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Pérez-Burgos M, Herfurth M, Kaczmarczyk A, Harms A, Huber K, Jenal U, Glatter T, Søgaard-Andersen L. A deterministic, c-di-GMP-dependent program ensures the generation of phenotypically similar, symmetric daughter cells during cytokinesis. Nat Commun 2024; 15:6014. [PMID: 39019889 PMCID: PMC11255338 DOI: 10.1038/s41467-024-50444-4] [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: 02/18/2024] [Accepted: 07/10/2024] [Indexed: 07/19/2024] Open
Abstract
Phenotypic heterogeneity in bacteria can result from stochastic processes or deterministic programs. The deterministic programs often involve the versatile second messenger c-di-GMP, and give rise to daughter cells with different c-di-GMP levels by deploying c-di-GMP metabolizing enzymes asymmetrically during cell division. By contrast, less is known about how phenotypic heterogeneity is kept to a minimum. Here, we identify a deterministic c-di-GMP-dependent program that is hardwired into the cell cycle of Myxococcus xanthus to minimize phenotypic heterogeneity and guarantee the formation of phenotypically similar daughter cells during division. Cells lacking the diguanylate cyclase DmxA have an aberrant motility behaviour. DmxA is recruited to the cell division site and its activity is switched on during cytokinesis, resulting in a transient increase in the c-di-GMP concentration. During cytokinesis, this c-di-GMP burst ensures the symmetric incorporation and allocation of structural motility proteins and motility regulators at the new cell poles of the two daughters, thereby generating phenotypically similar daughters with correct motility behaviours. Thus, our findings suggest a general c-di-GMP-dependent mechanism for minimizing phenotypic heterogeneity, and demonstrate that bacteria can ensure the formation of dissimilar or similar daughter cells by deploying c-di-GMP metabolizing enzymes to distinct subcellular locations.
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Affiliation(s)
- María Pérez-Burgos
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Marco Herfurth
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Andrea Harms
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Katrin Huber
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Urs Jenal
- Biozentrum, University of Basel, Basel, Switzerland
| | - Timo Glatter
- Core Facility for Mass Spectrometry & Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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2
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Loi JX, Syutsubo K, Rabuni MF, Takemura Y, Aoki M, Chua ASM. Downflow sponge biofilm reactors for polluted raw water treatment: Performance optimisation, kinetics, and microbial community. CHEMOSPHERE 2024; 358:142156. [PMID: 38679172 DOI: 10.1016/j.chemosphere.2024.142156] [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: 03/14/2024] [Revised: 04/16/2024] [Accepted: 04/24/2024] [Indexed: 05/01/2024]
Abstract
Water outages caused by elevated ammonium (NH4+-N) levels are a prevalent problem faced by conventional raw water treatment plants in developing countries. A treatment solution requires a short hydraulic retention time (HRT) to overcome nitrification rate limitation in oligotrophic conditions. In this study, the performance of polluted raw water treatment using a green downflow sponge biofilm (DSB) technology was evaluated. We operated two DSB reactors, DSB-1 and DSB-2 under different NH4+-N concentration ranges (DSB-1: 3.2-5.0 mg L-1; DSB-2: 1.7-2.6 mg L-1) over 360 days and monitored their performance under short HRT (60 min, 30 min, 20 min, and 15 min). The experimental results revealed vertical segregation of organic removal in the upper reactor depths and nitrification in the lower depths. Under the shortest HRT of 15 min, both DSB reactors achieved stable NH4+-N and chemical oxygen demand removal (≥95%) and produced minimal effluent nitrite (NO2--N). DSB system could facilitate complete NH4+-N oxidation to nitrate (NO3--N) without external aeration energy requirement. The 16S rRNA sequencing data revealed that nitrifying bacteria Nitrosomonas and Nitrospira in the reactor were stratified. Putative comammox bacteria with high ammonia affinity was successfully enriched in DSB-2 operating at a lower NH4+-N loading rate, which is advantageous in oligotrophic treatment. This study suggests that a high hydraulic rate DSB system with efficient ammonia removal could incorporate ammonia treatment capability into polluted raw water treatment process and ensure safe water supply in many developing countries.
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Affiliation(s)
- Jia Xing Loi
- Sustainable Process Engineering Centre, Department of Chemical Engineering, Faculty of Engineering, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Kazuaki Syutsubo
- Regional Environment Conservation Division, National Institute for Environmental Studies, Tsukuba, 305-8506, Japan; Research Centre of Water Environment Technology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
| | - Mohamad Fairus Rabuni
- Sustainable Process Engineering Centre, Department of Chemical Engineering, Faculty of Engineering, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Yasuyuki Takemura
- Department of Civil Engineering, National Institute of Technology, Wakayama College, Gobo, Wakayama, 644-0023, Japan.
| | - Masataka Aoki
- Regional Environment Conservation Division, National Institute for Environmental Studies, Tsukuba, 305-8506, Japan.
