1
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Corrales D, Alcántara C, Zúñiga M, Monedero V. Ppx1 putative exopolyphosphatase is essential for polyphosphate accumulation in Lacticaseibacillus paracasei. Appl Environ Microbiol 2024; 90:e0229023. [PMID: 38619267 PMCID: PMC11107151 DOI: 10.1128/aem.02290-23] [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: 12/22/2023] [Accepted: 03/27/2024] [Indexed: 04/16/2024] Open
Abstract
The linear polymer polyphosphate (poly-P) is present across all three domains of life and serves diverse physiological functions. The enzyme polyphosphate kinase (Ppk) is responsible for poly-P synthesis, whereas poly-P degradation is carried out by the enzyme exopolyphosphatase (Ppx). In many Lactobacillaceae, the Ppk-encoding gene (ppk) is found clustered together with two genes encoding putative exopolyphosphatases (ppx1 and ppx2) each having different domain compositions, with the gene order ppx1-ppk-ppx2. However, the specific function of these ppx genes remains unexplored. An in-frame deletion of ppx1 in Lacticaseibacillus paracasei BL23 resulted in bacteria unable to accumulate poly-P, whereas the disruption of ppx2 did not affect poly-P synthesis. The expression of ppk was not altered in the Δppx1 strain, and poly-P synthesis in this strain was only restored by expressing ppx1 in trans. Moreover, no poly-P synthesis was observed when ppk was expressed from a plasmid in the Δppx1 strain. Purified Ppx2 exhibited in vitro exopolyphosphatase activity, whereas no in vitro enzymatic activity could be demonstrated for Ppx1. This observation corresponds with the absence in Ppx1 of conserved motifs essential for catalysis found in characterized exopolyphosphatases. Furthermore, assays with purified Ppk and Ppx1 evidenced that Ppx1 enhanced Ppk activity. These results demonstrate that Ppx1 is essential for poly-P synthesis in Lc. paracasei and have unveiled, for the first time, an unexpected role of Ppx1 exopolyphosphatase in poly-P synthesis.IMPORTANCEPoly-P is a pivotal molecular player in bacteria, participating in a diverse array of processes ranging from stress resilience to pathogenesis while also serving as a functional component in probiotic bacteria. The synthesis of poly-P is tightly regulated, but the underlying mechanisms remain incompletely elucidated. Our study sheds light on the distinctive role played by the two exopolyphosphatases (Ppx) found in the Lactobacillaceae bacterial group, of relevance in food and health. This particular group is noteworthy for possessing two Ppx enzymes, supposedly involved in poly-P degradation. Remarkably, our investigation uncovers an unprecedented function of Ppx1 in Lacticaseibacillus paracasei, where its absence leads to the total cessation of poly-P synthesis, paralleling the impact observed upon eliminating the poly-P forming enzyme, poly-P kinase. Unlike the anticipated role as a conventional exopolyphosphatase, Ppx1 demonstrates an unexpected function. Our results added a layer of complexity to our understanding of poly-P dynamics in bacteria.
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Affiliation(s)
- Daniela Corrales
- Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Paterna, Spain
| | - Cristina Alcántara
- Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Paterna, Spain
| | - Manuel Zúñiga
- Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Paterna, Spain
| | - Vicente Monedero
- Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Paterna, Spain
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2
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Walker AM, Abbondanzieri EA, Meyer AS. Live to fight another day: The bacterial nucleoid under stress. Mol Microbiol 2024. [PMID: 38690745 DOI: 10.1111/mmi.15272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/03/2024]
Abstract
The bacterial chromosome is both highly supercoiled and bound by an ensemble of proteins and RNA, causing the DNA to form a compact structure termed the nucleoid. The nucleoid serves to condense, protect, and control access to the bacterial chromosome through a variety of mechanisms that remain incompletely understood. The nucleoid is also a dynamic structure, able to change both in size and composition. The dynamic nature of the bacterial nucleoid is particularly apparent when studying the effects of various stresses on bacteria, which require cells to protect their DNA and alter patterns of transcription. Stresses can lead to large changes in the organization and composition of the nucleoid on timescales as short as a few minutes. Here, we summarize some of the recent advances in our understanding of how stress can alter the organization of bacterial chromosomes.
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Affiliation(s)
- Azra M Walker
- Department of Biology, University of Rochester, Rochester, New York, USA
| | | | - Anne S Meyer
- Department of Biology, University of Rochester, Rochester, New York, USA
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3
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Linnik D, Maslov I, Punter CM, Poolman B. Dynamic structure of E. coli cytoplasm: supramolecular complexes and cell aging impact spatial distribution and mobility of proteins. Commun Biol 2024; 7:508. [PMID: 38678067 PMCID: PMC11055878 DOI: 10.1038/s42003-024-06216-3] [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: 12/06/2023] [Accepted: 04/18/2024] [Indexed: 04/29/2024] Open
Abstract
Protein diffusion is a critical factor governing the functioning and organization of a cell's cytoplasm. In this study, we investigate the influence of (poly)ribosome distribution, cell aging, protein aggregation, and biomolecular condensate formation on protein mobility within the E. coli cytoplasm. We employ nanoscale single-molecule displacement mapping (SMdM) to determine the spatial distribution of the proteins and to meticulously track their diffusion. We show that the distribution of polysomes does not impact the lateral diffusion coefficients of proteins. However, the degradation of mRNA induced by rifampicin treatment leads to an increase in protein mobility within the cytoplasm. Additionally, we establish a significant correlation between cell aging, the asymmetric localization of protein aggregates and reduced diffusion coefficients at the cell poles. Notably, we observe variations in the hindrance of diffusion at the poles and the central nucleoid region for small and large proteins, and we reveal differences between the old and new pole of the cell. Collectively, our research highlights cellular processes and mechanisms responsible for spatially organizing the bacterial cytoplasm into domains with different structural features and apparent viscosity.
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Affiliation(s)
- Dmitrii Linnik
- Department of Biochemistry, University of Groningen, Groningen, Nijenborgh 4, 9747 AG, the Netherlands
| | - Ivan Maslov
- Department of Biochemistry, University of Groningen, Groningen, Nijenborgh 4, 9747 AG, the Netherlands
| | - Christiaan Michiel Punter
- Department of Biochemistry, University of Groningen, Groningen, Nijenborgh 4, 9747 AG, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Groningen, Nijenborgh 4, 9747 AG, the Netherlands.
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4
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Khanna K, Welch MD. Cryo-electron tomography of stationary phase Burkholderia thailandensis. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001178. [PMID: 38725941 PMCID: PMC11079643 DOI: 10.17912/micropub.biology.001178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024]
Abstract
Burkholderia species belonging to the pseudomallei group include significant human and animal pathogens as well as the non-pathogenic species Burkholderia thailandensis . These bacteria co-opt the host cell machinery for their replication and spread between host cells. Thus, it is of interest to understand the structural features of these cells that contribute to host cell colonization and virulence. This study provides high-resolution cryo-electron tomograms of stationary phase Burkholderia thailandensis . It reveals the presence of compact nucleoids and storage granules, as well as examples of the type III secretion system and chemoreceptor arrays. The data can be used to investigate the near-atomic structure of stationary-phase bacterial macromolecules, such as ribosomes.
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Affiliation(s)
- Kanika Khanna
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States
| | - Matthew D. Welch
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States
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5
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Thappeta Y, Cañas-Duarte SJ, Kallem T, Fragasso A, Xiang Y, Gray W, Lee C, Cegelski L, Jacobs-Wagner C. Glycogen phase separation drives macromolecular rearrangement and asymmetric division in E. coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590186. [PMID: 38659787 PMCID: PMC11042326 DOI: 10.1101/2024.04.19.590186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Bacteria often experience nutrient limitation in nature and the laboratory. While exponential and stationary growth phases are well characterized in the model bacterium Escherichia coli, little is known about what transpires inside individual cells during the transition between these two phases. Through quantitative cell imaging, we found that the position of nucleoids and cell division sites becomes increasingly asymmetric during transition phase. These asymmetries were coupled with spatial reorganization of proteins, ribosomes, and RNAs to nucleoid-centric localizations. Results from live-cell imaging experiments, complemented with genetic and 13C whole-cell nuclear magnetic resonance spectroscopy studies, show that preferential accumulation of the storage polymer glycogen at the old cell pole leads to the observed rearrangements and asymmetric divisions. In vitro experiments suggest that these phenotypes are likely due to the propensity of glycogen to phase separate in crowded environments, as glycogen condensates exclude fluorescent proteins under physiological crowding conditions. Glycogen-associated differences in cell sizes between strains and future daughter cells suggest that glycogen phase separation allows cells to store large glucose reserves without counting them as cytoplasmic space.
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Affiliation(s)
- Yashna Thappeta
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Silvia J. Cañas-Duarte
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, USA
| | - Till Kallem
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Alessio Fragasso
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Yingjie Xiang
- Mechanical Engineering and Materials Science, Yale University, New Haven, CT
| | - William Gray
- Mechanical Engineering and Materials Science, Yale University, New Haven, CT
| | - Cheyenne Lee
- Mechanical Engineering and Materials Science, Yale University, New Haven, CT
| | | | - Christine Jacobs-Wagner
- Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, USA
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6
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Magkiriadou S, Stepp WL, Newman DK, Manley S, Racki LR. Polyphosphate affects cytoplasmic and chromosomal dynamics in nitrogen-starved Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2024; 121:e2313004121. [PMID: 38564631 PMCID: PMC11009631 DOI: 10.1073/pnas.2313004121] [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: 08/21/2023] [Accepted: 01/26/2024] [Indexed: 04/04/2024] Open
Abstract
Polyphosphate (polyP) synthesis is a ubiquitous stress and starvation response in bacteria. In diverse species, mutants unable to make polyP have a wide variety of physiological defects, but the mechanisms by which this simple polyanion exerts its effects remain unclear. One possibility is that polyP's many functions stem from global effects on the biophysical properties of the cell. We characterize the effect of polyphosphate on cytoplasmic mobility under nitrogen-starvation conditions in the opportunistic pathogen Pseudomonas aeruginosa. Using fluorescence microscopy and particle tracking, we quantify the motion of chromosomal loci and cytoplasmic tracer particles. In the absence of polyP and upon starvation, we observe a 2- to 10-fold increase in mean cytoplasmic diffusivity. Tracer particles reveal that polyP also modulates the partitioning between a "more mobile" and a "less mobile" population: Small particles in cells unable to make polyP are more likely to be "mobile" and explore more of the cytoplasm, particularly during starvation. Concomitant with this larger freedom of motion in polyP-deficient cells, we observe decompaction of the nucleoid and an increase in the steady-state concentration of ATP. The dramatic polyP-dependent effects we observe on cytoplasmic transport properties occur under nitrogen starvation, but not carbon starvation, suggesting that polyP may have distinct functions under different types of starvation.
