes, including two known cell division genes, ftsZ and sepF, a hydrolase of unknown substrate, and four genes that encode membrane-associated proteins of unknown function, which are required together to restore a phenotype similar to that of JCVI-syn1.0. This result emphasizes the polygenic nature of cell division and morphology in a genomically minimal cell.
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Affiliation(s)
- James F Pelletier
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Lijie Sun
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Kim S Wise
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Bogumil J Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, University of California-San Diego, La Jolla, CA 92037, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, University of California-San Diego, La Jolla, CA 92037, USA
| | - Andreas Mershin
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Neil Gershenfeld
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - John I Glass
- J. Craig Venter Institute, La Jolla, CA 92037, USA.
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21
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Phenotypic and Transcriptomic Analyses of Seven Clinical Stenotrophomonas maltophilia Isolates Identify a Small Set of Shared and Commonly Regulated Genes Involved in the Biofilm Lifestyle. Appl Environ Microbiol 2020; 86:AEM.02038-20. [PMID: 33097507 DOI: 10.1128/aem.02038-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/04/2020] [Indexed: 12/19/2022] Open
Abstract
Stenotrophomonas maltophilia is one of the most frequently isolated multidrug-resistant nosocomial opportunistic pathogens. It contributes to disease progression in cystic fibrosis (CF) patients and is frequently isolated from wounds, infected tissues, and catheter surfaces. On these diverse surfaces S. maltophilia lives in single-species or multispecies biofilms. Since very little is known about common processes in biofilms of different S. maltophilia isolates, we analyzed the biofilm profiles of 300 clinical and environmental isolates from Europe of the recently identified main lineages Sgn3, Sgn4, and Sm2 to Sm18. The analysis of the biofilm architecture of 40 clinical isolates revealed the presence of multicellular structures and high phenotypic variability at a strain-specific level. Further, transcriptome analyses of biofilm cells of seven clinical isolates identified a set of 106 shared strongly expressed genes and 33 strain-specifically expressed genes. Surprisingly, the transcriptome profiles of biofilm versus planktonic cells revealed that just 9.43% ± 1.36% of all genes were differentially regulated. This implies that just a small set of shared and commonly regulated genes is involved in the biofilm lifestyle. Strikingly, iron uptake appears to be a key factor involved in this metabolic shift. Further, metabolic analyses implied that S. maltophilia employs a mostly fermentative growth mode under biofilm conditions. The transcriptome data of this study together with the phenotypic and metabolic analyses represent so far the largest data set on S. maltophilia biofilm versus planktonic cells. This study will lay the foundation for the identification of strategies for fighting S. maltophilia biofilms in clinical and industrial settings.IMPORTANCE Microorganisms living in a biofilm are much more tolerant to antibiotics and antimicrobial substances than planktonic cells are. Thus, the treatment of infections caused by microorganisms living in biofilms is extremely difficult. Nosocomial infections (among others) caused by S. maltophilia, particularly lung infection among CF patients, have increased in prevalence in recent years. The intrinsic multidrug resistance of S. maltophilia and the increased tolerance to antimicrobial agents of its biofilm cells make the treatment of S. maltophilia infection difficult. The significance of our research is based on understanding the common mechanisms involved in biofilm formation of different S. maltophilia isolates, understanding the diversity of biofilm architectures among strains of this species, and identifying the differently regulated processes in biofilm versus planktonic cells. These results will lay the foundation for the treatment of S. maltophilia biofilms.
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22
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Molecular Characterization of the Burkholderia cenocepacia dcw Operon and FtsZ Interactors as New Targets for Novel Antimicrobial Design. Antibiotics (Basel) 2020; 9:antibiotics9120841. [PMID: 33255486 PMCID: PMC7761207 DOI: 10.3390/antibiotics9120841] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/18/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022] Open
Abstract
The worldwide spread of antimicrobial resistance highlights the need of new druggable cellular targets. The increasing knowledge of bacterial cell division suggested the potentiality of this pathway as a pool of alternative drug targets, mainly based on the essentiality of these proteins, as well as on the divergence from their eukaryotic counterparts. People suffering from cystic fibrosis are particularly challenged by the lack of antibiotic alternatives. Among the opportunistic pathogens that colonize the lungs of these patients, Burkholderia cenocepacia is a well-known multi-drug resistant bacterium, particularly difficult to treat. Here we describe the organization of its division cell wall (dcw) cluster: we found that 15 genes of the dcw operon can be transcribed as a polycistronic mRNA from mraZ to ftsZ and that its transcription is under the control of a strong promoter regulated by MraZ. B. cenocepacia J2315 FtsZ was also shown to interact with the other components of the divisome machinery, with a few differences respect to other bacteria, such as the direct interaction with FtsQ. Using an in vitro sedimentation assay, we validated the role of SulA as FtsZ inhibitor, and the roles of FtsA and ZipA as tethers of FtsZ polymers. Together our results pave the way for future antimicrobial design based on the divisome as pool of antibiotic cellular targets.
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23
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Wang Y, Huang JM, Zhou YL, Almeida A, Finn RD, Danchin A, He LS. Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli. BMC Genomics 2020; 21:408. [PMID: 32552739 PMCID: PMC7301438 DOI: 10.1186/s12864-020-06807-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/05/2020] [Indexed: 12/28/2022] Open
Abstract
Background The metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies have been largely focused on pathogenic species. In this study, we expanded analyses on Tenericutes lineages that inhabit various environments using a collection of 840 genomes. Results Several environmental lineages were discovered inhabiting the human gut, ground water, bioreactors and hypersaline lake and spanning the Haloplasmatales and Mycoplasmatales orders. A phylogenomics analysis of Bacilli and Tenericutes genomes revealed that some uncultured Tenericutes are affiliated with novel clades in Bacilli, such as RF39, RFN20 and ML615. Erysipelotrichales and two major gut lineages, RF39 and RFN20, were found to be neighboring clades of Mycoplasmatales. We detected habitat-specific functional patterns between the pathogenic, gut and the environmental Tenericutes, where genes involved in carbohydrate storage, carbon fixation, mutation repair, environmental response and amino acid cleavage are overrepresented in the genomes of environmental lineages, perhaps as a result of environmental adaptation. We hypothesize that the two major gut lineages, namely RF39 and RFN20, are probably acetate and hydrogen producers. Furthermore, deteriorating capacity of bactoprenol synthesis for cell wall peptidoglycan precursors secretion is a potential adaptive strategy employed by these lineages in response to the gut environment. Conclusions This study uncovers the characteristic functions of environmental Tenericutes and their relationships with Bacilli, which sheds new light onto the pathogenicity and evolutionary processes of Mycoplasmatales.