| | - Adeline Seak May Chua
- Sustainable Process Engineering Centre, Department of Chemical Engineering, Faculty of Engineering, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
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3
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Lipsman V, Shlakhter O, Rocha J, Segev E. Bacteria contribute exopolysaccharides to an algal-bacterial joint extracellular matrix. NPJ Biofilms Microbiomes 2024; 10:36. [PMID: 38561371 PMCID: PMC10984933 DOI: 10.1038/s41522-024-00510-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: 10/09/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
Marine ecosystems are influenced by phytoplankton aggregation, which affects processes like marine snow formation and harmful events such as marine mucilage outbreaks. Phytoplankton secrete exopolymers, creating an extracellular matrix (ECM) that promotes particle aggregation. This ECM attracts heterotrophic bacteria, providing a nutrient-rich and protective environment. In terrestrial environments, bacterial colonization near primary producers relies on attachment and the formation of multidimensional structures like biofilms. Bacteria were observed attaching and aggregating within algal-derived exopolymers, but it is unclear if bacteria produce an ECM that contributes to this colonization. This study, using Emiliania huxleyi algae and Phaeobacter inhibens bacteria in an environmentally relevant model system, reveals a shared algal-bacterial ECM scaffold that promotes algal-bacterial aggregation. Algal exudates play a pivotal role in promoting bacterial colonization, stimulating bacterial exopolysaccharide (EPS) production, and facilitating a joint ECM formation. A bacterial biosynthetic pathway responsible for producing a specific EPS contributing to bacterial ECM formation is identified. Genes from this pathway show increased expression in algal-rich environments. These findings highlight the underestimated role of bacteria in aggregate-mediated processes in marine environments, offering insights into algal-bacterial interactions and ECM formation, with implications for understanding and managing natural and perturbed aggregation events.
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Affiliation(s)
- Valeria Lipsman
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Olesia Shlakhter
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Jorge Rocha
- Programa de Agricultura en Zonas Áridas, Centro de Investigaciones Biológicas del Noroeste, La Paz, Baja California Sur, 23096, México
| | - Einat Segev
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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4
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França TC, Saïdi F, Ajamian A, Islam ST, LaPlante SR. Molecular Dynamics of Outer Membrane-Embedded Polysaccharide Secretion Porins Reveals Closed Resting-State Surface Gates Targetable by Virtual Fragment Screening for Drug Hotspot Identification. ACS OMEGA 2024; 9:13217-13226. [PMID: 38524450 PMCID: PMC10955716 DOI: 10.1021/acsomega.3c09970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/06/2024] [Accepted: 02/14/2024] [Indexed: 03/26/2024]
Abstract
Recent advances in iterative neural network analyses (e.g., AlphaFold2 and RoseTTA fold) have been revolutionary for protein 3D structure prediction, especially for difficult-to-manipulate α-helical/β-barrel integral membrane proteins. These model structures are calculated based on the coevolution of amino acids within the protein of interest and similarities to existing protein structures; the local effects of the membrane on folding and stability of the calculated model structures are not considered. We recently reported the discovery, 3D modeling, and characterization of 18-β-stranded outer-membrane (OM) WzpX, WzpS, and WzpB β-barrel secretion porins for the exopolysaccharide (EPS), major spore coat polysaccharide (MASC), and biosurfactant polysaccharide (BPS) pathways (respectively) in the Gram-negative social predatory bacterium Myxococcus xanthus DZ2. However, information was not obtained regarding the dynamic behavior of surface-gating WzpX/S/B loop domains or on potential treatments to inactivate these porins. Herein, we developed a molecular dynamics (MD) protocol to study the core stability and loop dynamism of neural network-based integral membrane protein structure models embedded in an asymmetric OM bilayer, using the M. xanthus WzpX, WzpS, and WzpB proteins as test candidates. This was accomplished through integration of the CHARMM-graphical user interface (GUI) and Molecular Operating Environment (MOE) workflows to allow for a rapid simulation system setup and facilitate data analysis. In addition to serving as a method of model structure validation, our molecular dynamics simulations revealed a minimal movement of extracellular WzpX/S/B loops in the absence of an external stimulus as well as druggable cavities between the loops. Virtual screening of a commercial fragment library against these cavities revealed putative fragment-binding hotspots on the cell-surface face of each β-barrel, along with key interacting residues, and identified promising hits for the design of potential binders capable of plugging the β-barrels and inhibiting polysaccharide secretion.