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Affiliation(s)
- Sofia Magkiriadou
- Laboratory of Experimental Biophysics, Institute of Physics, École Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Willi L. Stepp
- Laboratory of Experimental Biophysics, Institute of Physics, École Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Suliana Manley
- Laboratory of Experimental Biophysics, Institute of Physics, École Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Lisa R. Racki
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, San Diego, CA92037
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7
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Docampo R. Advances in the cellular biology, biochemistry, and molecular biology of acidocalcisomes. Microbiol Mol Biol Rev 2024; 88:e0004223. [PMID: 38099688 PMCID: PMC10966946 DOI: 10.1128/mmbr.00042-23] [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] [Indexed: 02/04/2024] Open
Abstract
SUMMARYAcidocalcisomes are organelles conserved during evolution and closely related to the so-called volutin granules of bacteria and archaea, to the acidocalcisome-like vacuoles of yeasts, and to the lysosome-related organelles of animal species. All these organelles have in common their acidity and high content of polyphosphate and calcium. They are characterized by a variety of functions from storage of phosphorus and calcium to roles in Ca2+ signaling, osmoregulation, blood coagulation, and inflammation. They interact with other organelles through membrane contact sites or by fusion, and have several enzymes, pumps, transporters, and channels.
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Affiliation(s)
- Roberto Docampo
- Department of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
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8
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Erkelens AM, van Erp B, Meijer WJJ, Dame RT. Rok from B. subtilis: Bridging genome structure and transcription regulation. Mol Microbiol 2024. [PMID: 38511404 DOI: 10.1111/mmi.15250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/02/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
Bacterial genomes are folded and organized into compact yet dynamic structures, called nucleoids. Nucleoid orchestration involves many factors at multiple length scales, such as nucleoid-associated proteins and liquid-liquid phase separation, and has to be compatible with replication and transcription. Possibly, genome organization plays an intrinsic role in transcription regulation, in addition to classical transcription factors. In this review, we provide arguments supporting this view using the Gram-positive bacterium Bacillus subtilis as a model. Proteins BsSMC, HBsu and Rok all impact the structure of the B. subtilis chromosome. Particularly for Rok, there is compelling evidence that it combines its structural function with a role as global gene regulator. Many studies describe either function of Rok, but rarely both are addressed at the same time. Here, we review both sides of the coin and integrate them into one model. Rok forms unusually stable DNA-DNA bridges and this ability likely underlies its repressive effect on transcription by either preventing RNA polymerase from binding to DNA or trapping it inside DNA loops. Partner proteins are needed to change or relieve Rok-mediated gene repression. Lastly, we investigate which features characterize H-NS-like proteins, a family that, at present, lacks a clear definition.
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Affiliation(s)
- Amanda M Erkelens
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, the Netherlands
| | - Bert van Erp
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, the Netherlands
| | - Wilfried J J Meijer
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Madrid, Spain
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, the Netherlands
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9
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Kuzminov A. Bacterial nucleoid is a riddle wrapped in a mystery inside an enigma. J Bacteriol 2024; 206:e0021123. [PMID: 38358278 PMCID: PMC10994824 DOI: 10.1128/jb.00211-23] [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] [Indexed: 02/16/2024] Open
Abstract
Bacterial chromosome, the nucleoid, is traditionally modeled as a rosette of DNA mega-loops, organized around proteinaceous central scaffold by nucleoid-associated proteins (NAPs), and mixed with the cytoplasm by transcription and translation. Electron microscopy of fixed cells confirms dispersal of the cloud-like nucleoid within the ribosome-filled cytoplasm. Here, I discuss evidence that the nucleoid in live cells forms DNA phase separate from riboprotein phase, the "riboid." I argue that the nucleoid-riboid interphase, where DNA interacts with NAPs, transcribing RNA polymerases, nascent transcripts, and ssRNA chaperones, forms the transcription zone. An active part of phase separation, transcription zone enforces segregation of the centrally positioned information phase (the nucleoid) from the surrounding action phase (the riboid), where translation happens, protein accumulates, and metabolism occurs. I speculate that HU NAP mostly tiles up the nucleoid periphery-facilitating DNA mobility but also supporting transcription in the interphase. Besides extruding plectonemically supercoiled DNA mega-loops, condensins could compact them into solenoids of uniform rings, while HU could support rigidity and rotation of these DNA rings. The two-phase cytoplasm arrangement allows the bacterial cell to organize the central dogma activities, where (from the cell center to its periphery) DNA replicates and segregates, DNA is transcribed, nascent mRNA is handed over to ribosomes, mRNA is translated into proteins, and finally, the used mRNA is recycled into nucleotides at the inner membrane. The resulting information-action conveyor, with one activity naturally leading to the next one, explains the efficiency of prokaryotic cell design-even though its main intracellular transportation mode is free diffusion.
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Affiliation(s)
- Andrei Kuzminov
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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10
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Monterroso B, Margolin W, Boersma AJ, Rivas G, Poolman B, Zorrilla S. Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions. Chem Rev 2024; 124:1899-1949. [PMID: 38331392 PMCID: PMC10906006 DOI: 10.1021/acs.chemrev.3c00622] [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: 08/31/2023] [Revised: 12/01/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.
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Affiliation(s)
- Begoña Monterroso
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - William Margolin
- Department
of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth-Houston, Houston, Texas 77030, United States
| | - Arnold J. Boersma
- Cellular
Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty
of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Germán Rivas
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - Bert Poolman
- Department
of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Silvia Zorrilla
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
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11
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Guan J, Jakob U. The Protein Scaffolding Functions of Polyphosphate. J Mol Biol 2024:168504. [PMID: 38423453 DOI: 10.1016/j.jmb.2024.168504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/31/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
Inorganic polyphosphate (polyP), one of the first high-energy compound on earth, defies its extreme compositional and structural simplicity with an astoundingly wide array of biological activities across all domains of life. However, the underlying mechanism of such functional pleiotropy remains largely elusive. In this review, we will summarize recent studies demonstrating that this simple polyanion stabilizes protein folding intermediates and scaffolds select native proteins. These functions allow polyP to act as molecular chaperone that protects cells against protein aggregation, as pro-amyloidogenic factor that accelerates both physiological and disease-associated amyloid formation, and as a modulator of liquid-liquid phase separation processes. These activities help to explain polyP's known roles in bacterial stress responses and pathogenicity, provide the mechanistic foundation for its potential role in human neurodegenerative diseases, and open a new direction regarding its influence on gene expression through condensate formation. We will highlight critical unanswered questions and point out potential directions that will help to further understand the pleiotropic functions of this ancient and ubiquitous biopolymer.
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Affiliation(s)
- Jian Guan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA; Biological Chemistry Department, University of Michigan Medical School, Ann Arbor, MI, USA.
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12
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Dai S, Xie Z, Wang B, Ye R, Ou X, Wang C, Yu N, Huang C, Zhao J, Cai C, Zhang F, Buratto D, Khan T, Qiao Y, Hua Y, Zhou R, Tian B. An inorganic mineral-based protocell with prebiotic radiation fitness. Nat Commun 2023; 14:7699. [PMID: 38052788 DOI: 10.1038/s41467-023-43272-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/06/2023] [Indexed: 12/07/2023] Open
Abstract
Protocell fitness under extreme prebiotic conditions is critical in understanding the origin of life. However, little is known about protocell's survival and fitness under prebiotic radiations. Here we present a radioresistant protocell model based on assembly of two types of coacervate droplets, which are formed through interactions of inorganic polyphosphate (polyP) with divalent metal cation and cationic tripeptide, respectively. Among the coacervate droplets, only the polyP-Mn droplet is radiotolerant and provides strong protection for recruited proteins. The radiosensitive polyP-tripeptide droplet sequestered with both proteins and DNA could be encapsulated inside the polyP-Mn droplet, and form into a compartmentalized protocell. The protocell protects the inner nucleoid-like condensate through efficient reactive oxygen species' scavenging capacity of intracellular nonenzymic antioxidants including Mn-phosphate and Mn-peptide. Our results demonstrate a radioresistant protocell model with redox reaction system in response to ionizing radiation, which might enable the protocell fitness to prebiotic radiation on the primitive Earth preceding the emergence of enzyme-based fitness. This protocell might also provide applications in synthetic biology as bioreactor or drug delivery system.
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Affiliation(s)
- Shang Dai
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
- Shanghai Institute for Advanced Study of Zhejiang University, Shanghai, China
| | - Zhenming Xie
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Binqiang Wang
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Rui Ye
- School of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou, China
| | - Xinwen Ou
- School of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou, China
| | - Chen Wang
- College of Pharmaceutical Science, Zhejiang University, Hangzhou, China
| | - Ning Yu
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Cheng Huang
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jie Zhao
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chunhui Cai
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Furong Zhang
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Damiano Buratto
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
- School of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou, China
| | - Taimoor Khan
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
- School of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou, China
| | - Yan Qiao
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.
| | - Yuejin Hua
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China.
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
| | - Ruhong Zhou
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China.
- Shanghai Institute for Advanced Study of Zhejiang University, Shanghai, China.
- School of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
| | - Bing Tian
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
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13
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Carnicer O, Hu YY, Ebenezer V, Irwin AJ, Finkel ZV. Genomic architecture constrains macromolecular allocation in dinoflagellates. Protist 2023; 174:125992. [PMID: 37738738 DOI: 10.1016/j.protis.2023.125992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/21/2023] [Accepted: 09/11/2023] [Indexed: 09/24/2023]
Abstract
Dinoflagellate genomes have a unique architecture that may constrain their physiological and biochemical responsiveness to environmental stressors. Here we quantified how nitrogen (N) starvation influenced macromolecular allocation and C:N:P of three photosynthetic marine dinoflagellates, representing different taxonomic classes and genome sizes. Dinoflagellates respond to nitrogen starvation by decreasing cellular nitrogen, protein and RNA content, but unlike many other eukaryotic phytoplankton examined RNA:protein is invariant. Additionally, 2 of the 3 species exhibit increases in cellular phosphorus and very little change in cellular carbon with N-starvation. As a consequence, N starvation induces moderate increases in C:N, but extreme decreases in N:P and C:P, relative to diatoms. Dinoflagellate DNA content relative to total C, N and P is much higher than similar sized diatoms, but similar to very small photosynthetic picoeukaryotes such as Ostreococcus. In aggregate these results indicate the accumulation of phosphate stores may be an important strategy employed by dinoflagellates to meet P requirements associated with the maintenance and replication of their large genomes.