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Affiliation(s)
- Yong Wang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.
| | - Jiao-Mei Huang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ying-Li Zhou
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China.,University of Chinese Academy of Sciences, Beijing, China
| | - Alexandre Almeida
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Antoine Danchin
- Kodikos, Department of Infection, Immunity and Inflammation, Institut Cochin INSERM U1016 - CNRS UMR8104 - Université Paris Descartes, 24 rue du Faubourg Saint-Jacques, 75014, Paris, France.,Li Kashing Faculty of Medicine, School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong, SAR, China
| | - Li-Sheng He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, Hai Nan, P.R. China
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24
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Klimina KM, Voroshilova VN, Poluektova EU, Veselovsky VA, Yunes RA, Kovtun AS, Kudryavtseva AV, Kasianov AS, Danilenko VN. Toxin-Antitoxin Systems: A Tool for Taxonomic Analysis of Human Intestinal Microbiota. Toxins (Basel) 2020; 12:toxins12060388. [PMID: 32545455 PMCID: PMC7354421 DOI: 10.3390/toxins12060388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 01/14/2023] Open
Abstract
The human gastrointestinal microbiota (HGM) is known for its rich diversity of bacterial species and strains. Yet many studies stop at characterizing the HGM at the family level. This is mainly due to lack of adequate methods for a high-resolution profiling of the HGM. One way to characterize the strain diversity of the HGM is to look for strain-specific functional markers. Here, we propose using type II toxin-antitoxin systems (TAS). To identify TAS systems in the HGM, we previously developed the software TAGMA. This software was designed to detect the TAS systems, MazEF and RelBE, in lactobacilli and bifidobacteria. In this study, we updated the gene catalog created previously and used it to test our software anew on 1346 strains of bacteria, which belonged to 489 species and 49 genera. We also sequenced the genomes of 20 fecal samples and analyzed the results with TAGMA. Although some differences were detected at the strain level, the results showed no particular difference in the bacterial species between our method and other classic analysis software. These results support the use of the updated catalog of genes encoding type II TAS as a useful tool for computer-assisted species and strain characterization of the HGM.
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Affiliation(s)
- Ksenia M. Klimina
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia;
- Correspondence:
| | - Viktoriya N. Voroshilova
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
| | - Elena U. Poluektova
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
| | - Vladimir A. Veselovsky
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia;
| | - Roman A. Yunes
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
| | - Aleksey S. Kovtun
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Artem S. Kasianov
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
| | - Valery N. Danilenko
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; (V.N.V.); (E.U.P.); (R.A.Y.); (A.S.K.); (A.S.K.); (V.N.D.)
- Faculty of Ecology, International Institute for Strategic Development of Sectoral Economics, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
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25
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Abstract
The bacterial cell envelope provides many important functions. It protects cells from harsh environments, serves as a selective permeability barrier, houses bioenergetic functions, defines sensitivity to antibacterial agents, and plays a crucial role in biofilm formation, symbiosis, and virulence. Despite the important roles of this cellular compartment, we lack a detailed understanding of the biosynthesis and remodeling of the cell envelope. Here, we report that the R. sphaeroides two-component signaling system NtrYX is a previously undescribed regulator of cell envelope processes, providing evidence that it is directly involved in controlling transcription of genes involved in cell envelope assembly, structure, and function in this and possibly other bacteria. Thus, our data report on a newly discovered process used by bacteria to assemble and remodel the cell envelope. Activity of the NtrYX two-component system has been associated with important processes in diverse bacteria, ranging from symbiosis to nitrogen and energy metabolism. In the facultative alphaproteobacterium Rhodobacter sphaeroides, loss of the two-component system NtrYX results in increased lipid production and sensitivity to some known cell envelope-active compounds. In this study, we show that NtrYX directly controls multiple properties of the cell envelope. We find that the response regulator NtrX binds upstream of cell envelope genes, including those involved in peptidoglycan biosynthesis and modification and in cell division. We show that loss of NtrYX impacts the cellular levels of peptidoglycan precursors and lipopolysaccharide and alters cell envelope structure, increasing cell length and the thickness of the periplasm. Cell envelope function is also disrupted in the absence of NtrYX, resulting in increased outer membrane permeability. Based on the properties of R. sphaeroides cells lacking NtrYX and the target genes under direct control of this two-component system, we propose that NtrYX plays a previously undescribed, and potentially conserved, role in the assembly, structure, and function of the cell envelope in a variety of bacteria.
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26
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Abstract
The FtsZ protein is a highly conserved bacterial tubulin homolog. In vivo, the functional form of FtsZ is the polymeric, ring-like structure (Z-ring) assembled at the future division site during cell division. While it is clear that the Z-ring plays an essential role in orchestrating cytokinesis, precisely what its functions are and how these functions are achieved remain elusive. In this article, we review what we have learned during the past decade about the Z-ring's structure, function, and dynamics, with a particular focus on insights generated by recent high-resolution imaging and single-molecule analyses. We suggest that the major function of the Z-ring is to govern nascent cell pole morphogenesis by directing the spatiotemporal distribution of septal cell wall remodeling enzymes through the Z-ring's GTP hydrolysis-dependent treadmilling dynamics. In this role, FtsZ functions in cell division as the counterpart of the cell shape-determining actin homolog MreB in cell elongation.
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Affiliation(s)
- Ryan McQuillen
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; ,
| | - Jie Xiao
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; ,
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27
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Suppression of antibiotic resistance evolution by single-gene deletion. Sci Rep 2020; 10:4178. [PMID: 32144279 PMCID: PMC7060189 DOI: 10.1038/s41598-020-60663-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 02/12/2020] [Indexed: 11/08/2022] Open
Abstract
Antibiotic treatment generally results in the selection of resistant bacterial strains, and the dynamics of resistance evolution is dependent on complex interactions between cellular components. To better characterize the mechanisms of antibiotic resistance and evaluate its dependence on gene regulatory networks, we performed systematic laboratory evolution of Escherichia coli strains with single-gene deletions of 173 transcription factors under three different antibiotics. This resulted in the identification of several genes whose deletion significantly suppressed resistance evolution, including arcA and gutM. Analysis of double-gene deletion strains suggested that the suppression of resistance evolution caused by arcA and gutM deletion was not caused by epistatic interactions with mutations known to confer drug resistance. These results provide a methodological basis for combinatorial drug treatments that may help to suppress the emergence of resistant pathogens by inhibiting resistance evolution.