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Affiliation(s)
- Tanos
C. C. França
- Institut
National de la Recherche Scientifique (INRS), Centre Armand-Frappier
Santé Biotechnologie, Université
du Québec, Institut Pasteur International Network, Laval, QC H7V 1B7, Canada
- PROTEO,
the Quebec Network for Research on Protein Function, Engineering,
and Applications, Université Laval, Quebec, QC G1V 0A6, Canada
- Laboratory
of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro 22290-270, Brazil
- Department
of Chemistry, Faculty of Science, University
of Hradec Kralove, Rokitanskeho
62, 50003 Hradec
Kralove, Czech Republic
| | - Fares Saïdi
- Institut
National de la Recherche Scientifique (INRS), Centre Armand-Frappier
Santé Biotechnologie, Université
du Québec, Institut Pasteur International Network, Laval, QC H7V 1B7, Canada
- PROTEO,
the Quebec Network for Research on Protein Function, Engineering,
and Applications, Université Laval, Quebec, QC G1V 0A6, Canada
| | - Alain Ajamian
- Chemical
Computing Group, Montreal, Quebec H3A 2R7, Canada
| | - Salim T. Islam
- Institut
National de la Recherche Scientifique (INRS), Centre Armand-Frappier
Santé Biotechnologie, Université
du Québec, Institut Pasteur International Network, Laval, QC H7V 1B7, Canada
- PROTEO,
the Quebec Network for Research on Protein Function, Engineering,
and Applications, Université Laval, Quebec, QC G1V 0A6, Canada
| | - Steven R. LaPlante
- Institut
National de la Recherche Scientifique (INRS), Centre Armand-Frappier
Santé Biotechnologie, Université
du Québec, Institut Pasteur International Network, Laval, QC H7V 1B7, Canada
- PROTEO,
the Quebec Network for Research on Protein Function, Engineering,
and Applications, Université Laval, Quebec, QC G1V 0A6, Canada
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5
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Zhang X, Xu J, Dai J, Zhang L, Feng L, Tian X, Yang Q. Taxonomic, Phylogenomic and Bioactivity Profiling of Novel Phycosphere Bacterium from Model Cyanobacterium Synechococcus elongatus PCC 7942. Mar Drugs 2024; 22:36. [PMID: 38248661 PMCID: PMC10817584 DOI: 10.3390/md22010036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
Phycosphere niches host rich microbial consortia that harbor dynamic algae-bacteria interactions with fundamental significance in varied natural ecosystems. Hence, culturing the uncultured microbial majority of the phycosphere microbiota is vital for deep understanding of the intricate mechanisms governing the dynamic interactions, and also to provide novel and rich microbial resources, and to discover new natural bioactive metabolites. Synechococcus elongatus PCC 7942 is a robust model cyanobacterium widely used in environment, synthesis biology, and biotechnology research. To expand the number of novel phycosphere species that were brought into culture and to discover the natural bioactivities, we presented a new yellow-pigmented bacterium named ABI-127-1, which was recovered from the phycosphere of PCC 7942, using an optimized bacterial isolation procedure. Combined polyphasic taxonomic and phylogenomic characterization was performed to confidently identify the new isolate as a potential novel species belonging to the genus Qipengyuania. The observed bioactivity of strain ABI-127-1 with promoting potential towards the growth and CO2 fixation efficiency of the host microalgae was measured. Additionally, the bacterial production of active bioflocculant exopolysaccharides was evaluated after culture optimization. Thus, these findings revealed the potential environmental and biotechnological implications of this new microalgae growth-promoting bacterium isolated from the phycosphere microenvironment.
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Affiliation(s)
- Xiaoling Zhang
- Department of Marine Chemistry, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National “111” Center for Cellular Regulation and Molecular Pharmaceutics, College of Bioengineering, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
- ABI Group, Laboratory of Phycosphere Microbiology, Zhejiang Ocean University, Zhoushan 316021, China
| | - Jiaquan Xu
- Department of Marine Chemistry, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China
- Zhejiang Provincial Key Laboratory of Petrochemical Pollution Control, Zhejiang Ocean University, Zhoushan 316022, China
- Donghai Laboratory, Zhoushan 316022, China
| | - Jun Dai
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National “111” Center for Cellular Regulation and Molecular Pharmaceutics, College of Bioengineering, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Lei Zhang
- Zhejiang Provincial Key Laboratory of Petrochemical Pollution Control, Zhejiang Ocean University, Zhoushan 316022, China
| | - Lijuan Feng
- Zhejiang Provincial Key Laboratory of Petrochemical Pollution Control, Zhejiang Ocean University, Zhoushan 316022, China
| | - Xiaoqing Tian
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
| | - Qiao Yang
- ABI Group, Laboratory of Phycosphere Microbiology, Zhejiang Ocean University, Zhoushan 316021, China
- Zhejiang Provincial Key Laboratory of Petrochemical Pollution Control, Zhejiang Ocean University, Zhoushan 316022, China
- Donghai Laboratory, Zhoushan 316022, China
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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6
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Dye KJ, Salar S, Allen U, Smith W, Yang Z. Myxococcus xanthus PilB interacts with c-di-GMP and modulates motility and biofilm formation. J Bacteriol 2023; 205:e0022123. [PMID: 37695853 PMCID: PMC10521364 DOI: 10.1128/jb.00221-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 08/02/2023] [Indexed: 09/13/2023] Open
Abstract
The regulation of biofilm and motile states as alternate bacterial lifestyles has been studied extensively in flagellated bacteria, where the second messenger cyclic-di-GMP (cdG) plays a crucial role. However, much less is known about the mechanisms of such regulation in motile bacteria without flagella. The bacterial type IV pilus (T4P) serves as a motility apparatus that enables Myxococcus xanthus to move on solid surfaces. PilB, the T4P assembly ATPase, is, therefore, required for T4P-dependent motility in M. xanthus. Interestingly, T4P is also involved in the regulation of exopolysaccharide as the biofilm matrix material in this bacterium. A newly discovered cdG-binding domain, MshEN, is conserved in the N-terminus of PilB (PilBN) in M. xanthus and other bacteria. This suggests that cdG may bind to PilB to control the respective outputs that regulate biofilm development and T4P-powered motility. In this study, we aimed to validate M. xanthus PilB as a cdG effector protein. We performed a systematic mutational analysis of its cdG-binding domain to investigate its relationship with motility, piliation, and biofilm formation. Excluding those resulting in low levels of PilB protein, all other substitution mutations in PilBN resulted in pilB mutants with distinct and differential phenotypes in piliation and biofilm levels in M. xanthus. This suggests that the PilBN domain plays dual roles in modulating motility and biofilm levels, and these two functions of PilB can be dependent on and independent of each other in M. xanthus. IMPORTANCE The regulation of motility and biofilm by cyclic-di-GMP in flagellated bacteria has been extensively investigated. However, our knowledge regarding this regulation in motile bacteria without flagella remains limited. Here, we aimed to address this gap by investigating a non-flagellated bacterium with motility powered by bacterial type-IV pilus (T4P). Previous studies hinted at the possibility of Myxococcus xanthus PilB, the T4P assembly ATPase, serving as a cyclic-di-GMP effector involved in regulating both motility and biofilm. Our findings strongly support the hypothesis that PilB directly interacts with cyclic-di-GMP to act as a potential switch to promote biofilm formation or T4P-dependent motility. These results shed light on the bifurcation of PilB functions and its pivotal role in coordinating biofilm formation and T4P-mediated motility.