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Affiliation(s)
- Olga Carnicer
- Department of Oceanography, Dalhousie University, Halifax, Canada
| | - Ying-Yu Hu
- Department of Oceanography, Dalhousie University, Halifax, Canada
| | - Vinitha Ebenezer
- Department of Oceanography, Dalhousie University, Halifax, Canada
| | - Andrew J Irwin
- Department of Mathematics & Statistics, Dalhousie University, Halifax, Canada
| | - Zoe V Finkel
- Department of Oceanography, Dalhousie University, Halifax, Canada.
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14
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Chawla R, Tom JKA, Boyd T, Grotjahn DA, Park D, Deniz AA, Racki LR. Reentrant DNA shells tune polyphosphate condensate size. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557044. [PMID: 37745474 PMCID: PMC10515899 DOI: 10.1101/2023.09.13.557044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The ancient, inorganic biopolymer polyphosphate (polyP) occurs in all three domains of life and affects myriad cellular processes. An intriguing feature of polyP is its frequent proximity to chromatin, and in the case of many bacteria, its occurrence in the form of magnesium-enriched condensates embedded in the nucleoid, particularly in response to stress. The physical basis of the interaction between polyP and DNA, two fundamental anionic biopolymers, and the resulting effects on the organization of both the nucleoid and polyP condensates remain poorly understood. Given the essential role of magnesium ions in the coordination of polymeric phosphate species, we hypothesized that a minimal system of polyP, magnesium ions, and DNA (polyP-Mg2+-DNA) would capture key features of the interplay between the condensates and bacterial chromatin. We find that DNA can profoundly affect polyP-Mg2+ coacervation even at concentrations several orders of magnitude lower than found in the cell. The DNA forms shells around polyP-Mg2+ condensates and these shells show reentrant behavior, primarily forming in the concentration range close to polyP-Mg2+ charge neutralization. This surface association tunes both condensate size and DNA morphology in a manner dependent on DNA properties, including length and concentration. Our work identifies three components that could form the basis of a central and tunable interaction hub that interfaces with cellular interactors. These studies will inform future efforts to understand the basis of polyP granule composition and consolidation, as well as the potential capacity of these mesoscale assemblies to remodel chromatin in response to diverse stressors at different length and time scales.
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Affiliation(s)
| | | | - Tumara Boyd
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Danielle A. Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Donghyun Park
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Ashok A. Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Lisa R. Racki
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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15
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Ortiz Camargo AR, van Mastrigt O, Bongers RS, Ben-Amor K, Knol J, Abee T, Smid EJ. Quantitative Physiology and Proteome Adaptations of Bifidobacterium breve NRBB57 at Near-Zero Growth Rates. Microbiol Spectr 2023; 11:e0256822. [PMID: 37184421 PMCID: PMC10269484 DOI: 10.1128/spectrum.02568-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 04/26/2023] [Indexed: 05/16/2023] Open
Abstract
In natural environments, nutrients are usually scarce, causing microorganisms to grow slowly while staying metabolically active. These natural conditions can be simulated using retentostat cultivations. The present study describes the physiological and proteome adaptations of the probiotic Bifidobacterium breve NRBB57 from high (0.4 h-1) to near-zero growth rates. Lactose-limited retentostat cultivations were carried out for 21 days in which the bacterial growth rate progressively reduced to 0.00092 h-1, leading to a 3.4-fold reduction of the maintenance energy requirement. Lactose was mainly converted into acetate, formate, and ethanol at high growth rates, while in the retentostat, lactate production increased. Interestingly, the consumption of several amino acids (serine, aspartic acid, and glutamine/arginine) and glycerol increased over time in the retentostat. Morphological changes and viable but nonculturable cells were also observed in the retentostat. Proteomes were compared for all growth rates, revealing a downregulation of ribosomal proteins at near-zero growth rates and an upregulation of proteins involved in the catabolism of alternative energy sources. Finally, we observed induction of the stringent response and stress defense systems. Retentostat cultivations were proven useful to study the physiology of B. breve, mimicking the nutrient scarcity of its complex habitat, the human gut. IMPORTANCE In natural environments, nutrients are usually scarce, causing microorganisms to grow slowly while staying metabolically active. In this study we used retentostat cultivation to investigate how the probiotic Bifidobacterium breve adapts its physiology and proteome under severe nutrient limitation resulting in near-zero growth rates (<0.001 h-1). We showed that the nutrient limitation induced a multifaceted response including stress defense and stringent response, metabolic shifts, and the activation of novel alternative energy-producing pathways.
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Affiliation(s)
| | - Oscar van Mastrigt
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | | | | | - Jan Knol
- Danone Nutricia Research, Utrecht, The Netherlands
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Eddy J. Smid
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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16
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Palmer M, Covington JK, Zhou EM, Thomas SC, Habib N, Seymour CO, Lai D, Johnston J, Hashimi A, Jiao JY, Muok AR, Liu L, Xian WD, Zhi XY, Li MM, Silva LP, Bowen BP, Louie K, Briegel A, Pett-Ridge J, Weber PK, Tocheva EI, Woyke T, Northen TR, Mayali X, Li WJ, Hedlund BP. Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past. THE ISME JOURNAL 2023:10.1038/s41396-023-01405-0. [PMID: 37041326 DOI: 10.1038/s41396-023-01405-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/13/2023]
Abstract
Although the phylum Chloroflexota is ubiquitous, its biology and evolution are poorly understood due to limited cultivability. Here, we isolated two motile, thermophilic bacteria from hot spring sediments belonging to the genus Tepidiforma and class Dehalococcoidia within the phylum Chloroflexota. A combination of cryo-electron tomography, exometabolomics, and cultivation experiments using stable isotopes of carbon revealed three unusual traits: flagellar motility, a peptidoglycan-containing cell envelope, and heterotrophic activity on aromatics and plant-associated compounds. Outside of this genus, flagellar motility has not been observed in Chloroflexota, and peptidoglycan-containing cell envelopes have not been described in Dehalococcoidia. Although these traits are unusual among cultivated Chloroflexota and Dehalococcoidia, ancestral character state reconstructions showed flagellar motility and peptidoglycan-containing cell envelopes were ancestral within the Dehalococcoidia, and subsequently lost prior to a major adaptive radiation of Dehalococcoidia into marine environments. However, despite the predominantly vertical evolutionary histories of flagellar motility and peptidoglycan biosynthesis, the evolution of enzymes for degradation of aromatics and plant-associated compounds was predominantly horizontal and complex. Together, the presence of these unusual traits in Dehalococcoidia and their evolutionary histories raise new questions about the timing and selective forces driving their successful niche expansion into global oceans.
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Affiliation(s)
- Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - Jonathan K Covington
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - En-Min Zhou
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
| | - Scott C Thomas
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Neeli Habib
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
- Department of Microbiology, Shaheed Benazir Bhutto Women University, Peshawar, Khyber Pakhtunkhwa (KPK), Pakistan
| | - Cale O Seymour
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Dengxun Lai
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Juliet Johnston
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Ameena Hashimi
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Alise R Muok
- Institute of Biology, Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Leslie P Silva
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Benjamin P Bowen
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katherine Louie
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ariane Briegel
- Institute of Biology, Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Tanja Woyke
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Trent R Northen
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
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17
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Genome-wide screen in human plasma identifies multifaceted complement evasion of Pseudomonas aeruginosa. PLoS Pathog 2023; 19:e1011023. [PMID: 36696456 PMCID: PMC9901815 DOI: 10.1371/journal.ppat.1011023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 02/06/2023] [Accepted: 11/23/2022] [Indexed: 01/26/2023] Open
Abstract
Pseudomonas aeruginosa, an opportunistic Gram-negative pathogen, is a leading cause of bacteremia with a high mortality rate. We recently reported that P. aeruginosa forms a persister-like sub-population of evaders in human plasma. Here, using a gain-of-function transposon sequencing (Tn-seq) screen in plasma, we identified and validated previously unknown factors affecting bacterial persistence in plasma. Among them, we identified a small periplasmic protein, named SrgA, whose expression leads to up to a 100-fold increase in resistance to killing. Additionally, mutants in pur and bio genes displayed higher tolerance and persistence, respectively. Analysis of several steps of the complement cascade and exposure to an outer-membrane-impermeable drug, nisin, suggested that the mutants impede membrane attack complex (MAC) activity per se. Electron microscopy combined with energy-dispersive X-ray spectroscopy (EDX) revealed the formation of polyphosphate (polyP) granules upon incubation in plasma of different size in purD and wild-type strains, implying the bacterial response to a stress signal. Indeed, inactivation of ppk genes encoding polyP-generating enzymes lead to significant elimination of persisting bacteria from plasma. Through this study, we shed light on a complex P. aeruginosa response to the plasma conditions and discovered the multifactorial origin of bacterial resilience to MAC-induced killing.
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18
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Shi X, Zarkan A. Bacterial survivors: evaluating the mechanisms of antibiotic persistence. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748698 DOI: 10.1099/mic.0.001266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacteria withstand antibiotic onslaughts by employing a variety of strategies, one of which is persistence. Persistence occurs in a bacterial population where a subpopulation of cells (persisters) survives antibiotic treatment and can regrow in a drug-free environment. Persisters may cause the recalcitrance of infectious diseases and can be a stepping stone to antibiotic resistance, so understanding persistence mechanisms is critical for therapeutic applications. However, current understanding of persistence is pervaded by paradoxes that stymie research progress, and many aspects of this cellular state remain elusive. In this review, we summarize the putative persister mechanisms, including toxin-antitoxin modules, quorum sensing, indole signalling and epigenetics, as well as the reasons behind the inconsistent body of evidence. We highlight present limitations in the field and underscore a clinical context that is frequently neglected, in the hope of supporting future researchers in examining clinically important persister mechanisms.