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28
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Kaya D, Kjellerup BV, Chourey K, Hettich RL, Taggart DM, Löffler FE. Impact of Fixed Nitrogen Availability on Dehalococcoides mccartyi Reductive Dechlorination Activity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:14548-14558. [PMID: 31693350 DOI: 10.1021/acs.est.9b04463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biostimulation to promote reductive dechlorination is widely practiced, but the value of adding an exogenous nitrogen (N) source (e.g., NH4+) during treatment is unclear. This study investigates the effect of NH4+ availability on organohalide-respiring Dehalococcoides mccartyi (Dhc) growth and reductive dechlorination in enrichment cultures derived from groundwater (PW4) and river sediment (TC) impacted with chlorinated ethenes. In PW4 cultures, the addition of NH4+ increased cis-1,2-dichloroethene (cDCE)-to-ethene dechlorination rates about 5-fold (20.6 ± 1.6 versus 3.8 ± 0.5 μM Cl- d-1), and the total number of Dhc 16S rRNA gene copies were about 43-fold higher in incubations with NH4+ ((1.8 ± 0.9) × 108 mL-1) compared to incubations without NH4+ ((4.1 ± 0.8) × 107 mL-1). In TC cultures, NH4+ also stimulated cDCE-to-ethene dechlorination and Dhc growth. Quantitative polymerase chain reaction (qPCR) revealed that Cornell-type Dhc capable of N2 fixation dominated PW4 cultures without NH4+, but their relative abundance decreased in cultures with NH4+ amendment (i.e., 99 versus 54% of total Dhc). Pinellas-type Dhc incapable of N2 fixation were responsible for cDCE dechlorination in TC cultures, and diazotrophic community members met their fixed N requirement in the medium without NH4+. Responses to NH4+ were apparent at the community level, and N2-fixing bacterial populations increased in incubations without NH4+. Quantitative assessment of Dhc nitrogenase genes, transcripts, and proteomics data linked Cornell-type Dhc nifD and nifK expression with fixed N limitation. NH4+ additions also demonstrated positive effects on Dhc in situ dechlorination activity in the vicinity of well PW4. These findings demonstrate that biostimulation with NH4+ can enhance Dhc reductive dechlorination rates; however, a "do nothing" approach that relies on indigenous diazotrophs can achieve similar dechlorination end points and avoids the potential for stalled dechlorination due to inhibitory levels of NH4+ or transformation products (i.e., nitrous oxide).
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Affiliation(s)
- Devrim Kaya
- Biosciences Division and ⊥Chemical Sciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
- Department of Civil and Environmental Engineering , University of Maryland College Park , College Park , Maryland 20742 , United States
| | - Birthe V Kjellerup
- Department of Civil and Environmental Engineering , University of Maryland College Park , College Park , Maryland 20742 , United States
| | | | | | - Dora M Taggart
- Microbial Insights, Inc. , Knoxville , Tennessee 37932 , United States
| | - Frank E Löffler
- Biosciences Division and ⊥Chemical Sciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
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29
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Xu X, Zhang H, Huang Y, Zhang Y, Wu C, Gao P, Teng Z, Luo X, Peng X, Wang X, Wang D, Pu J, Zhao H, Lu X, Lu S, Ye C, Dong Y, Lan R, Xu J. Beyond a Ribosomal RNA Methyltransferase, the Wider Role of MraW in DNA Methylation, Motility and Colonization in Escherichia coli O157:H7. Front Microbiol 2019; 10:2520. [PMID: 31798540 PMCID: PMC6863780 DOI: 10.3389/fmicb.2019.02520] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 10/18/2019] [Indexed: 12/31/2022] Open
Abstract
MraW is a 16S rRNA methyltransferase and plays a role in the fine-tuning of the ribosomal decoding center. It was recently found to contribute to the virulence of Staphylococcus aureus. In this study, we examined the function of MraW in Escherichia coli O157:H7 and found that the deletion of mraW led to decreased motility, flagellar production and DNA methylation. Whole-genome bisulfite sequencing showed a genome wide decrease of methylation of 336 genes and 219 promoters in the mraW mutant including flagellar genes. The methylation level of flagellar genes was confirmed by bisulfite PCR sequencing. Quantitative reverse transcription PCR results indicated that the transcription of these genes was also affected. MraW was furtherly observed to directly bind to the four flagellar gene sequences by electrophoretic mobility shift assay (EMSA). A common flexible motif in differentially methylated regions (DMRs) of promoters and coding regions of the four flagellar genes was identified. Reduced methylation was correlated with altered expression of 21 of the 24 genes tested. DNA methylation activity of MraW was confirmed by DNA methyltransferase activity assay in vitro and repressed by DNA methylation inhibitor 5-aza-2'-deoxycytidine (5-aza). In addition, the mraW mutant colonized poorer than wild type in mice. We also found that the expression of mraZ in the mraW mutant was increased confirming the antagonistic effect of mraW on mraZ. In conclusion, mraW was found to be a DNA methylase and have a wide-ranging effect on E. coli O157:H7 including motility and virulence in vivo via genome wide methylation and mraZ antagonism.
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Affiliation(s)
- Xuefang Xu
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Heng Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Ying Huang
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Yuan Zhang
- China Institute of Veterinary Drug Control, Haidian, China
| | - Changde Wu
- College of Animal Sciences and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Pengya Gao
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,College of Animal Sciences and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhongqiu Teng
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xuelian Luo
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiaojing Peng
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiaoyuan Wang
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Dai Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Ji Pu
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Hongqing Zhao
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xuancheng Lu
- Laboratory Animal Center, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuangshuang Lu
- Laboratory Animal Center, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Changyun Ye
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Yuhui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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30
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Vedyaykin AD, Ponomareva EV, Khodorkovskii MA, Borchsenius SN, Vishnyakov IE. Mechanisms of Bacterial Cell Division. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719030159] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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31
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Wang C, Wang Z, You Y, Xu W, Lv Z, Liu Z, Chen W, Shi Y. Response of Arthrobacter QD 15-4 to dimethyl phthalate by regulating energy metabolism and ABC transporters. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 174:146-152. [PMID: 30825737 DOI: 10.1016/j.ecoenv.2019.02.078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
Ubiquitous dimethyl phthalate (DMP) has severely threatened environmental safety and the health of organisms. Therefore, it is necessary to degrade DMP, removing it from the environment. Microbiological degradation is an efficient and safe method for degrading DMP. In this study, the response of Arthrobacter QD 15-4 to DMP was investigated. The results showed that the growth of Arthrobacter QD 15-4 was not impacted by DMP and Arthrobacter QD 15-4 could degrade DMP. RNA-Seq and RT-qPCR results showed that DMP treatment caused some changes in the expression of key genes in Arthrobacter QD 15-4. The transcriptional expressions of pstSCAB and phoU were downregulated by DMP. The transcriptional expressions of potACD, gluBC, oppAB, pdhAB, aceAF, gltA were upregulated by DMP. The genes are mainly involved in regulating energy metabolism and ATP-binding cassette (ABC) transporters. The increasing of pyruvic acid and citrate in Arthrobacter QD 15-4 further supported the energy metabolism was improved by DMP. It was clearly shown that Arthrobacter QD 15-4 made response to dimethyl phthalate by regulating energy metabolism and ABC transporters.