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Affiliation(s)
- Keane J. Dye
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Safoura Salar
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Uvina Allen
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Wraylyn Smith
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Zhaomin Yang
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
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7
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Murali R, Yu H, Speth DR, Wu F, Metcalfe KS, Crémière A, Laso-Pèrez R, Malmstrom RR, Goudeau D, Woyke T, Hatzenpichler R, Chadwick GL, Connon SA, Orphan VJ. Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea. PLoS Biol 2023; 21:e3002292. [PMID: 37747940 PMCID: PMC10553843 DOI: 10.1371/journal.pbio.3002292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 10/05/2023] [Accepted: 08/08/2023] [Indexed: 09/27/2023] Open
Abstract
Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.
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Affiliation(s)
- Ranjani Murali
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, Unites Stated of America
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, United States of America
| | - Daan R. Speth
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Fabai Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Kyle S. Metcalfe
- Department of Plant and Molecular Biology, University of California, Berkeley. Berkeley, California, United States of America
| | - Antoine Crémière
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, Unites Stated of America
| | - Rafael Laso-Pèrez
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Rex R. Malmstrom
- DOE Joint Genome Institute, Department of Energy, Berkeley, California, United States of America
| | - Danielle Goudeau
- DOE Joint Genome Institute, Department of Energy, Berkeley, California, United States of America
| | - Tanja Woyke
- DOE Joint Genome Institute, Department of Energy, Berkeley, California, United States of America
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
| | - Grayson L. Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, Unites Stated of America
- Department of Plant and Molecular Biology, University of California, Berkeley. Berkeley, California, United States of America
| | - Stephanie A. Connon
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, Unites Stated of America
| | - Victoria J. Orphan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, Unites Stated of America
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8
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Baria DM, Patel NY, Yagnik SM, Panchal RR, Rajput KN, Raval VH. Exopolysaccharides from marine microbes with prowess for environment cleanup. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:76611-76625. [PMID: 36166130 DOI: 10.1007/s11356-022-23198-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
A variety of both small and large biologically intriguing compounds can be found abundantly in the marine environment. Researchers are particularly interested in marine bacteria because they can produce classes of bioactive secondary metabolites that are structurally diverse. The main secondary metabolites produced by marine bacteria are regarded as steroids, alkaloids, peptides, terpenoids, biopolymers, and polyketides. The global urbanization leads to the increased use of organic pollutants that are both persistent and toxic for humans, other life forms and tend to biomagnified in environment. The issue can be addressed, by using marine microbial biopolymers with ability for increased bioremediation. Amongst biopolymers, the exopolysaccharides (EPS) are the most prominent under adverse environmental stress conditions. The present review emphasizes the use of EPS as a bio-flocculent for wastewater treatment, as an adsorbent for the removal of textile dye and heavy metals from industrial effluents. The biofilm-forming ability of EPS helps with soil reclamation and reduces soil erosion. EPS are an obvious choice being environmentally friendly and cost-effective in processes for developing sustainable technology. However, a better understanding of EPS biosynthetic pathways and further developing novel sustainable technologies is desirable and certainly will pave the way for efficient usage of EPS for environment cleanup.
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Affiliation(s)
- Dhritiksha Mansukhlal Baria
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, 380 009, Ahmedabad, Gujarat, India
| | - Nidhi Yogeshbhai Patel
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, 380 009, Ahmedabad, Gujarat, India
| | | | - Rakeshkumar Ramanlal Panchal
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, 380 009, Ahmedabad, Gujarat, India
| | - Kiransinh Narendrasinh Rajput
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, 380 009, Ahmedabad, Gujarat, India
| | - Vikram Hiren Raval
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, 380 009, Ahmedabad, Gujarat, India.