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Affiliation(s)
- Xiaoyi Shi
- Cambridge Centre for International Research, Cambridge CB4 0PZ, UK
| | - Ashraf Zarkan
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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19
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Cossa A, Trépout S, Wien F, Groen J, Le Brun E, Turbant F, Besse L, Pereiro E, Arluison V. Cryo soft X-ray tomography to explore Escherichia coli nucleoid remodeling by Hfq master regulator. J Struct Biol 2022; 214:107912. [PMID: 36283630 DOI: 10.1016/j.jsb.2022.107912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/28/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022]
Abstract
The bacterial chromosomic DNA is packed within a membrane-less structure, the nucleoid, due to the association of DNA with proteins called Nucleoid Associated Proteins (NAPs). Among these NAPs, Hfq is one of the most intriguing as it plays both direct and indirect roles on DNA structure. Indeed, Hfq is best known to mediate post-transcriptional regulation by using small noncoding RNA (sRNA). Although Hfq presence in the nucleoid has been demonstrated for years, its precise role is still unclear. Recently, it has been shown in vitro that Hfq forms amyloid-like structures through its C-terminal region, hence belonging to the bridging family of NAPs. Here, using cryo soft X-ray tomography imaging of native unlabeled cells and using a semi-automatic analysis and segmentation procedure, we show that Hfq significantly remodels the Escherichia coli nucleoid. More specifically, Hfq influences nucleoid density especially during the stationary growth phase when it is more abundant. Our results indicate that Hfq could regulate nucleoid compaction directly via its interaction with DNA, but also at the post-transcriptional level via its interaction with RNAs. Taken together, our findings reveal a new role for this protein in nucleoid remodeling in vivo, that may serve in response to stress conditions and in adapting to changing environments.
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Affiliation(s)
- Antoine Cossa
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France; Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Sylvain Trépout
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France; Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Victoria 3800, Australia.
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
| | - Johannes Groen
- Mistral Beamline, Alba Light Source, Cerdanyola del Valles, 08290 Barcelona, Spain
| | - Etienne Le Brun
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France; Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Laetitia Besse
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France
| | - Eva Pereiro
- Mistral Beamline, Alba Light Source, Cerdanyola del Valles, 08290 Barcelona, Spain
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France; Université Paris Cité, UFR Sciences du vivant, 75006 Paris cedex, France.
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20
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Wang J, Tao Y, Juan Y, Zhou H, Zhao X, Cheng X, Wang X, Quan X, Li J, Huang K, Wei W, Zhao J. Hierarchical Assembly of Flexible Biopolymer Polyphosphate-Manganese into Nanosheets. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2203200. [PMID: 36084167 DOI: 10.1002/smll.202203200] [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: 05/28/2022] [Revised: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Polyphosphate (polyP) is one of the most compact inorganic polyanionic biopolymers that participates in various physiological processes. However, the development of polyP-based nanomaterials is still in its infancy. Here, biocompatible polyphosphate-manganese nanosheets are designed and synthesized by a hierarchical assembly strategy. The thickness and the lateral size of the resulting polyP-Mn nanosheets (PMNSs) are 5 nm and 120-130 nm, respectively. Molecular dynamics simulations suggested that the polyP-hexadecyl trimethyl ammonium bromide flat structure possesses a strong aggregating capacity and serves as the template for the 2D assembly of polyP-Mn. The PMNSs can activate the inflammatory response of macrophages resulting in the recovery of innate immunological functions to inhibit tumor proliferation. This work has initiated a new direction in constructing layered polyP-based nanomaterials and provides guidance for biocompatible and biodegradable biopolymer-based materials in the regulation of innate responses.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210008, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210008, China
| | - Yucheng Tao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210008, China
| | - Yewen Juan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210008, China
| | - Hang Zhou
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210008, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210008, China
| | - Xinyang Zhao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210008, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210008, China
| | - Xiaomei Cheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210008, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210008, China
| | - Xiuxiu Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210008, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210008, China
| | - Xuebo Quan
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518067, China
| | - Junyan Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518067, China
| | - Kai Huang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518067, China
| | - Wei Wei
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210008, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210008, China
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210008, China
- Shenzhen Research Institute, Nanjing University, Shenzhen, 518057, China
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210008, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210008, China
- Shenzhen Research Institute, Nanjing University, Shenzhen, 518057, China
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21
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Moon SJ, Hwang J, Kang WK, Ahn JP, Kim HJ. Administration of the probiotic Lactiplantibacillus paraplantarum is effective in controlling hyperphosphatemia in 5/6 nephrectomy rat model. Life Sci 2022; 306:120856. [PMID: 35926592 DOI: 10.1016/j.lfs.2022.120856] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/20/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022]
Abstract
AIMS Several studies have linked gut microbes to human diseases. Most of the mechanisms by which lactic acid bacteria have beneficial effects on the human body are related to immune modulation. Controlled studies of the ability of lactic acid bacteria to absorb phosphorus directly from the intestine and thereby control serum phosphorus level in in vivo uremic animal models are limited. MATERIALS AND METHODS We screened lactic acid bacteria living in Korean fermented foods to identify those that absorb the most phosphorus and noted Lactiplantibacillus paraplantarum KCCM 11826P. The mechanism through which better intracellular absorption of phosphorus occurs in this strain was studied using genomic DNA sequencing. After the strain was administered to 5/6 nephrectomized rats for 6 weeks, it was observed whether hyperphosphatemia had improved. KEY FINDINGS The L. paraplantarum KCCM 11826P strain has a polyP gene cluster; thus, it absorbs phosphorus better than other bacteria and can suppress strains that produce indole. Supplementing the diets of 5/6 nephrectomized rats with this L. paraplantarum strain significantly decreased serum phosphate level (by 22 %) and reduced blood indoxyl sulphate concentration (by 40 %) compared with vehicle treatment. SIGNIFICANCE These results suggest that Lactiplantibacillus preparations can be used for multiple purposes, such as the removal of phosphorus and uremic toxins from patients with chronic kidney disease (CKD). This study also demonstrates the novel concept of a probiotic phosphate binder.
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Affiliation(s)
- Sung Jin Moon
- Department of Internal Medicine, International St. Mary's Hospital, Catholic Kwandong University, Incheon, Republic of Korea.
| | - Junsang Hwang
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Republic of Korea; Institute for Food Industrialization, Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
| | - Woo Kyung Kang
- Institute for Food Industrialization, Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
| | - Jeong-Pin Ahn
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Republic of Korea; Institute for Food Industrialization, Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Republic of Korea
| | - Hyo Jin Kim
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Republic of Korea; Institute for Food Industrialization, Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Republic of Korea.
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22
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Bacterial Membrane Vesicles as a Novel Strategy for Extrusion of Antimicrobial Bismuth Drug in Helicobacter pylori. mBio 2022; 13:e0163322. [PMID: 36154274 PMCID: PMC9601102 DOI: 10.1128/mbio.01633-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacterial antibiotic resistance is a major threat to human health. A combination of antibiotics with metals is among the proposed alternative treatments. Only one such combination is successfully used in clinics; it associates antibiotics with the metal bismuth to treat infections by Helicobacter pylori. This bacterial pathogen colonizes the human stomach and is associated with gastric cancer, killing 800,000 individuals yearly. The effect of bismuth in H. pylori treatment is not well understood in particular for sublethal doses such as those measured in the plasma of treated patients. We addressed this question and observed that bismuth induces the formation of homogeneously sized membrane vesicles (MVs) with unique protein cargo content enriched in bismuth-binding proteins, as shown by quantitative proteomics. Purified MVs of bismuth-exposed bacteria were strongly enriched in bismuth as measured by inductively coupled plasma optical emission spectrometry (ICP-OES), unlike bacterial cells from which they originate. Thus, our results revealed a novel function of MVs in bismuth detoxification, where secreted MVs act as tool to discard bismuth from the bacteria. Bismuth also induces the formation of intracellular polyphosphate granules that are associated with changes in nucleoid structure. Nucleoid compaction in response to bismuth was established by immunogold electron microscopy and refined by the first chromosome conformation capture (Hi-C) analysis of H. pylori. Our results reveal that even low doses of bismuth induce profound changes in H. pylori physiology and highlight a novel defense mechanism that involves MV-mediated bismuth extrusion from the bacteria and a probable local DNA protective response where polyphosphate granules are associated with nucleoid compaction.
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Wan J, Monteil CL, Taoka A, Ernie G, Park K, Amor M, Taylor-Cornejo E, Lefevre CT, Komeili A. McaA and McaB control the dynamic positioning of a bacterial magnetic organelle. Nat Commun 2022; 13:5652. [PMID: 36163114 PMCID: PMC9512821 DOI: 10.1038/s41467-022-32914-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Magnetotactic bacteria are a diverse group of microorganisms that use intracellular chains of ferrimagnetic nanocrystals, produced within magnetosome organelles, to align and navigate along the geomagnetic field. Several conserved genes for magnetosome formation have been described, but the mechanisms leading to distinct species-specific magnetosome chain configurations remain unclear. Here, we show that the fragmented nature of magnetosome chains in Magnetospirillum magneticum AMB-1 is controlled by genes mcaA and mcaB. McaA recognizes the positive curvature of the inner cell membrane, while McaB localizes to magnetosomes. Along with the MamK actin-like cytoskeleton, McaA and McaB create space for addition of new magnetosomes in between pre-existing magnetosomes. Phylogenetic analyses suggest that McaA and McaB homologs are widespread among magnetotactic bacteria and may represent an ancient strategy for magnetosome positioning.
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Affiliation(s)
- Juan Wan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Caroline L Monteil
- Aix-Marseille Université, CEA, CNRS, Institute of Biosciences and Biotechnologies of Aix-Marseille, 13108, Saint-Paul-lez-Durance, France
| | - Azuma Taoka
- Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Gabriel Ernie
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Kieop Park
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA
| | - Matthieu Amor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Aix-Marseille Université, CEA, CNRS, Institute of Biosciences and Biotechnologies of Aix-Marseille, 13108, Saint-Paul-lez-Durance, France
| | - Elias Taylor-Cornejo
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Department of Biology, Randolph-Macon College, Ashland, VA, 23005, USA
| | - Christopher T Lefevre
- Aix-Marseille Université, CEA, CNRS, Institute of Biosciences and Biotechnologies of Aix-Marseille, 13108, Saint-Paul-lez-Durance, France
| | - Arash Komeili
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
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24
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Getting Closer to Decrypting the Phase Transitions of Bacterial Biomolecules. Biomolecules 2022; 12:biom12070907. [PMID: 35883463 PMCID: PMC9312465 DOI: 10.3390/biom12070907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/24/2022] [Accepted: 06/26/2022] [Indexed: 12/31/2022] Open
Abstract
Liquid–liquid phase separation (LLPS) of biomolecules has emerged as a new paradigm in cell biology, and the process is one proposed mechanism for the formation of membraneless organelles (MLOs). Bacterial cells have only recently drawn strong interest in terms of studies on both liquid-to-liquid and liquid-to-solid phase transitions. It seems that these processes drive the formation of prokaryotic cellular condensates that resemble eukaryotic MLOs. In this review, we present an overview of the key microbial biomolecules that undergo LLPS, as well as the formation and organization of biomacromolecular condensates within the intracellular space. We also discuss the current challenges in investigating bacterial biomacromolecular condensates. Additionally, we highlight a summary of recent knowledge about the participation of bacterial biomolecules in a phase transition and provide some new in silico analyses that can be helpful for further investigations.