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Affiliation(s)
- Chunlong Wang
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Zhigang Wang
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China.
| | - Yimin You
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Weihui Xu
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Zhihang Lv
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Zeping Liu
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Wenjing Chen
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Yiran Shi
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
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32
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Karasev ES, Andronov EE, Aksenova TS, Chizhevskaya EP, Tupikin AE, Provorov NA. Evolution of Goat’s Rue Rhizobia (Neorhizobium galegae): Analysis of Polymorphism of the Nitrogen Fixation and Nodule Formation Genes. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419020078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Far-reaching cellular consequences of tat deletion in Escherichia coli revealed by comprehensive proteome analyses. Microbiol Res 2019; 218:97-107. [DOI: 10.1016/j.micres.2018.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/21/2018] [Accepted: 10/27/2018] [Indexed: 11/22/2022]
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34
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Competitive Fitness of Essential Gene Knockdowns Reveals a Broad-Spectrum Antibacterial Inhibitor of the Cell Division Protein FtsZ. Antimicrob Agents Chemother 2018; 62:AAC.01231-18. [PMID: 30297366 PMCID: PMC6256756 DOI: 10.1128/aac.01231-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/01/2018] [Indexed: 12/26/2022] Open
Abstract
To streamline the elucidation of antibacterial compounds' mechanism of action, comprehensive high-throughput assays interrogating multiple putative targets are necessary. However, current chemogenomic approaches for antibiotic target identification have not fully utilized the multiplexing potential of next-generation sequencing. Here, we used Illumina sequencing of transposon insertions to track the competitive fitness of a Burkholderia cenocepacia library containing essential gene knockdowns. Using this method, we characterized a novel benzothiadiazole derivative, 10126109 (C109), with antibacterial activity against B. cenocepacia, for which whole-genome sequencing of low-frequency spontaneous drug-resistant mutants had failed to identify the drug target. By combining the identification of hypersusceptible mutants and morphology screening, we show that C109 targets cell division. Furthermore, fluorescence microscopy of bacteria harboring green fluorescent protein (GFP) cell division protein fusions revealed that C109 prevents divisome formation by altering the localization of the essential cell division protein FtsZ. In agreement with this, C109 inhibited both the GTPase and polymerization activities of purified B. cenocepacia FtsZ. C109 displayed antibacterial activity against Gram-positive and Gram-negative cystic fibrosis pathogens, including Mycobacterium abscessus C109 effectively cleared B. cenocepacia infection in the Caenorhabditis elegans model and exhibited additive interactions with clinically relevant antibiotics. Hence, C109 is an enticing candidate for further drug development.
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Campos M, Govers SK, Irnov I, Dobihal GS, Cornet F, Jacobs-Wagner C. Genomewide phenotypic analysis of growth, cell morphogenesis, and cell cycle events in Escherichia coli. Mol Syst Biol 2018; 14:e7573. [PMID: 29941428 PMCID: PMC6018989 DOI: 10.15252/msb.20177573] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Cell size, cell growth, and cell cycle events are necessarily intertwined to achieve robust bacterial replication. Yet, a comprehensive and integrated view of these fundamental processes is lacking. Here, we describe an image‐based quantitative screen of the single‐gene knockout collection of Escherichia coli and identify many new genes involved in cell morphogenesis, population growth, nucleoid (bulk chromosome) dynamics, and cell division. Functional analyses, together with high‐dimensional classification, unveil new associations of morphological and cell cycle phenotypes with specific functions and pathways. Additionally, correlation analysis across ~4,000 genetic perturbations shows that growth rate is surprisingly not predictive of cell size. Growth rate was also uncorrelated with the relative timings of nucleoid separation and cell constriction. Rather, our analysis identifies scaling relationships between cell size and nucleoid size and between nucleoid size and the relative timings of nucleoid separation and cell division. These connections suggest that the nucleoid links cell morphogenesis to the cell cycle.
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Affiliation(s)
- Manuel Campos
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.,Laboratoire de Microbiologie et Génétique Moléculaires (LMGM; UMR5100), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, Toulouse, France
| | - Sander K Govers
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Irnov Irnov
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Genevieve S Dobihal
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
| | - François Cornet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM; UMR5100), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, Toulouse, France
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT, USA .,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.,Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
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36
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Zorz JK, Kozlowski JA, Stein LY, Strous M, Kleiner M. Comparative Proteomics of Three Species of Ammonia-Oxidizing Bacteria. Front Microbiol 2018; 9:938. [PMID: 29867847 PMCID: PMC5960693 DOI: 10.3389/fmicb.2018.00938] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/23/2018] [Indexed: 12/30/2022] Open
Abstract
Ammonia-oxidizing bacteria (AOB) are important members of terrestrial, marine, and industrial microbial communities and play a fundamental role in the Nitrogen cycle within these systems. They are responsible for the first step of nitrification, ammonia oxidation to nitrite. Although AOB are widespread and essential to environmental and industrial systems, where they regularly experience fluctuations in ammonia availability, no comparative studies of the physiological response of diverse AOB species at the protein level exist. In the present study, we used 1D-LC-MS/MS proteomics to compare the metabolism and physiology of three species of ammonia AOB, Nitrosomonas europaea, Nitrosospira multiformis, and Nitrosomonas ureae, under ammonia replete and ammonia starved conditions. Additionally, we compared the expression of orthologous genes to determine the major differences in the proteome composition of the three species. We found that approximately one-third of the predicted proteome was expressed in each species and that proteins for the key metabolic processes, ammonia oxidation and carbon fixation, were among the most abundant. The red copper protein, nitrosocyanin was highly abundant in all three species hinting toward its possible role as a central metabolic enzyme in AOB. The proteomic data also allowed us to identify pyrophosphate-dependent 6-phosphofructokinase as the potential enzyme replacing the Calvin-Benson-Bassham cycle enzyme Fructose-1,6-bisphosphatase missing in N. multiformis and N. ureae. Additionally, between species, there were statistically significant differences in the expression of many abundant proteins, including those related to nitrogen metabolism (nitrite reductase), motility (flagellin), cell growth and division (FtsH), and stress response (rubrerythrin). The three species did not exhibit a starvation response at the proteome level after 24 h of ammonia starvation, however, the levels of the RuBisCO enzyme were consistently reduced after the starvation period, suggesting a decrease in capacity for biomass accumulation. This study presents the first published proteomes of N. ureae and N. multiformis, and the first comparative proteomics study of ammonia-oxidizing bacteria, which gives new insights into consistent metabolic features and differences between members of this environmentally and industrially important group.