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9
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Saïdi F, Mahanta U, Panda A, Kezzo AA, Jolivet NY, Bitazar R, John G, Martinez M, Mellouk A, Calmettes C, Chang YW, Sharma G, Islam ST. Bacterial Outer Membrane Polysaccharide Export (OPX) Proteins Occupy Three Structural Classes with Selective β-Barrel Porin Requirements for Polymer Secretion. Microbiol Spectr 2022; 10:e0129022. [PMID: 36200915 PMCID: PMC9603273 DOI: 10.1128/spectrum.01290-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/08/2022] [Indexed: 12/30/2022] Open
Abstract
Secretion of high-molecular-weight polysaccharides across the bacterial envelope is ubiquitous, as it enhances prokaryotic survival in (a)biotic settings. Such polymers are often assembled by Wzx/Wzy- or ABC transporter-dependent schemes implicating outer membrane (OM) polysaccharide export (OPX) proteins in cell-surface polymer translocation. In the social predatory bacterium Myxococcus xanthus, the exopolysaccharide (EPS) pathway WzaX, major spore coat (MASC) pathway WzaS, and biosurfactant polysaccharide (BPS) pathway WzaB were herein found to be truncated OPX homologues of Escherichia coli Wza lacking OM-spanning α-helices. Comparative genomics across all bacteria (>91,000 OPX proteins identified and analyzed), complemented with cryo-electron tomography cell-envelope analyses, revealed such "truncated" WzaX/S/B architecture to be the most common among three defined OPX-protein structural classes independent of periplasm thickness. Fold recognition and deep learning revealed the conserved M. xanthus proteins MXAN_7418/3226/1916 (encoded beside wzaX/S/B, respectively) to be integral OM β-barrels, with structural homology to the poly-N-acetyl-d-glucosamine synthase-dependent pathway porin PgaA. Such bacterial porins were identified near numerous genes for all three OPX protein classes. Interior MXAN_7418/3226/1916 β-barrel electrostatics were found to match properties of their associated polymers. With MXAN_3226 essential for MASC export, and MXAN_7418 herein shown to mediate EPS translocation, we have designated this new secretion machinery component "Wzp" (i.e., Wz porin), with the final step of M. xanthus EPS/MASC/BPS secretion across the OM now proposed to be mediated by WzpX/S/B (i.e., MXAN_7418/3226/1916). Importantly, these data support a novel and widespread secretion paradigm for polysaccharide biosynthesis pathways in which those containing OPX components that cannot span the OM instead utilize β-barrel porins to mediate polysaccharide transport across the OM. IMPORTANCE Diverse bacteria assemble and secrete polysaccharides that alter their physiologies through modulation of motility, biofilm formation, and host immune system evasion. Most such pathways require outer membrane (OM) polysaccharide export (OPX) proteins for sugar-polymer transport to the cell surface. In the prototypic Escherichia coli Group-1-capsule biosynthesis system, eight copies of this canonical OPX protein cross the OM with an α-helix, forming a polysaccharide-export pore. Herein, we instead reveal that most OPX proteins across all bacteria lack this α-helix, raising questions as to the manner by which most secreted polysaccharides actually exit cells. In the model developmental bacterium Myxococcus xanthus, we show this process to depend on OPX-coupled OM-spanning β-barrel porins, with similar porins encoded near numerous OPX genes in diverse bacteria. Knowledge of the terminal polysaccharide secretion step will enable development of antimicrobial compounds targeted to blocking polymer export from outside the cell, thus bypassing any requirements for antimicrobial compound uptake by the cell.
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Affiliation(s)
- Fares Saïdi
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
| | - Utkarsha Mahanta
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| | - Adyasha Panda
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| | - Ahmad A. Kezzo
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
| | - Nicolas Y. Jolivet
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
| | - Razieh Bitazar
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
| | - Gavin John
- Department of Pediatrics, Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Matthew Martinez
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Abdelkader Mellouk
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
| | - Charles Calmettes
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gaurav Sharma
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| | - Salim T. Islam
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
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Evidence for a Widespread Third System for Bacterial Polysaccharide Export across the Outer Membrane Comprising a Composite OPX/β-Barrel Translocon. mBio 2022; 13:e0203222. [PMID: 35972145 PMCID: PMC9601211 DOI: 10.1128/mbio.02032-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Gram-negative bacteria, secreted polysaccharides have multiple critical functions. In Wzx/Wzy- and ABC transporter-dependent pathways, an outer membrane (OM) polysaccharide export (OPX) type translocon exports the polysaccharide across the OM. The paradigm OPX protein Wza of Escherichia coli is an octamer in which the eight C-terminal domains form an α-helical OM pore and the eight copies of the three N-terminal domains (D1 to D3) form a periplasmic cavity. In synthase-dependent pathways, the OM translocon is a 16- to 18-stranded β-barrel protein. In Myxococcus xanthus, the secreted polysaccharide EPS (exopolysaccharide) is synthesized in a Wzx/Wzy-dependent pathway. Here, using experiments, phylogenomics, and computational structural biology, we identify and characterize EpsX as an OM 18-stranded β-barrel protein important for EPS synthesis and identify AlgE, a β-barrel translocon of a synthase-dependent pathway, as its closest structural homolog. We also find that EpsY, the OPX protein of the EPS pathway, consists only of the periplasmic D1 and D2 domains and completely lacks the domain for spanning the OM (herein termed a D1D2OPX protein). In vivo, EpsX and EpsY mutually stabilize each other and interact in in vivo pulldown experiments supporting their direct interaction. Based on these observations, we propose that EpsY and EpsX make up and represent a third type of translocon for polysaccharide export across the OM. Specifically, in this composite translocon, EpsX functions as the OM-spanning β-barrel translocon together with the periplasmic D1D2OPX protein EpsY. Based on computational genomics, similar composite systems are widespread in Gram-negative bacteria. IMPORTANCE Bacteria secrete a wide variety of polysaccharides that have critical functions in, e.g., fitness, surface colonization, and biofilm formation and in beneficial and pathogenic human-, animal-, and plant-microbe interactions. In Gram-negative bacteria, export of these chemically diverse polysaccharides across the outer membrane depends on two known translocons, i.e., an outer membrane OPX protein in Wzx/Wzy- and ABC transporter-dependent pathways and an outer membrane 16- to 18-stranded β-barrel protein in synthase-dependent pathways. Here, using a combination of experiments in Myxococcus xanthus, phylogenomics, and computational structural biology, we provide evidence supporting that a third type of translocon can export polysaccharides across the outer membrane. Specifically, in this translocon, an outer membrane-spanning β-barrel protein functions together with an entirely periplasmic OPX protein that completely lacks the domain for spanning the OM. Computational genomics support that similar composite systems are widespread in Gram-negative bacteria.