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25
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The Histone H1-Like Protein AlgP Facilitates Even Spacing of Polyphosphate Granules in Pseudomonas aeruginosa. mBio 2022; 13:e0246321. [PMID: 35435704 PMCID: PMC9239181 DOI: 10.1128/mbio.02463-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Synthesis of polyphosphate (polyP) is an ancient and universal stress and starvation response in bacteria. In many bacteria, polyP chains come together to form granular superstructures within cells. Some species appear to regulate polyP granule subcellular organization. Despite the critical role of polyP in starvation fitness, the composition of these structures, mechanism(s) underpinning their organization, and functional significance of such organization are poorly understood. We previously determined that granules become transiently evenly spaced on the cell’s long axis during nitrogen starvation in the opportunistic human pathogen Pseudomonas aeruginosa. Here, we developed a granule-enrichment protocol to screen for polyP granule-localizing proteins. We identified AlgP as a protein that associates with polyP granules. We further discovered that AlgP is required for the even spacing of polyP granules. AlgP is a DNA-binding protein with a 154 amino acid C-terminal domain enriched in “KPAA” repeats and variants of this repeat, with an overall sequence composition similar to the C-terminal tail of eukaryotic histone H1. Granule size, number, and spacing are significantly perturbed in the absence of AlgP, or when AlgP is truncated to remove the C-terminus. The ΔalgP and algPΔCTD mutants have fewer, larger granules. We speculate that AlgP may contribute to spacing by tethering polyP granules to the chromosome, thereby inhibiting fusion with neighboring granules. Our discovery that AlgP facilitates granule spacing allows us for the first time to directly uncouple granule biogenesis from even spacing, and will inform future efforts to explore the functional significance of granule organization on fitness during starvation.
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Bowlin MQ, Long AR, Huffines JT, Gray MJ. The role of nitrogen-responsive regulators in controlling inorganic polyphosphate synthesis in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001185. [PMID: 35482529 PMCID: PMC10233264 DOI: 10.1099/mic.0.001185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/10/2022] [Indexed: 12/22/2022]
Abstract
Inorganic polyphosphate (polyP) is synthesized by bacteria under stressful environmental conditions and acts by a variety of mechanisms to promote cell survival. While the kinase that synthesizes polyP (PPK, encoded by the ppk gene) is well known, ppk transcription is not activated by environmental stress and little is understood about how environmental stress signals lead to polyP accumulation. Previous work has shown that the transcriptional regulators DksA, RpoN (σ54) and RpoE (σ24) positively regulate polyP production, but not ppk transcription, in Escherichia coli. In this work, we examine the role of the alternative sigma factor RpoN and nitrogen starvation stress response pathways in controlling polyP synthesis. We show that the RpoN enhancer binding proteins GlnG and GlrR impact polyP production, and uncover a new role for the nitrogen phosphotransferase regulator PtsN (EIIANtr) as a positive regulator of polyP production, acting upstream of DksA, downstream of RpoN and apparently independently of RpoE. However, neither these regulatory proteins nor common nitrogen metabolites appear to act directly on PPK, and the precise mechanism(s) by which polyP production is modulated after stress remain(s) unclear. Unexpectedly, we also found that the genes that impact polyP production vary depending on the composition of the rich media in which the cells were grown before exposure to polyP-inducing stress. These results constitute progress towards deciphering the regulatory networks driving polyP production under stress, and highlight the remarkable complexity of this regulation and its connections to a broad range of stress-sensing pathways.
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Affiliation(s)
- Marvin Q. Bowlin
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Abagail Renee Long
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Joshua T. Huffines
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michael Jeffrey Gray
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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27
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Frank C, Pfeiffer D, Aktas M, Jendrossek D. Migration of Polyphosphate Granules in Agrobacterium tumefaciens. Microb Physiol 2022; 32:71-82. [PMID: 35168233 DOI: 10.1159/000521970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/12/2022] [Indexed: 01/29/2023]
Abstract
Agrobacterium tumefaciens has two polyphosphate (polyP) kinases, one of which (PPK1AT) is responsible for the formation of polyP granules, while the other (PPK2AT) is used for replenishing the NTP pools by using polyP as a phosphate donor to phosphorylate nucleoside diphosphates. Fusions of eYFP with PPK2AT or of the polyP granule-associated phosin PptA from Ralstonia eutropha always co-localized with polyP granules in A. tumefaciens and allowed the tracking of polyP granules in time-lapse microscopy experiments without the necessity to label the cells with the toxic dye DAPI. Fusions of PPK1AT with mCherry formed fluorescent signals often attached to, but not completely co-localizing with, polyP granules in wild-type cells. Time-lapse microscopy revealed that polyP granules in about one-third of a cell population migrated from the old pole to the new cell pole shortly before or during cell division. Many cells de novo formed a second (nonmigrating) polyP granule at the opposite cell pole before cell division was completed, resulting in two daughter cells each having a polyP granule at the old pole after septum formation. Migration of polyP granules was disordered in mitomycin C-treated or in PopZ-depleted cells, suggesting that polyP granules can associate with DNA or with other molecules that are segregated during the cell cycle.
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Affiliation(s)
- Celina Frank
- Institute of Microbiology, University of Stuttgart, Stuttgart, Germany
| | - Daniel Pfeiffer
- Department of Microbiology, University Bayreuth, Bayreuth, Germany
| | - Meriyem Aktas
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Dieter Jendrossek
- Institute of Microbiology, University of Stuttgart, Stuttgart, Germany
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28
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Neville N, Roberge N, Jia Z. Polyphosphate Kinase 2 (PPK2) Enzymes: Structure, Function, and Roles in Bacterial Physiology and Virulence. Int J Mol Sci 2022; 23:ijms23020670. [PMID: 35054854 PMCID: PMC8776046 DOI: 10.3390/ijms23020670] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 01/27/2023] Open
Abstract
Inorganic polyphosphate (polyP) has been implicated in an astonishing array of biological functions, ranging from phosphorus storage to molecular chaperone activity to bacterial virulence. In bacteria, polyP is synthesized by polyphosphate kinase (PPK) enzymes, which are broadly subdivided into two families: PPK1 and PPK2. While both enzyme families are capable of catalyzing polyP synthesis, PPK1s preferentially synthesize polyP from nucleoside triphosphates, and PPK2s preferentially consume polyP to phosphorylate nucleoside mono- or diphosphates. Importantly, many pathogenic bacteria such as Pseudomonas aeruginosa and Acinetobacter baumannii encode at least one of each PPK1 and PPK2, suggesting these enzymes may be attractive targets for antibacterial drugs. Although the majority of bacterial polyP studies to date have focused on PPK1s, PPK2 enzymes have also begun to emerge as important regulators of bacterial physiology and downstream virulence. In this review, we specifically examine the contributions of PPK2s to bacterial polyP homeostasis. Beginning with a survey of the structures and functions of biochemically characterized PPK2s, we summarize the roles of PPK2s in the bacterial cell, with a particular emphasis on virulence phenotypes. Furthermore, we outline recent progress on developing drugs that inhibit PPK2 enzymes and discuss this strategy as a novel means of combatting bacterial infections.
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29
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Karasz DC, Weaver AI, Buckley DH, Wilhelm RC. Conditional filamentation as an adaptive trait of bacteria and its ecological significance in soils. Environ Microbiol 2021; 24:1-17. [PMID: 34929753 DOI: 10.1111/1462-2920.15871] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/30/2022]
Abstract
Bacteria can regulate cell morphology in response to environmental conditions, altering their physiological and metabolic characteristics to improve survival. Conditional filamentation, in which cells suspend division while continuing lateral growth, is a strategy with a range of adaptive benefits. Here, we review the causes and consequences of conditional filamentation with respect to bacterial physiology, ecology and evolution. We describe four major benefits from conditional filamentation: stress tolerance, surface colonization, gradient spanning and the facilitation of biotic interactions. Adopting a filamentous growth habit involves fitness trade-offs which are also examined. We focus on the role of conditional filamentation in soil habitats, where filamentous morphotypes are highly prevalent and where environmental heterogeneity can benefit a conditional response. To illustrate the use of information presented in our review, we tested the conditions regulating filamentation by the forest soil isolate Paraburkholderia elongata 5NT . Filamentation by P. elongata was induced at elevated phosphate concentrations, and was associated with the accumulation of intracellular polyphosphate, highlighting the role of filamentation in a phosphate-solubilizing bacterium. Conditional filamentation enables bacteria to optimize their growth and metabolism in environments that are highly variable, a trait that can impact succession, symbioses, and biogeochemistry in soil environments.
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Affiliation(s)
- David C Karasz
- School of Integrative Plant Science, Bradfield Hall, Cornell University, Ithaca, New York, 14853, USA
| | - Anna I Weaver
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, New York, 14853, USA.,Weill Institute for Cell and Molecular Biology, Weill Hall, Cornell University, Ithaca, New York, 14853, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Bradfield Hall, Cornell University, Ithaca, New York, 14853, USA
| | - Roland C Wilhelm
- School of Integrative Plant Science, Bradfield Hall, Cornell University, Ithaca, New York, 14853, USA
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30
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Roberge N, Neville N, Douchant K, Noordhof C, Boev N, Sjaarda C, Sheth PM, Jia Z. Broad-Spectrum Inhibitor of Bacterial Polyphosphate Homeostasis Attenuates Virulence Factors and Helps Reveal Novel Physiology of Klebsiella pneumoniae and Acinetobacter baumannii. Front Microbiol 2021; 12:764733. [PMID: 34764949 PMCID: PMC8576328 DOI: 10.3389/fmicb.2021.764733] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/04/2021] [Indexed: 12/26/2022] Open
Abstract
Acinetobacter baumannii and Klebsiella pneumoniae currently rank amongst the most antibiotic-resistant pathogens, responsible for millions of infections each year. In the wake of this crisis, anti-virulence therapeutics targeting bacterial polyphosphate (polyP) homeostasis have been lauded as an attractive alternative to traditional antibiotics. In this work, we show that the small molecule gallein, a known G-protein βγ subunit modulator, also recently proven to have dual-specificity polyphosphate kinase (PPK) inhibition in Pseudomonas aeruginosa, in turn exhibits broad-spectrum PPK inhibition in other priority pathogens. Gallein treatment successfully attenuated virulence factors of K. pneumoniae and A. baumannii including biofilm formation, surface associated motility, and offered protection against A. baumannii challenge in a Caenorhabditis elegans model of infection. This was highlighted most importantly in the critically understudied A. baumannii, where gallein treatment phenocopied a ppk1 knockout strain of a previously uncharacterized PPK1. Subsequent analysis revealed a unique instance of two functionally and phenotypically distinct PPK1 isoforms encoded by a single bacterium. Finally, gallein was administered to a defined microbial community comprising over 30 commensal species of the human gut microbiome, demonstrating the non-disruptive properties characteristic of anti-virulence treatments as microbial biodiversity was not adversely influenced. Together, these results emphasize that gallein is a promising avenue for the development of broad-spectrum anti-virulence therapeutics.