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Affiliation(s)
- Jackie K Zorz
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Jessica A Kozlowski
- Department of Ecogenomics and Systems Biology, Division Archaea Biology and Ecogenomics, University of Vienna, Vienna, Austria
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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Chowdhury-Paul S, Pando-Robles V, Jiménez-Jacinto V, Segura D, Espín G, Núñez C. Proteomic analysis revealed proteins induced upon Azotobacter vinelandii encystment. J Proteomics 2018; 181:47-59. [PMID: 29605291 DOI: 10.1016/j.jprot.2018.03.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 03/09/2018] [Accepted: 03/27/2018] [Indexed: 01/22/2023]
Affiliation(s)
- Sangita Chowdhury-Paul
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad, 2001, Col Chamilpa, C.P. 62210 Cuernavaca, Morelos, México
| | - Victoria Pando-Robles
- Instituto Nacional de Salud Pública, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Universidad No. 655 Colonia Santa María Ahuacatitlán, Cerrada Los Pinos y Caminera, C.P. 62100 Cuernavaca, Morelos, México
| | - Verónica Jiménez-Jacinto
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnologia, UNAM, Av. Universidad, 2001, Col Chamilpa, C.P. 62210 Cuernavaca, Morelos, México
| | - Daniel Segura
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad, 2001, Col Chamilpa, C.P. 62210 Cuernavaca, Morelos, México
| | - Guadalupe Espín
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad, 2001, Col Chamilpa, C.P. 62210 Cuernavaca, Morelos, México
| | - Cinthia Núñez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, UNAM, Av. Universidad, 2001, Col Chamilpa, C.P. 62210 Cuernavaca, Morelos, México.
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38
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Peng H, Zhang Y, Palmer LD, Kehl-Fie TE, Skaar EP, Trinidad JC, Giedroc DP. Hydrogen Sulfide and Reactive Sulfur Species Impact Proteome S-Sulfhydration and Global Virulence Regulation in Staphylococcus aureus. ACS Infect Dis 2017; 3:744-755. [PMID: 28850209 DOI: 10.1021/acsinfecdis.7b00090] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Hydrogen sulfide (H2S) is thought to protect bacteria from oxidative stress, but a comprehensive understanding of its function in bacteria is largely unexplored. In this study, we show that the human pathogen Staphylococcus aureus (S. aureus) harbors significant effector molecules of H2S signaling, reactive sulfur species (RSS), as low molecular weight persulfides of bacillithiol, coenzyme A, and cysteine, and significant inorganic polysulfide species. We find that proteome S-sulfhydration, a post-translational modification (PTM) in H2S signaling, is widespread in S. aureus. RSS levels modulate the expression of secreted virulence factors and the cytotoxicity of the secretome, consistent with an S-sulfhydration-dependent inhibition of DNA binding by MgrA, a global virulence regulator. Two previously uncharacterized thioredoxin-like proteins, denoted TrxP and TrxQ, are S-sulfhydrated in sulfide-stressed cells and are capable of reducing protein hydrodisulfides, suggesting that this PTM is potentially regulatory in S. aureus. In conclusion, our results reveal that S. aureus harbors a pool of proteome- and metabolite-derived RSS capable of impacting protein activities and gene regulation and that H2S signaling can be sensed by global regulators to affect the expression of virulence factors.
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Affiliation(s)
- Hui Peng
- Department of Chemistry, Indiana University, 800 E. Kirkwood Drive, Bloomington, Indiana 47405-7102, United States
- Graduate Program in Biochemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, Indiana 47405, United States
| | - Yixiang Zhang
- Department of Chemistry, Indiana University, 800 E. Kirkwood Drive, Bloomington, Indiana 47405-7102, United States
- Laboratory for Biological Mass Spectrometry,
Department of Chemistry, Indiana University, Simon Hall 120B, 212 S. Hawthorne
Drive, Bloomington, Indiana 47405, United States
| | - Lauren D. Palmer
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, Nashville, Tennessee 37232-2363, United States
| | - Thomas E. Kehl-Fie
- Department of Microbiology, University of Illinois Urbana−Champaign, 601 South Goodwin Avenue, Urbana, Illinois 61801, United States
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, Nashville, Tennessee 37232-2363, United States
| | - Jonathan C. Trinidad
- Department of Chemistry, Indiana University, 800 E. Kirkwood Drive, Bloomington, Indiana 47405-7102, United States
- Laboratory for Biological Mass Spectrometry,
Department of Chemistry, Indiana University, Simon Hall 120B, 212 S. Hawthorne
Drive, Bloomington, Indiana 47405, United States
| | - David P. Giedroc
- Department of Chemistry, Indiana University, 800 E. Kirkwood Drive, Bloomington, Indiana 47405-7102, United States
- Department
of Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, Indiana 47405, United States
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39
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Sánchez-Osuna M, Barbé J, Erill I. Comparative genomics of the DNA damage-inducible network in the Patescibacteria. Environ Microbiol 2017; 19:3465-3474. [DOI: 10.1111/1462-2920.13826] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/09/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Miquel Sánchez-Osuna
- Departament de Genètica i de Microbiologia; Universitat Autònoma de Barcelona; Spain
| | - Jordi Barbé
- Departament de Genètica i de Microbiologia; Universitat Autònoma de Barcelona; Spain
| | - Ivan Erill
- Department of Biological Sciences; University of Maryland Baltimore County; Baltimore Maryland USA
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40
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Venturelli OS, Tei M, Bauer S, Chan LJG, Petzold CJ, Arkin AP. Programming mRNA decay to modulate synthetic circuit resource allocation. Nat Commun 2017; 8:15128. [PMID: 28443619 PMCID: PMC5414051 DOI: 10.1038/ncomms15128] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 03/02/2017] [Indexed: 01/03/2023] Open
Abstract
Synthetic circuits embedded in host cells compete with cellular processes for limited intracellular resources. Here we show how funnelling of cellular resources, after global transcriptome degradation by the sequence-dependent endoribonuclease MazF, to a synthetic circuit can increase production. Target genes are protected from MazF activity by recoding the gene sequence to eliminate recognition sites, while preserving the amino acid sequence. The expression of a protected fluorescent reporter and flux of a high-value metabolite are significantly enhanced using this genome-scale control strategy. Proteomics measurements discover a host factor in need of protection to improve resource redistribution activity. A computational model demonstrates that the MazF mRNA-decay feedback loop enables proportional control of MazF in an optimal operating regime. Transcriptional profiling of MazF-induced cells elucidates the dynamic shifts in transcript abundance and discovers regulatory design elements. Altogether, our results suggest that manipulation of cellular resource allocation is a key control parameter for synthetic circuit design. Synthetic circuits in host cells compete with endogenous processes for limited resources. Here the authors use MazF to funnel cellular resources to a synthetic circuit to increase product production and demonstrate how resource allocation can be manipulated.