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11
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Dye KJ, Yang Z. Analysis of Myxococcus xanthus Vegetative Biofilms With Microtiter Plates. Front Microbiol 2022; 13:894562. [PMID: 35572678 PMCID: PMC9100584 DOI: 10.3389/fmicb.2022.894562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
The bacterium Myxococcus xanthus forms both developmental and vegetative types of biofilms. While the former has been studied on both agar plates and submerged surfaces, the latter has been investigated predominantly on agar surfaces as swarming colonies. Here we describe the development of a microplate-based assay for the submerged biofilms of M. xanthus under vegetative conditions. We examined the impacts of inoculation, aeration, and temperature to optimize the conditions for the assay. Aeration was observed to be critical for the effective development of submerged biofilms by M. xanthus, an obligate aerobic bacterium. In addition, temperature plays an important role in the development of M. xanthus submerged biofilms. It is well established that the formation of submerged biofilms by many bacteria requires both exopolysaccharide (EPS) and the type IV pilus (T4P). EPS constitutes part of the biofilm matrix that maintains and organizes bacterial biofilms while the T4P facilitates surface attachment as adhesins. For validation, we used our biofilm assay to examine a multitude of M. xanthus strains with various EPS and T4P phenotypes. The results indicate that the levels of EPS, but not of piliation, positively correlate with submerged biofilm formation in M. xanthus.
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12
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A DnaK(Hsp70) Chaperone System Connects Type IV Pilus Activity to Polysaccharide Secretion in Cyanobacteria. mBio 2022; 13:e0051422. [PMID: 35420478 PMCID: PMC9239167 DOI: 10.1128/mbio.00514-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Surface motility powered by type IV pili (T4P) is widespread among bacteria, including the photosynthetic cyanobacteria. This form of movement typically requires the deposition of a motility-associated polysaccharide, and several studies indicate that there is complex coregulation of T4P motor activity and polysaccharide production, although a mechanistic understanding of this coregulation is not fully defined. Here, using a combination of genetic, comparative genomic, transcriptomic, protein-protein interaction, and cytological approaches in the model filamentous cyanobacterium N. punctiforme, we provided evidence that a DnaK-type chaperone system coupled the activity of the T4P motors to the production of the motility-associated hormogonium polysaccharide (HPS). The results from these studies indicated that DnaK1 and DnaJ3 along with GrpE comprised a chaperone system that interacted specifically with active T4P motors and was required to produce HPS. Genomic conservation in cyanobacteria and the conservation of the protein-protein interaction network in the model unicellular cyanobacterium Synechocystis sp. strain PCC 6803 imply that this system is conserved among nearly all motile cyanobacteria and provides a mechanism to coordinate polysaccharide secretion and T4P activity in these organisms.
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13
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Saïdi F, Bitazar R, Bradette NY, Islam ST. Bacterial Glycocalyx Integrity Impacts Tolerance of Myxococcus xanthus to Antibiotics and Oxidative-Stress Agents. Biomolecules 2022; 12:571. [PMID: 35454160 PMCID: PMC9029694 DOI: 10.3390/biom12040571] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 02/07/2023] Open
Abstract
The presence of an exopolysaccharide (EPS) layer surrounding bacterial cells, termed a "glycocalyx", confers protection against toxic molecules. However, the effect of glycocalyx integrity on the tolerance to such agents is poorly understood. Using a modified disc-diffusion assay, we tested the susceptibility to a panel of antibiotics and oxidative stress-inducing compounds of various mutant strains of the social predatory Gram-negative soil bacterium Myxococcus xanthus; the selected mutants were those that manifest different physical states of their respective EPS glycocalyces. While the overall presence of an EPS layer was indeed beneficial for tolerance, the integrity of this layer was also found to affect the susceptibility of the bacterium to killing; however, this finding was not universal, and instead was dependent on the specific compound tested. Thus, the integrity of the cell-surface EPS glycocalyx plays an important role in the tolerance of M. xanthus to harmful compounds.
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Affiliation(s)
- Fares Saïdi
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Institut Pasteur International Network, Laval, QC H7V 1B7, Canada; (F.S.); (R.B.); (N.Y.B.)
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, QC G1V 0A6, Canada
| | - Razieh Bitazar
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Institut Pasteur International Network, Laval, QC H7V 1B7, Canada; (F.S.); (R.B.); (N.Y.B.)
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, QC G1V 0A6, Canada
| | - Nicholas Y. Bradette
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Institut Pasteur International Network, Laval, QC H7V 1B7, Canada; (F.S.); (R.B.); (N.Y.B.)
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, QC G1V 0A6, Canada
| | - Salim T. Islam
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Institut Pasteur International Network, Laval, QC H7V 1B7, Canada; (F.S.); (R.B.); (N.Y.B.)