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Affiliation(s)
- Nathan Roberge
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Nolan Neville
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Katya Douchant
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada.,Gastrointestinal Disease Research Unit (GIDRU), Department of Medicine, Queen's University, Kingston, ON, Canada
| | - Curtis Noordhof
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada.,Gastrointestinal Disease Research Unit (GIDRU), Department of Medicine, Queen's University, Kingston, ON, Canada
| | - Nadejda Boev
- Queen's Genomics Lab at Ongwanada (Q-GLO), Ongwanada Resource Center, Kingston, ON, Canada
| | - Calvin Sjaarda
- Queen's Genomics Lab at Ongwanada (Q-GLO), Ongwanada Resource Center, Kingston, ON, Canada.,Department of Psychiatry, Queen's University, Kingston, ON, Canada
| | - Prameet M Sheth
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada.,Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada.,Gastrointestinal Disease Research Unit (GIDRU), Department of Medicine, Queen's University, Kingston, ON, Canada.,Division of Microbiology, Kingston Health Science Center, Kingston, ON, Canada
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
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31
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Gao Z, Zhang W, Chang R, Zhang S, Yang G, Zhao G. Liquid-Liquid Phase Separation: Unraveling the Enigma of Biomolecular Condensates in Microbial Cells. Front Microbiol 2021; 12:751880. [PMID: 34759902 PMCID: PMC8573418 DOI: 10.3389/fmicb.2021.751880] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/06/2021] [Indexed: 12/12/2022] Open
Abstract
Numerous examples of microbial phase-separated biomolecular condensates have now been identified following advances in fluorescence imaging and single molecule microscopy technologies. The structure, function, and potential applications of these microbial condensates are currently receiving a great deal of attention. By neatly compartmentalizing proteins and their interactors in membrane-less organizations while maintaining free communication between these macromolecules and the external environment, microbial cells are able to achieve enhanced metabolic efficiency. Typically, these condensates also possess the ability to rapidly adapt to internal and external changes. The biological functions of several phase-separated condensates in small bacterial cells show evolutionary convergence with the biological functions of their eukaryotic paralogs. Artificial microbial membrane-less organelles are being constructed with application prospects in biocatalysis, biosynthesis, and biomedicine. In this review, we provide an overview of currently known biomolecular condensates driven by liquid-liquid phase separation (LLPS) in microbial cells, and we elaborate on their biogenesis mechanisms and biological functions. Additionally, we highlight the major challenges and future research prospects in studying microbial LLPS.
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Affiliation(s)
| | | | | | | | - Guiwen Yang
- College of Life Science, Shandong Normal University, Jinan, China
| | - Guoyan Zhao
- College of Life Science, Shandong Normal University, Jinan, China
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32
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Abstract
Polyphosphate (polyP) is a universally conserved molecule that plays critical roles in managing bacterial stress responses, in addition to biofilm formation and virulence. The enzymes that make polyphosphate molecules are called polyphosphate kinases (PPKs). Since these enzymes are not conserved in higher eukaryotes, PPKs make excellent therapeutic targets. In a recent paper in mBio, Neville and colleagues described gallein, a commercially available G-protein antagonist, as a novel dual-specificity inhibitor against two families of PPK enzymes in Pseudomonas aeruginosa. In this commentary, we discuss the impact of this discovery, outline potential challenges of implementing gallein use in the clinic, and describe how gallein will serve as a fantastic new tool to further fundamental PPK and polyP research in bacteria.
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33
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Xiang Y, Surovtsev IV, Chang Y, Govers SK, Parry BR, Liu J, Jacobs-Wagner C. Interconnecting solvent quality, transcription, and chromosome folding in Escherichia coli. Cell 2021; 184:3626-3642.e14. [PMID: 34186018 DOI: 10.1016/j.cell.2021.05.037] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/09/2020] [Accepted: 05/25/2021] [Indexed: 12/12/2022]
Abstract
All cells fold their genomes, including bacterial cells, where the chromosome is compacted into a domain-organized meshwork called the nucleoid. How compaction and domain organization arise is not fully understood. Here, we describe a method to estimate the average mesh size of the nucleoid in Escherichia coli. Using nucleoid mesh size and DNA concentration estimates, we find that the cytoplasm behaves as a poor solvent for the chromosome when the cell is considered as a simple semidilute polymer solution. Monte Carlo simulations suggest that a poor solvent leads to chromosome compaction and DNA density heterogeneity (i.e., domain formation) at physiological DNA concentration. Fluorescence microscopy reveals that the heterogeneous DNA density negatively correlates with ribosome density within the nucleoid, consistent with cryoelectron tomography data. Drug experiments, together with past observations, suggest the hypothesis that RNAs contribute to the poor solvent effects, connecting chromosome compaction and domain formation to transcription and intracellular organization.
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Affiliation(s)
- Yingjie Xiang
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, CT 06520, USA; Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
| | - Ivan V Surovtsev
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Yunjie Chang
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sander K Govers
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA; Department of Biology and Institute of Chemistry, Engineering and Medicine for Human Health, Stanford University, Palo Alto, CA 94305, USA
| | - Bradley R Parry
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Jun Liu
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA; Department of Biology and Institute of Chemistry, Engineering and Medicine for Human Health, Stanford University, Palo Alto, CA 94305, USA.
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34
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A Dual-Specificity Inhibitor Targets Polyphosphate Kinase 1 and 2 Enzymes To Attenuate Virulence of Pseudomonas aeruginosa. mBio 2021; 12:e0059221. [PMID: 34126765 PMCID: PMC8262977 DOI: 10.1128/mbio.00592-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa is a leading cause of nosocomial infections, which are becoming increasingly difficult to treat due to antibiotic resistance. Polyphosphate (polyP) plays a key role in P. aeruginosa virulence, stress response, and antibiotic tolerance, suggesting an attractive drug target. Here, we show that the small molecule gallein disrupts polyphosphate homeostasis by inhibiting all members of both polyphosphate kinase (PPK) families (PPK1 and PPK2) encoded by P. aeruginosa, demonstrating dual-specificity PPK inhibition for the first time. Inhibitor treatment phenocopied ppk deletion to reduce cellular polyP accumulation and attenuate biofilm formation, motility, and pyoverdine and pyocyanin production. Most importantly, gallein attenuated P. aeruginosa virulence in a Caenorhabditis elegans infection model and synergized with antibiotics while exhibiting negligible toxicity toward the nematodes or HEK293T cells, suggesting our discovery of dual-specificity PPK inhibitors as a promising starting point for the development of new antivirulence therapeutics.
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35
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Rosigkeit H, Kneißle L, Obruča S, Jendrossek D. The Multiple Roles of Polyphosphate in Ralstonia eutropha and Other Bacteria. Microb Physiol 2021; 31:163-177. [PMID: 34015783 DOI: 10.1159/000515741] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/06/2021] [Indexed: 11/19/2022]
Abstract
An astonishing variety of functions has been attributed to polyphosphate (polyP) in prokaryotes. Besides being a reservoir of phosphorus, functions in exopolysaccharide formation, motility, virulence and in surviving various forms of stresses such as exposure to heat, extreme pH, oxidative agents, high osmolarity, heavy metals and others have been ascribed to polyP. In this contribution, we will provide a historical overview on polyP, will then describe the key proteins of polyP synthesis, the polyP kinases, before we will critically assess of the underlying data on the multiple functions of polyP and provide evidence that - with the exception of a P-storage-function - most other functions of polyP are not relevant for survival of Ralstonia eutropha, a biotechnologically important beta-proteobacterial species.
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Affiliation(s)
- Hanna Rosigkeit
- Institute of Microbiology, University of Stuttgart, Stuttgart, Germany
| | - Lea Kneißle
- Institute of Microbiology, University of Stuttgart, Stuttgart, Germany
| | - Stanislav Obruča
- Faculty of Chemistry, Brno University of Technology, Brno, Czechia
| | - Dieter Jendrossek
- Institute of Microbiology, University of Stuttgart, Stuttgart, Germany
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Di Caprio F. A fattening factor to quantify the accumulation ability of microorganisms under N-starvation. N Biotechnol 2021; 66:70-78. [PMID: 33862285 DOI: 10.1016/j.nbt.2021.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 04/06/2021] [Accepted: 04/10/2021] [Indexed: 01/04/2023]
Abstract
Many microorganisms can accumulate biomass in the form of lipids and polysaccharides, which can be used for biofuels, bioplastics, food and feed. Some innovative bioprocesses exploit the competitive advantage provided by such accumulation ability, mainly under N-starvation, to select high-accumulating strains against biological contaminants, by using uncoupled nutrient feeding. However, there is no general and easily comparable parameter available to compare biomass accumulation ability among different microbial strains, which could measure the competitive advantage. Here, a parameter termed "fattening factor" (ηx) is described to quantify such strain-specific biomass accumulation ability in bacteria, yeasts and microalgae. This parameter measures how many fold a microbial population can increase its biomass just as the result of accumulation. It is derived from considerations about the main metabolic aspects of cells' response to N-starvation, which induces variations in cell cycle, biomass production and biochemical composition. The fattening factor described here should be easily estimatable in N-starvation for every culturable microbial strain, by measuring the amount of accumulated biomass.
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Affiliation(s)
- Fabrizio Di Caprio
- Department of Chemistry, University Sapienza of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy.