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Affiliation(s)
- Ophelia S Venturelli
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94158, USA.,Department of Bioengineering, University of California Berkeley, Berkeley, California 94720, USA
| | - Mika Tei
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94158, USA.,Department of Bioengineering, University of California Berkeley, Berkeley, California 94720, USA
| | - Stefan Bauer
- Energy Biosciences Institute, University of California Berkeley, Berkeley, California 94704, USA
| | - Leanne Jade G Chan
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Adam P Arkin
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94158, USA.,Department of Bioengineering, University of California Berkeley, Berkeley, California 94720, USA.,Energy Biosciences Institute, University of California Berkeley, Berkeley, California 94704, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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41
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Fisunov GY, Garanina IA, Evsyutina DV, Semashko TA, Nikitina AS, Govorun VM. Reconstruction of Transcription Control Networks in Mollicutes by High-Throughput Identification of Promoters. Front Microbiol 2016; 7:1977. [PMID: 27999573 PMCID: PMC5138195 DOI: 10.3389/fmicb.2016.01977] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/25/2016] [Indexed: 01/05/2023] Open
Abstract
Bacteria of the class Mollicutes have significantly reduced genomes and gene expression control systems. They are also efficient pathogens that can colonize a broad range of hosts including plants and animals. Despite their simplicity, Mollicutes demonstrate complex transcriptional responses to various conditions, which contradicts their reduction in gene expression regulation mechanisms. We analyzed the conservation and distribution of transcription regulators across the 50 Mollicutes species. The majority of the transcription factors regulate transport and metabolism, and there are four transcription factors that demonstrate significant conservation across the analyzed bacteria. These factors include repressors of chaperone HrcA, cell cycle regulator MraZ and two regulators with unclear function from the WhiA and YebC/PmpR families. We then used three representative species of the major clades of Mollicutes (Acholeplasma laidlawii, Spiroplasma melliferum, and Mycoplasma gallisepticum) to perform promoter mapping and activity quantitation. We revealed that Mollicutes evolved towards a promoter architecture simplification that correlates with a diminishing role of transcription regulation and an increase in transcriptional noise. Using the identified operons structure and a comparative genomics approach, we reconstructed the transcription control networks for these three species. The organization of the networks reflects the adaptation of bacteria to specific conditions and hosts.
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Affiliation(s)
- Gleb Y Fisunov
- Federal Research and Clinical Centre of Physical-Chemical Medicine Moscow, Russia
| | - Irina A Garanina
- Federal Research and Clinical Centre of Physical-Chemical MedicineMoscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of SciencesMoscow, Russia
| | - Daria V Evsyutina
- Federal Research and Clinical Centre of Physical-Chemical Medicine Moscow, Russia
| | - Tatiana A Semashko
- Federal Research and Clinical Centre of Physical-Chemical Medicine Moscow, Russia
| | - Anastasia S Nikitina
- Federal Research and Clinical Centre of Physical-Chemical MedicineMoscow, Russia; Moscow Institute of Physics and TechnologyMoscow, Russia
| | - Vadim M Govorun
- Federal Research and Clinical Centre of Physical-Chemical MedicineMoscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of SciencesMoscow, Russia; Moscow Institute of Physics and TechnologyMoscow, Russia
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42
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Keseler IM, Mackie A, Santos-Zavaleta A, Billington R, Bonavides-Martínez C, Caspi R, Fulcher C, Gama-Castro S, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Peralta-Gil M, Subhraveti P, Velázquez-Ramírez DA, Weaver D, Collado-Vides J, Paulsen I, Karp PD. The EcoCyc database: reflecting new knowledge about Escherichia coli K-12. Nucleic Acids Res 2016; 45:D543-D550. [PMID: 27899573 PMCID: PMC5210515 DOI: 10.1093/nar/gkw1003] [Citation(s) in RCA: 377] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 11/07/2016] [Indexed: 12/16/2022] Open
Abstract
EcoCyc (EcoCyc.org) is a freely accessible, comprehensive database that collects and summarizes experimental data for Escherichia coli K-12, the best-studied bacterial model organism. New experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc. New SmartTable tools allow users to browse collections of related EcoCyc content. SmartTables can also serve as repositories for user- or curator-generated lists. EcoCyc now supports running and modifying E. coli metabolic models directly on the EcoCyc website.
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Affiliation(s)
- Ingrid M Keseler
- SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
| | - Amanda Mackie
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Alberto Santos-Zavaleta
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico
| | | | - César Bonavides-Martínez
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico
| | - Ron Caspi
- SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
| | - Carol Fulcher
- SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
| | - Socorro Gama-Castro
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico
| | - Anamika Kothari
- SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
| | | | | | - Luis Muñiz-Rascado
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico
| | - Quang Ong
- SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
| | - Suzanne Paley
- SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
| | - Martin Peralta-Gil
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico
| | | | - David A Velázquez-Ramírez
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico
| | - Daniel Weaver
- SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
| | - Julio Collado-Vides
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico
| | - Ian Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Peter D Karp
- SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
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43
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Waters EM, Rudkin JK, Coughlan S, Clair GC, Adkins JN, Gore S, Xia G, Black NS, Downing T, O'Neill E, Kadioglu A, O'Gara JP. Redeploying β-Lactam Antibiotics as a Novel Antivirulence Strategy for the Treatment of Methicillin-Resistant Staphylococcus aureus Infections. J Infect Dis 2016; 215:80-87. [PMID: 28077586 DOI: 10.1093/infdis/jiw461] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 09/08/2016] [Indexed: 12/13/2022] Open
Abstract
Innovative approaches to the use of existing antibiotics is an important strategy in efforts to address the escalating antimicrobial resistance crisis. We report a new approach to the treatment of methicillin-resistant Staphylococcus aureus (MRSA) infections by demonstrating that oxacillin can be used to significantly attenuate the virulence of MRSA despite the pathogen being resistant to this drug. Using mechanistic in vitro assays and in vivo models of invasive pneumonia and sepsis, we show that oxacillin-treated MRSA strains are significantly attenuated in virulence. This effect is based primarily on the oxacillin-dependent repression of the accessory gene regulator quorum-sensing system and altered cell wall architecture, which in turn lead to increased susceptibility to host killing of MRSA. Our data indicate that β-lactam antibiotics should be included in the treatment regimen as an adjunct antivirulence therapy for patients with MRSA infections. This would represent an important change to current clinical practice for treatment of MRSA infection, with the potential to significantly improve patient outcomes in a safe, cost-effective manner.