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, QC G1V 0A6, Canada
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14
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Ashraf KU, Nygaard R, Vickery ON, Erramilli SK, Herrera CM, McConville TH, Petrou VI, Giacometti SI, Dufrisne MB, Nosol K, Zinkle AP, Graham CLB, Loukeris M, Kloss B, Skorupinska-Tudek K, Swiezewska E, Roper DI, Clarke OB, Uhlemann AC, Kossiakoff AA, Trent MS, Stansfeld PJ, Mancia F. Structural basis of lipopolysaccharide maturation by the O-antigen ligase. Nature 2022; 604:371-376. [PMID: 35388216 PMCID: PMC9884178 DOI: 10.1038/s41586-022-04555-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 02/16/2022] [Indexed: 01/31/2023]
Abstract
The outer membrane of Gram-negative bacteria has an external leaflet that is largely composed of lipopolysaccharide, which provides a selective permeation barrier, particularly against antimicrobials1. The final and crucial step in the biosynthesis of lipopolysaccharide is the addition of a species-dependent O-antigen to the lipid A core oligosaccharide, which is catalysed by the O-antigen ligase WaaL2. Here we present structures of WaaL from Cupriavidus metallidurans, both in the apo state and in complex with its lipid carrier undecaprenyl pyrophosphate, determined by single-particle cryo-electron microscopy. The structures reveal that WaaL comprises 12 transmembrane helices and a predominantly α-helical periplasmic region, which we show contains many of the conserved residues that are required for catalysis. We observe a conserved fold within the GT-C family of glycosyltransferases and hypothesize that they have a common mechanism for shuttling the undecaprenyl-based carrier to and from the active site. The structures, combined with genetic, biochemical, bioinformatics and molecular dynamics simulation experiments, offer molecular details on how the ligands come in apposition, and allows us to propose a mechanistic model for catalysis. Together, our work provides a structural basis for lipopolysaccharide maturation in a member of the GT-C superfamily of glycosyltransferases.
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Affiliation(s)
- Khuram U Ashraf
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Rie Nygaard
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Owen N Vickery
- School of Life Sciences, University of Warwick, Coventry, UK
- Department of Chemistry, University of Warwick, Coventry, UK
| | - Satchal K Erramilli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Carmen M Herrera
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Thomas H McConville
- Department of Medicine, Division of Infectious Diseases, Columbia University Medical Center, New York, NY, USA
| | - Vasileios I Petrou
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ, USA
| | - Sabrina I Giacometti
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Meagan Belcher Dufrisne
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Kamil Nosol
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Allen P Zinkle
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Michael Loukeris
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY, USA
| | - Brian Kloss
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY, USA
| | | | - Ewa Swiezewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - David I Roper
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Anne-Catrin Uhlemann
- Department of Medicine, Division of Infectious Diseases, Columbia University Medical Center, New York, NY, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - M Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA.
| | - Phillip J Stansfeld
- School of Life Sciences, University of Warwick, Coventry, UK.
- Department of Chemistry, University of Warwick, Coventry, UK.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
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15
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Zhao Y, Wang Y, Xia C, Li X, Ye X, Fan Q, Huang Y, Li Z, Zhu C, Cui Z. Whole-Genome Sequencing of Corallococcus sp. Strain EGB Reveals the Genetic Determinants Linking Taxonomy and Predatory Behavior. Genes (Basel) 2021; 12:genes12091421. [PMID: 34573403 PMCID: PMC8466578 DOI: 10.3390/genes12091421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022] Open
Abstract
Corallococcus sp. strain EGB is a Gram-negative myxobacteria isolated from saline soil, and has considerable potential for the biocontrol of phytopathogenic fungi. However, the detailed mechanisms related to development and predatory behavior are unclear. To obtain a comprehensive overview of genetic features, the genome of strain EGB was sequenced, annotated, and compared with 10 other Corallococcus species. The strain EGB genome was assembled as a single circular chromosome of 9.4 Mb with 7916 coding genes. Phylogenomics analysis showed that strain EGB was most closely related to Corallococcus interemptor AB047A, and it was inferred to be a novel species within the Corallococcus genus. Comparative genomic analysis revealed that the pan-genome of Corallococcus genus was large and open. Only a small proportion of genes were specific to strain EGB, and most of them were annotated as hypothetical proteins. Subsequent analyses showed that strain EGB produced abundant extracellular enzymes such as chitinases and β-(1,3)-glucanases, and proteases to degrade the cell-wall components of phytopathogenic fungi. In addition, 35 biosynthetic gene clusters potentially coding for antimicrobial compounds were identified in the strain EGB, and the majority of them were present in the dispensable pan-genome with unexplored metabolites. Other genes related to secretion and regulation were also explored for strain EGB. This study opens new perspectives in the greater understanding of the predatory behavior of strain EGB, and facilitates a potential application in the biocontrol of fungal plant diseases in the future.
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Affiliation(s)
- Yuqiang Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Yanxin Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chengyao Xia
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xu Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiwen Fan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Cancan Zhu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
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16
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Saïdi F, Jolivet NY, Lemon DJ, Nakamura A, Belgrave AM, Garza AG, Veyrier FJ, Islam ST. Bacterial glycocalyx integrity drives multicellular swarm biofilm dynamism. Mol Microbiol 2021; 116:1151-1172. [PMID: 34455651 DOI: 10.1111/mmi.14803] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/24/2022]
Abstract
Exopolysaccharide (EPS) layers on the bacterial cell surface are key determinants of biofilm establishment and maintenance, leading to the formation of higher-order 3D structures that confer numerous survival benefits to a cell community. In addition to a specific cell-associated EPS glycocalyx, we recently revealed that the social δ-proteobacterium Myxococcus xanthus secretes a novel biosurfactant polysaccharide (BPS) to the extracellular milieu. Together, secretion of the two polymers (EPS and BPS) is required for type IV pilus (T4P)-dependent swarm expansion via spatio-specific biofilm expression profiles. Thus the synergy between EPS and BPS secretion somehow modulates the multicellular lifecycle of M. xanthus. Herein, we demonstrate that BPS secretion functionally alters the EPS glycocalyx via destabilization of the latter, fundamentally changing the characteristics of the cell surface. This impacts motility behaviors at the single-cell level and the aggregative capacity of cells in groups via cell-surface EPS fibril formation as well as T4P production, stability, and positioning. These changes modulate the structure of swarm biofilms via cell layering, likely contributing to the formation of internal swarm polysaccharide architecture. Together, these data reveal the manner by which the combined secretion of two distinct polymers induces single-cell changes that modulate swarm biofilm communities.