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Di Caprio F. Cultivation processes to select microorganisms with high accumulation ability. Biotechnol Adv 2021; 49:107740. [PMID: 33838283 DOI: 10.1016/j.biotechadv.2021.107740] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/26/2021] [Accepted: 03/26/2021] [Indexed: 10/21/2022]
Abstract
The microbial ability to accumulate biomolecules is fundamental for different biotechnological applications aiming at the production of biofuels, food and bioplastics. However, high accumulation is a selective advantage only under certain stressful conditions, such as nutrient depletion, characterized by lower growth rate. Conventional bioprocesses maintain an optimal and stable environment for large part of the cultivation, that doesn't reward cells for their accumulation ability, raising the risk of selection of contaminant strains with higher growth rate, but lower accumulation of products. Here in this work the physiological responses of different microorganisms (microalgae, bacteria, yeasts) under N-starvation and energy starvation are reviewed, with the aim to furnish relevant insights exploitable to develop tailored bioprocesses to select specific strains for their higher accumulation ability. Microorganism responses to starvation are reviewed focusing on cell cycle, biomass production and variations in biochemical composition. Then, the work describes different innovative bioprocess configurations exploiting uncoupled nutrient feeding strategies (feast-famine), tailored to maintain a selective pressure to reward the strains with higher accumulation ability in mixed microbial populations. Finally, the main models developed in recent studies to describe and predict microbial growth and intracellular accumulation upon N-starvation and feast-famine conditions have been reviewed.
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Affiliation(s)
- Fabrizio Di Caprio
- Department of Chemistry, University Sapienza of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
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Azaldegui CA, Vecchiarelli AG, Biteen JS. The emergence of phase separation as an organizing principle in bacteria. Biophys J 2021; 120:1123-1138. [PMID: 33186556 PMCID: PMC8059088 DOI: 10.1016/j.bpj.2020.09.023] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
Recent investigations in bacteria suggest that membraneless organelles play a crucial role in the subcellular organization of bacterial cells. However, the biochemical functions and assembly mechanisms of these compartments have not yet been completely characterized. This article assesses the current methodologies used in the study of membraneless organelles in bacteria, highlights the limitations in determining the phase of complexes in cells that are typically an order of magnitude smaller than a eukaryotic cell, and identifies gaps in our current knowledge about the functional role of membraneless organelles in bacteria. Liquid-liquid phase separation (LLPS) is one proposed mechanism for membraneless organelle assembly. Overall, we outline the framework to evaluate LLPS in vivo in bacteria, we describe the bacterial systems with proposed LLPS activity, and we comment on the general role LLPS plays in bacteria and how it may regulate cellular function. Lastly, we provide an outlook for super-resolution microscopy and single-molecule tracking as tools to assess condensates in bacteria.
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Affiliation(s)
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan.
| | - Julie S Biteen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan.
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Dynamic Polyphosphate Metabolism Coordinating with Manganese Ions Defends against Oxidative Stress in the Extreme Bacterium Deinococcus radiodurans. Appl Environ Microbiol 2021; 87:AEM.02785-20. [PMID: 33452031 DOI: 10.1128/aem.02785-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/08/2021] [Indexed: 02/05/2023] Open
Abstract
Deinococcus radiodurans is an extreme bacterium with unparalleled resistance to oxidative stresses. Accumulation of intracellular Mn2+ complexing with small metabolites is the key contributor to the tolerance of D. radiodurans against oxidative stress. However, the intracellular reservoir of Mn ions and homeostatic regulation of the Mn complex in D. radiodurans remain unclear. We identified an evolutionarily ancient and negatively charged phosphate polymer (polyphosphate [PolyP]) in D. radiodurans We investigated PolyP metabolism in the response of D. radiodurans to oxidative stress. The genes dr1939, encoding polyphosphatase kinase (PPKDr; the subscript "Dr" refers to D. radiodurans), and dra0185, encoding exopolyphosphatase (PPXDr), were identified. PPXDr is a novel exopolyphosphatase with a cofactor preference to Mn2+, which enhances the dimerization and activity of PPXDr to allow the effective cleavage of PolyP-Mn. PPKDr and PPXDr exhibited different dynamic expression profiles under oxidative stress. First, ppkDr was upregulated leading to the accumulation of PolyP, which chelated large amounts of intracellular Mn ions. Subsequently, the expression level of ppkDr decreased while ppxDr was substantially upregulated and effectively hydrolyzed inactive PolyP-Mn to release phosphate (Pi) and Mn2+, which could form into Mn-Pi complexes to scavenge O2 - and protect proteins from oxidative damage. Hence, dynamic cellular PolyP metabolites complexed with free Mn ions highlight a defense strategy of D. radiodurans in response to oxidative stress.IMPORTANCE The Mn-phosphate complex (Mn-Pi) plays a key role in the cellular resistance of radioresistant bacteria. The evolutionarily ancient polyphosphate polymers (polyphosphate [PolyP]) could effectively chelate Mn2+ and donate phosphates. However, the intracellular reservoir of Mn ions and homeostatic regulation of the Mn-Pi complex remain unclear. Here, we investigated the relationship of PolyP metabolites and Mn2+ homeostasis and how they function to defend against oxidative stress in the radioresistant bacterium Deinococcus radiodurans We found that PPXDr (the subscript "Dr" refers to D. radiodurans) is a novel exopolyphosphatase with a cofactor preference for Mn2+, mediating PolyP-Mn degradation into Pi and Mn ions. The formed Mn-Pi complexes effectively protect proteins. The dynamic PolyP metabolism coordinating with Mn ions is a defense strategy of D. radiodurans in response to oxidative stress. The findings not only provide new insights into the resistance mechanism of the extreme bacterium D. radiodurans but also broaden our understanding of the functions of PolyP metabolism in organisms.
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Shropshire H, Jones RA, Aguilo-Ferretjans MM, Scanlan DJ, Chen Y. Proteomics insights into the Burkholderia cenocepacia phosphorus stress response. Environ Microbiol 2021; 23:5069-5086. [PMID: 33684254 DOI: 10.1111/1462-2920.15451] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 03/02/2021] [Indexed: 11/26/2022]
Abstract
The Burkholderia cepacia complex is a group of Burkholderia species that are opportunistic pathogens causing high mortality rates in patients with cystic fibrosis. An environmental stress often encountered by these soil-dwelling and pathogenic bacteria is phosphorus limitation, an essential element for cellular processes. Here, we describe cellular and extracellular proteins differentially regulated between phosphate-deplete (0 mM, no added phosphate) and phosphate-replete (1 mM) growth conditions using a comparative proteomics (LC-MS/MS) approach. We observed a total of 128 and 65 unique proteins were downregulated and upregulated respectively, in the B. cenocepacia proteome. Of those downregulated proteins, many have functions in amino acid transport/metabolism. We have identified 24 upregulated proteins that are directly/indirectly involved in inorganic phosphate or organic phosphorus acquisition. Also, proteins involved in virulence and antimicrobial resistance were differentially regulated, suggesting B. cenocepacia experiences a dramatic shift in metabolism under these stress conditions. Overall, this study provides a baseline for further research into the biology of Burkholderia in response to phosphorus stress.
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Affiliation(s)
- Holly Shropshire
- BBSRC Midlands Integrative Biosciences Training Partnership, University of Warwick, Coventry, CV4 7AL, UK.,School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Rebekah A Jones
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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Single- or double-membrane-bound vesicles and P, Ca, and Fe-containing granules in Xanthomonas citri cultured on a solid medium. Micron 2021; 143:103024. [PMID: 33549851 DOI: 10.1016/j.micron.2021.103024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 11/21/2022]
Abstract
The organelle-like structures of Xanthomonas citri, a bacterial pathogen that causes citrus canker, were investigated using an analytical transmission electron microscope. After high-pressure freezing, the bacteria were then freeze-substituted for imaging and element analysis. Miniscule electron-dense structures of varying shapes without a membrane enclosure were frequently observed near the cell poles in a 3-day culture. The bacteria formed cytoplasmic electron-dense spherical structures measuring approximately 50 nm in diameter. Furthermore, X. citri produced electron-dense or translucent ellipsoidal intracellular or extracellular granules. Single- or double-membrane-bound vesicles, including outer-inner membrane vesicles, were observed both inside and outside the cells. Most cells had been lysed in the 3-week X. citri culture, but they harbored one or two electron-dense spherical structures. Contrast-inverted scanning transmission electron microscopy images revealed distinct white spherical structures within the cytoplasm of X. citri. Likewise, energy-dispersive X-ray spectrometry showed the spatial heterogeneity and co-localization of phosphorus, oxygen, calcium, and iron only in the cytoplasmic electron-dense spherical structures, thus corroborating the nature of polyphosphate granules.
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Denoncourt A, Downey M. Model systems for studying polyphosphate biology: a focus on microorganisms. Curr Genet 2021; 67:331-346. [PMID: 33420907 DOI: 10.1007/s00294-020-01148-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 12/19/2022]
Abstract
Polyphosphates (polyP) are polymers of inorganic phosphates joined by high-energy bonds to form long chains. These chains are present in all forms of life but were once disregarded as 'molecular fossils'. PolyP has gained attention in recent years following new links to diverse biological roles ranging from energy storage to cell signaling. PolyP research in humans and other higher eukaryotes is limited by a lack of suitable tools and awaits the identification of enzymatic players that would enable more comprehensive studies. Therefore, many of the most important insights have come from single-cell model systems. Here, we review determinants of polyP metabolism, regulation, and function in major microbial systems, including bacteria, fungi, protozoa, and algae. We highlight key similarities and differences that may aid in our understanding of how polyP impacts cell physiology at a molecular level.
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Affiliation(s)
- Alix Denoncourt
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, K1H 8M5, Canada.,Ottawa Institute of Systems Biology, Ottawa, K1H 8M5, Canada
| | - Michael Downey
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, K1H 8M5, Canada. .,Ottawa Institute of Systems Biology, Ottawa, K1H 8M5, Canada.