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Affiliation(s)
- Elaine M Waters
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool
| | | | - Simone Coughlan
- School of Mathematics, Statistics, and Applied Mathematics, National University of Ireland, Galway
| | - Geremy C Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Joshua N Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Suzanna Gore
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool
| | - Guoqing Xia
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| | - Nikki S Black
- Department of Microbiology, School of Natural Sciences
| | - Tim Downing
- School of Mathematics, Statistics, and Applied Mathematics, National University of Ireland, Galway.,School of Biotechnology, Dublin City University
| | - Eoghan O'Neill
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Connolly Hospital, Dublin
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool
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44
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Weber L, Thoelken C, Volk M, Remes B, Lechner M, Klug G. The Conserved Dcw Gene Cluster of R. sphaeroides Is Preceded by an Uncommonly Extended 5' Leader Featuring the sRNA UpsM. PLoS One 2016; 11:e0165694. [PMID: 27802301 PMCID: PMC5089854 DOI: 10.1371/journal.pone.0165694] [Citation(s) in RCA: 14] [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: 06/16/2016] [Accepted: 10/17/2016] [Indexed: 11/18/2022] Open
Abstract
Cell division and cell wall synthesis mechanisms are similarly conserved among bacteria. Consequently some bacterial species have comparable sets of genes organized in the dcw (division andcellwall) gene cluster. Dcw genes, their regulation and their relative order within the cluster are outstandingly conserved among rod shaped and gram negative bacteria to ensure an efficient coordination of growth and division. A well studied representative is the dcw gene cluster of E. coli. The first promoter of the gene cluster (mraZ1p) gives rise to polycistronic transcripts containing a 38 nt long 5’ UTR followed by the first gene mraZ. Despite reported conservation we present evidence for a much longer 5’ UTR in the gram negative and rod shaped bacterium Rhodobacter sphaeroides and in the family of Rhodobacteraceae. This extended 268 nt long 5’ UTR comprises a Rho independent terminator, which in case of termination gives rise to a non-coding RNA (UpsM). This sRNA is conditionally cleaved by RNase E under stress conditions in an Hfq- and very likely target mRNA-dependent manner, implying its function in trans. These results raise the question for the regulatory function of this extended 5’ UTR. It might represent the rarely described case of a trans acting sRNA derived from a riboswitch with exclusive presence in the family of Rhodobacteraceae.
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Affiliation(s)
- Lennart Weber
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-University Giessen, Giessen, Germany
| | - Clemens Thoelken
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Marcel Volk
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-University Giessen, Giessen, Germany
| | - Bernhard Remes
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-University Giessen, Giessen, Germany
| | - Marcus Lechner
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-University Giessen, Giessen, Germany
- * E-mail:
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Mwita L, Chan WY, Pretorius T, Lyantagaye SL, Lapa SV, Avdeeva LV, Reva ON. Gene expression regulation in the plant growth promoting Bacillus atrophaeus UCMB-5137 stimulated by maize root exudates. Gene 2016; 590:18-28. [PMID: 27259668 DOI: 10.1016/j.gene.2016.05.045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/04/2016] [Accepted: 05/31/2016] [Indexed: 12/17/2022]
Abstract
Despite successful use of Plant Growth Promoting Rhizobacteria (PGPR) in agriculture, little is known about specific mechanisms of gene regulation facilitating the effective communication between bacteria and plants during plant colonization. Active PGPR strain Bacillus atrophaeus UCMB-5137 was studied in this research. RNA sequencing profiles were generated in experiments where root exudate stimulations were used to mimic interactions between bacteria and plants. It was found that the gene regulation in B. atrophaeus UCMB-5137 in response to the root exudate stimuli differed from the reported gene regulation at similar conditions in B. amyloliquefaciens FZB42, which was considered as a paradigm PGPR. This difference was explained by hypersensitivity of UCMB-5137 to the root exudate stimuli impelling it to a sessile root colonization behavior through the CcpA-CodY-AbrB regulation. It was found that the transcriptional factor DegU also could play an important role in gene regulations during plant colonization. A significant stress caused by the root exudates on in vitro cultivated B. atrophaeus UCMB-5137 was noticed and discussed. Multiple cases of conflicted gene regulations showed scantiness of our knowledge on the regulatory network in Bacillus. Some of these conflicted regulations could be explained by interference of non-coding RNA (ncRNA). Search through differential expressed intergenic regions revealed 49 putative loci of ncRNA regulated by the root exudate stimuli. Possible target mRNA were predicted and a general regulatory network of B. atrophaeus UCMB-5137 genome was designed.
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Affiliation(s)
- Liberata Mwita
- Centre for Bioinformatics and Computational Biology, Dep. Biochemistry, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria 0002, South Africa
| | - Wai Yin Chan
- Department of Microbiology and Plant Pathology, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria 0002, South Africa
| | - Theresa Pretorius
- Department of Microbiology and Plant Pathology, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria 0002, South Africa
| | - Sylvester L Lyantagaye
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 35179, Dar es Salaam, Tanzania
| | - Svitlana V Lapa
- Dep. Antibiotics, D. K. Zabolotnogo Institute of Microbiology and Virology, 154 Zabolotnogo Str., Kiev, Ukraine
| | - Lilia V Avdeeva
- Dep. Antibiotics, D. K. Zabolotnogo Institute of Microbiology and Virology, 154 Zabolotnogo Str., Kiev, Ukraine
| | - Oleg N Reva
- Centre for Bioinformatics and Computational Biology, Dep. Biochemistry, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria 0002, South Africa.
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Arun PVPS, Miryala SK, Chattopadhyay S, Thiyyagura K, Bawa P, Bhattacharjee M, Yellaboina S. Identification and functional analysis of essential, conserved, housekeeping and duplicated genes. FEBS Lett 2016; 590:1428-37. [PMID: 27129600 DOI: 10.1002/1873-3468.12192] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/13/2016] [Accepted: 04/22/2016] [Indexed: 01/09/2023]
Abstract
Gene conservation, duplication and constitutive expression are intricately linked and strong predictors of essentiality. Here, we introduce metrics based on diversity indices to measure gene conservation, duplication and constitutive expression and validate them by measuring their performance in prediction of essential genes. Conservation and duplication were measured using the diversity indices on the bit score profile of Escherichia coli K12 orthologues, across the genomes, and paralogues, within the genome respectively. Constitutive expression was measured using expression diversity of E. coli K12 genes across different conditions. In addition, we developed a systematic method for enrichment analysis of gene-sets in a given ranked list of genes. The method was used to identify genome-wide functions of essential, conserved, constitutively expressed and duplicated genes. Furthermore, we also ranked various operons, complexes and pathways according to their essentiality, conservation, constitutive expression and duplication.
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Affiliation(s)
- P V Parvati Sai Arun
- CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, University of Hyderabad Campus, Hyderabad, Telangana, India
| | - Sravan Kumar Miryala
- CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, University of Hyderabad Campus, Hyderabad, Telangana, India.,National Institute of Animal Biotechnology, Hyderabad, Telangana, India
| | - Subhayan Chattopadhyay
- School of Mathematics and Statistics, University of Hyderabad, Hyderabad, Telangana, India
| | - Kranthi Thiyyagura
- CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, University of Hyderabad Campus, Hyderabad, Telangana, India
| | - Payal Bawa
- CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, University of Hyderabad Campus, Hyderabad, Telangana, India
| | | | - Sailu Yellaboina
- CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, University of Hyderabad Campus, Hyderabad, Telangana, India
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Fisunov GY, Evsyutina DV, Semashko TA, Arzamasov AA, Manuvera VA, Letarov AV, Govorun VM. Binding site of MraZ transcription factor in Mollicutes. Biochimie 2016; 125:59-65. [PMID: 26945841 DOI: 10.1016/j.biochi.2016.02.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/29/2016] [Indexed: 10/22/2022]
Abstract
Mollicutes (mycoplasmas) feature a significant loss of known regulators of gene expression. Here, we identified the recognition site of the MraZ-family regulator of Mycoplasma gallisepticum, which is conserved in many species of different clades within class Mollicutes. The MraZ binding site is AAAGTG[T/G], in the promoter of mraZ gene it forms a series of direct repeats with a structure (AAAGTG[T/G]N3)k, where k = 3 most frequently. MraZ binds to a single repeat as an octamer complex. MraZ can also bind a single binding site or a series of repeats with different spacer lengths (2-4 nt); thus, it may play a role in the regulation of multiple operons in Mollicutes. In M. gallisepticum, MraZ acts as a transcriptional activator. The overexpression of MraZ leads to moderate filamentation of cells and the formation of aggregates, likely as a result of incomplete cytokinesis.