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Affiliation(s)
- Fares Saïdi
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada.,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
| | - Nicolas Y Jolivet
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada.,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
| | - David J Lemon
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Arnaldo Nakamura
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada
| | - Akeisha M Belgrave
- Integrated Sciences Program, Harrisburg University of Science & Technology, Harrisburg, Pennsylvania, USA
| | - Anthony G Garza
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Frédéric J Veyrier
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada
| | - Salim T Islam
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada.,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
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17
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Three PilZ Domain Proteins, PlpA, PixA, and PixB, Have Distinct Functions in Regulation of Motility and Development in Myxococcus xanthus. J Bacteriol 2021; 203:e0012621. [PMID: 33875546 PMCID: PMC8316039 DOI: 10.1128/jb.00126-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In bacteria, the nucleotide-based second messenger bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) binds to effectors to generate outputs in response to changes in the environment. In Myxococcus xanthus, c-di-GMP regulates type IV pilus-dependent motility and the starvation-induced developmental program that results in formation of spore-filled fruiting bodies; however, little is known about the effectors that bind c-di-GMP. Here, we systematically inactivated all 24 genes encoding PilZ domain-containing proteins, which are among the most common c-di-GMP effectors. We confirm that the stand-alone PilZ domain protein PlpA is important for regulation of motility independently of the Frz chemosensory system and that Pkn1, which is composed of a Ser/Thr kinase domain and a PilZ domain, is specifically important for development. Moreover, we identify two PilZ domain proteins that have distinct functions in regulating motility and development. PixB, which is composed of two PilZ domains and an acetyltransferase domain, binds c-di-GMP in vitro and regulates type IV pilus-dependent and gliding motility in a Frz-dependent manner as well as development. The acetyltransferase domain is required and sufficient for function during growth, while all three domains and c-di-GMP binding are essential for PixB function during development. PixA is a response regulator composed of a PilZ domain and a receiver domain, binds c-di-GMP in vitro, and regulates motility independently of the Frz system, likely by setting up the polarity of the two motility systems. Our results support a model whereby PlpA, PixA, and PixB act in independent pathways and have distinct functions in regulation of motility. IMPORTANCE c-di-GMP signaling controls bacterial motility in many bacterial species by binding to downstream effector proteins. Here, we identify two PilZ domain-containing proteins in Myxococcus xanthus that bind c-di-GMP. We show that PixB, which contains two PilZ domains and an acetyltransferase domain, acts in a manner that depends on the Frz chemosensory system to regulate motility via the acetyltransferase domain, while the intact protein and c-di-GMP binding are essential for PixB to support development. In contrast, PixA acts in a Frz-independent manner to regulate motility. Taking our results together with previous observations, we conclude that PilZ domain proteins and c-di-GMP act in multiple independent pathways to regulate motility and development in M. xanthus.
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Mohd Nadzir M, Nurhayati RW, Idris FN, Nguyen MH. Biomedical Applications of Bacterial Exopolysaccharides: A Review. Polymers (Basel) 2021; 13:530. [PMID: 33578978 PMCID: PMC7916691 DOI: 10.3390/polym13040530] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 12/11/2022] Open
Abstract
Bacterial exopolysaccharides (EPSs) are an essential group of compounds secreted by bacteria. These versatile EPSs are utilized individually or in combination with different materials for a broad range of biomedical field functions. The various applications can be explained by the vast number of derivatives with useful properties that can be controlled. This review offers insight on the current research trend of nine commonly used EPSs, their biosynthesis pathways, their characteristics, and the biomedical applications of these relevant bioproducts.
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Affiliation(s)
- Masrina Mohd Nadzir
- School of Chemical Engineering, Engineering Campus, Universiti Sains Malaysia, Nibong Tebal 14300, Malaysia;
| | - Retno Wahyu Nurhayati
- Department of Chemical Engineering, Faculty of Engineering, Universitas Indonesia, Depok 16424, Indonesia;
- Stem Cell and Tissue Engineering Research Cluster, Indonesian Medical Education and Research Institute, Faculty of Medicine, Universitas Indonesia, Jl. Salemba Raya No. 6, Jakarta 10430, Indonesia
| | - Farhana Nazira Idris
- School of Chemical Engineering, Engineering Campus, Universiti Sains Malaysia, Nibong Tebal 14300, Malaysia;
| | - Minh Hong Nguyen
- Faculty of Biotechnology, Chemistry and Environmental Engineering, Phenikaa University, Hanoi 12116, Vietnam;
- Bioresource Research Center, Phenikaa University, Hanoi 12116, Vietnam
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