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Affiliation(s)
- G Y Fisunov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119992, Russia.
| | - D V Evsyutina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119992, Russia; Department of Bioinformatics and Bioengineering, Lomonosov Moscow State University, Leninskiye Gory, GSP-1, 73, Moscow 119234, Russia
| | - T A Semashko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119992, Russia
| | - A A Arzamasov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119992, Russia
| | - V A Manuvera
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119992, Russia; Moscow Institute of Physics and Technology, Institutsky 9, Dolgoprudny 141700, Russia
| | - A V Letarov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, Bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - V M Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119992, Russia; Moscow Institute of Physics and Technology, Institutsky 9, Dolgoprudny 141700, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
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48
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Maeda T, Tanaka Y, Takemoto N, Hamamoto N, Inui M. RNase III mediated cleavage of the coding region of mraZ mRNA is required for efficient cell division in Corynebacterium glutamicum. Mol Microbiol 2016; 99:1149-66. [PMID: 26713407 DOI: 10.1111/mmi.13295] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/02/2015] [Indexed: 12/30/2022]
Abstract
The Corynebacterium glutamicum R cgR_1959 gene encodes an endoribonuclease of the RNase III family. Deletion mutant of cgR_1959 (Δrnc mutant) showed an elongated cell shape, and presence of several lines on the cell surface, indicating a required of RNase III for maintaining normal cell morphology in C. glutamicum. The level of mraZ mRNA was increased, whereas cgR_1596 mRNA encoding a putative cell wall hydrolase and ftsEX mRNA were decreased in the Δrnc mutant. The half-life of mraZ mRNA was significantly prolonged in the Δrnc and the Δpnp mutant strains. This indicated that the degradation of mraZ mRNA was performed by RNase III and the 3'-to-5' exoribonuclease, PNPase. Northern hybridization and primer extension analysis revealed that the cleavage site for mraZ mRNA by RNase III is in the coding region. Overproduction of MraZ resulted in an elongated cell shape. The expression of ftsEX decreased while that of cgR_1596 unchanged in an MraZ-overexpressing strain. An electrophoretic mobility shift assay and a transcriptional reporter assay indicate that MraZ is a transcriptional repressor of ftsEX in C. glutamicum. These results indicate that RNase III is required for efficient expression of MraZ-dependent ftsEX and MraZ-independent cgR_1596.
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Affiliation(s)
- Tomoya Maeda
- Research Institute of Innovative Technology for the Earth, Kyoto, Japan
| | - Yuya Tanaka
- Research Institute of Innovative Technology for the Earth, Kyoto, Japan
| | - Norihiko Takemoto
- Research Institute of Innovative Technology for the Earth, Kyoto, Japan
| | - Nagisa Hamamoto
- Research Institute of Innovative Technology for the Earth, Kyoto, Japan.,Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth, Kyoto, Japan.,Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
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Identification of the Avian Pasteurella multocida phoP Gene and Evaluation of the Effects of phoP Deletion on Virulence and Immunogenicity. Int J Mol Sci 2015; 17:ijms17010012. [PMID: 26703595 PMCID: PMC4730259 DOI: 10.3390/ijms17010012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/14/2015] [Accepted: 12/15/2015] [Indexed: 12/16/2022] Open
Abstract
Pasteurella multocida (P. multocida) is an animal pathogen of worldwide economic significance that causes fowl cholera in poultry and wild birds. Global gene regulators, including PhoP are important in regulating bacterial virulence and are good targets for developing attenuated vaccines against many pathogenic bacteria. However, the biological significance of phoP gene has not been identified in P. multocida. Here, we identified the phoP gene in P. multocida, and we evaluated the roles of phoP in P. multocida by deleting the phoP gene. The P. multocida phoP mutant exhibited similar growth curves and lipopolysaccharide and outer membrane protein profiles but displayed defective polymyxin resistance in vitro compared with the parent strain. Additionally, the phoP deletion resulted in decreased virulence. The LD50 of the ΔphoP mutant was 32- and 154-fold higher than the parent strain via the oral and intranasal routes, respectively. Transcriptome sequencing analysis showed that 161 genes were up-regulated and 173 genes were down-regulated in the absence of the phoP gene. Finally, the immunogenicity and protective efficacy of the ΔphoP mutant were evaluated. Immunized ducks produced significantly higher levels of serum IgY and bile IgA compared to the control ducks, and immunization with the ΔphoP mutant conferred 54.5% protection efficiency against challenge with the virulent P. multocida. This work provides a platform to dissect the function of phoP and develop a new vaccine against P. multocida.
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Staphylococcus aureus transcriptomic response to inhibition by H2O2-producing Lactococcus garvieae. Food Microbiol 2015; 51:163-70. [PMID: 26187841 DOI: 10.1016/j.fm.2015.05.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 05/26/2015] [Accepted: 05/28/2015] [Indexed: 12/19/2022]
Abstract
Growth of the foodborne pathogen Staphylococcus aureus can be inhibited in milk and in cheese by the hydrogen peroxide-producing Lactococcus garvieae N201 dairy strain. Transcriptomic responses of two S. aureus strains, the S. aureus SA15 dairy strain and the MW2 human pathogenic strain, to this growth inhibition were investigated in Brain-Heart Infusion broth under a high or a low aeration level. We demonstrated that S. aureus MW2 had a higher resistance to L. garvieae inhibition under the high aeration level: this correlated to a higher survival under hydrogen peroxide exposure. Conversely, the two strains were similarly inhibited under the low aeration level. Expression of S. aureus genes involved in response to H2O2 or other stresses as well as in cell division was generally repressed by L. garvieae. However, differential expressions between the two S. aureus strains were observed, especially under the high aeration level. Additionally, expression of virulence-related genes (enterotoxins, regulatory genes) was modulated by L. garvieae depending on the aeration level and on the S. aureus strain. This study led to new insights into potential molecular mechanisms of S. aureus inhibition by Lactic Acid Bacteria via H2O2 production.
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