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Brito LF, López MG, Straube L, Passaglia LMP, Wendisch VF. Inorganic Phosphate Solubilization by Rhizosphere Bacterium Paenibacillus sonchi: Gene Expression and Physiological Functions. Front Microbiol 2020; 11:588605. [PMID: 33424789 PMCID: PMC7793946 DOI: 10.3389/fmicb.2020.588605] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Due to the importance of phosphorus (P) in agriculture, crop inoculation with phosphate-solubilizing bacteria is a relevant subject of study. Paenibacillus sonchi genomovar Riograndensis SBR5 is a promising candidate for crop inoculation, as it can fix nitrogen and excrete ammonium at a remarkably high rate. However, its trait of phosphate solubilization (PS) has not yet been studied in detail. Here, differential gene expression and functional analyses were performed to characterize PS in this bacterium. SBR5 was cultivated with two distinct P sources: NaH2PO4 as soluble phosphate source (SPi) and hydroxyapatite as insoluble phosphate source (IPi). Total RNA of SBR5 cultivated in those two conditions was isolated and sequenced, and bacterial growth and product formation were monitored. In the IPi medium, the expression of 68 genes was upregulated, whereas 100 genes were downregulated. Among those, genes involved in carbon metabolism, including those coding for subunits of 2-oxoglutarate dehydrogenase, were identified. Quantitation of organic acids showed that the production of tricarboxylic acid cycle-derived organic acids was reduced in IPi condition, whereas acetate and gluconate were overproduced. Increased concentrations of proline, trehalose, and glycine betaine revealed active osmoprotection during growth in IPi. The cultivation with hydroxyapatite also caused the reduction in the motility of SBR5 cells as a response to Pi depletion at the beginning of its growth. SBR5 was able to solubilize hydroxyapatite, which suggests that this organism is a promising phosphate-solubilizing bacterium. Our findings are the initial step in the elucidation of the PS process in P. sonchi SBR5 and will be a valuable groundwork for further studies of this organism as a plant growth-promoting rhizobacterium.
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Affiliation(s)
- Luciana F. Brito
- Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Marina Gil López
- Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Lucas Straube
- Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Volker F. Wendisch
- Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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44
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Theng S, Williamson KS, Franklin MJ. Role of Hibernation Promoting Factor in Ribosomal Protein Stability during Pseudomonas aeruginosa Dormancy. Int J Mol Sci 2020; 21:E9494. [PMID: 33327444 PMCID: PMC7764885 DOI: 10.3390/ijms21249494] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 01/02/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes biofilm-associated infections. P. aeruginosa can survive in a dormant state with reduced metabolic activity in nutrient-limited environments, including the interiors of biofilms. When entering dormancy, the bacteria undergo metabolic remodeling, which includes reduced translation and degradation of cellular proteins. However, a supply of essential macromolecules, such as ribosomes, are protected from degradation during dormancy. The small ribosome-binding proteins, hibernation promoting factor (HPF) and ribosome modulation factor (RMF), inhibit translation by inducing formation of inactive 70S and 100S ribosome monomers and dimers. The inactivated ribosomes are protected from the initial steps in ribosome degradation, including endonuclease cleavage of the ribosomal RNA (rRNA). Here, we characterized the role of HPF in ribosomal protein (rProtein) stability and degradation during P. aeruginosa nutrient limitation. We determined the effect of the physiological status of P. aeruginosa prior to starvation on its ability to recover from starvation, and on its rRNA and rProtein stability during cell starvation. The results show that the wild-type strain and a stringent response mutant (∆relA∆spoT strain) maintain high cellular abundances of the rProteins L5 and S13 over the course of eight days of starvation. In contrast, the abundances of L5 and S13 reduce in the ∆hpf mutant cells. The loss of rProteins in the ∆hpf strain is dependent on the physiology of the cells prior to starvation. The greatest rProtein loss occurs when cells are first cultured to stationary phase prior to starvation, with less rProtein loss in the ∆hpf cells that are first cultured to exponential phase or in balanced minimal medium. Regardless of the pre-growth conditions, P. aeruginosa recovery from starvation and the integrity of its rRNA are impaired in the absence of HPF. The results indicate that protein remodeling during P. aeruginosa starvation includes the degradation of rProteins, and that HPF is essential to prevent rProtein loss in starved P. aeruginosa. The results also indicate that HPF is produced throughout cell growth, and that regardless of the cellular physiological status, HPF is required to protect against ribosome loss when the cells subsequently enter starvation phase.
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Affiliation(s)
- Sokuntheary Theng
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA; (S.T.); (K.S.W.)
| | - Kerry S. Williamson
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA; (S.T.); (K.S.W.)
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA
| | - Michael J. Franklin
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA; (S.T.); (K.S.W.)
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA
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45
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Ropelewska M, Gross MH, Konieczny I. DNA and Polyphosphate in Directed Proteolysis for DNA Replication Control. Front Microbiol 2020; 11:585717. [PMID: 33123115 PMCID: PMC7566177 DOI: 10.3389/fmicb.2020.585717] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/10/2020] [Indexed: 12/03/2022] Open
Abstract
The strict control of bacterial cell proliferation by proteolysis is vital to coordinate cell cycle processes and to adapt to environmental changes. ATP-dependent proteases of the AAA + family are molecular machineries that contribute to cellular proteostasis. Their activity is important to control the level of various proteins, including those that are essential for the regulation of DNA replication. Since the process of proteolysis is irreversible, the protease activity must be tightly regulated and directed toward a specific substrate at the exact time and space in a cell. In our mini review, we discuss the impact of phosphate-containing molecules like DNA and inorganic polyphosphate (PolyP), accumulated during stress, on protease activities. We describe how the directed proteolysis of essential replication proteins contributes to the regulation of DNA replication under normal and stress conditions in bacteria.
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Affiliation(s)
- Malgorzata Ropelewska
- Laboratory of Molecular Biology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Marta H Gross
- Laboratory of Molecular Biology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Igor Konieczny
- Laboratory of Molecular Biology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
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46
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Frank C, Teleki A, Jendrossek D. Characterization of Agrobacterium tumefaciens PPKs reveals the formation of oligophosphorylated products up to nucleoside nona-phosphates. Appl Microbiol Biotechnol 2020; 104:9683-9692. [PMID: 33025129 PMCID: PMC7595981 DOI: 10.1007/s00253-020-10891-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/28/2020] [Accepted: 09/04/2020] [Indexed: 12/29/2022]
Abstract
Agrobacterium tumefaciens synthesizes polyphosphate (polyP) in the form of one or two polyP granules per cell during growth. The A. tumefaciens genome codes for two polyphosphate kinase genes, ppk1AT and ppk2AT, of which only ppk1AT is essential for polyP granule formation in vivo. Biochemical characterization of the purified PPK1AT and PPK2AT proteins revealed a higher substrate specificity of PPK1AT (in particular for adenine nucleotides) than for PPK2AT. In contrast, PPK2AT accepted all nucleotides at comparable rates. Most interestingly, PPK2AT catalyzed also the formation of tetra-, penta-, hexa-, hepta-, and octa-phosphorylated nucleosides from guanine, cytosine, desoxy-thymidine, and uridine nucleotides and even nona-phosphorylated adenosine. Our data-in combination with in vivo results-suggest that PPK1AT is important for the formation of polyP whereas PPK2AT has the function to replenish nucleoside triphosphate pools during times of enhanced demand. The potential physiological function(s) of the detected oligophosphorylated nucleotides await clarification. KEY POINTS: •PPK1AT and PPK2AT have different substrate specificities, •PPK2AT is a subgroup 1 member of PPK2s, •PPK2AT catalyzes the formation of polyphosphorylated nucleosides.
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Affiliation(s)
- Celina Frank
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Dieter Jendrossek
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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Bondy-Chorney E, Abramchuk I, Nasser R, Holinier C, Denoncourt A, Baijal K, McCarthy L, Khacho M, Lavallée-Adam M, Downey M. A Broad Response to Intracellular Long-Chain Polyphosphate in Human Cells. Cell Rep 2020; 33:108318. [PMID: 33113373 DOI: 10.1016/j.celrep.2020.108318] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/27/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022] Open
Abstract
Polyphosphates (polyPs) are long chains of inorganic phosphates linked by phosphoanhydride bonds. They are found in all kingdoms of life, playing roles in cell growth, infection, and blood coagulation. Unlike in bacteria and lower eukaryotes, the mammalian enzymes responsible for polyP metabolism are largely unexplored. We use RNA sequencing (RNA-seq) and mass spectrometry to define a broad impact of polyP produced inside of mammalian cells via ectopic expression of the E. coli polyP synthetase PPK. We find that multiple cellular compartments can support accumulation of polyP to high levels. Overproduction of polyP is associated with reprogramming of both the transcriptome and proteome, including activation of the ERK1/2-EGR1 signaling axis. Finally, fractionation analysis shows that polyP accumulation results in relocalization of nuclear/cytoskeleton proteins, including targets of non-enzymatic lysine polyphosphorylation. Our work demonstrates that internally produced polyP can activate diverse signaling pathways in human cells.
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Affiliation(s)
- Emma Bondy-Chorney
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
| | - Iryna Abramchuk
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Rawan Nasser
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Charlotte Holinier
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Alix Denoncourt
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Kanchi Baijal
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Liam McCarthy
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Mireille Khacho
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Mathieu Lavallée-Adam
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Michael Downey
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
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48
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Mahajan M, Seeger C, Yee B, Andersson SGE. Evolutionary Remodeling of the Cell Envelope in Bacteria of the Planctomycetes Phylum. Genome Biol Evol 2020; 12:1528-1548. [PMID: 32761170 DOI: 10.1093/gbe/evaa159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2020] [Indexed: 01/09/2023] Open
Abstract
Bacteria of the Planctomycetes phylum have many unique cellular features, such as extensive membrane invaginations and the ability to import macromolecules. These features raise intriguing questions about the composition of their cell envelopes. In this study, we have used microscopy, phylogenomics, and proteomics to examine the composition and evolution of cell envelope proteins in Tuwongella immobilis and other members of the Planctomycetes. Cryo-electron tomography data indicated a distance of 45 nm between the inner and outer membranes in T. immobilis. Consistent with the wide periplasmic space, our bioinformatics studies showed that the periplasmic segments of outer-membrane proteins in type II secretion systems are extended in bacteria of the order Planctomycetales. Homologs of two highly abundant cysteine-rich cell wall proteins in T. immobilis were identified in all members of the Planctomycetales, whereas genes for peptidoglycan biosynthesis and cell elongation have been lost in many members of this bacterial group. The cell wall proteins contain multiple copies of the YTV motif, which is the only domain that is conserved and unique to the Planctomycetales. Earlier diverging taxa in the Planctomycetes phylum contain genes for peptidoglycan biosynthesis but no homologs to the YTV cell wall proteins. The major remodeling of the cell envelope in the ancestor of the Planctomycetales coincided with the emergence of budding and other unique cellular phenotypes. The results have implications for hypotheses about the process whereby complex cellular features evolve in bacteria.
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Affiliation(s)
- Mayank Mahajan
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Sweden
| | - Christian Seeger
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Sweden
| | - Benjamin Yee
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Sweden
| | - Siv G E Andersson
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Sweden
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Guilhas B, Walter JC, Rech J, David G, Walliser NO, Palmeri J, Mathieu-Demaziere C, Parmeggiani A, Bouet JY, Le Gall A, Nollmann M. ATP-Driven Separation of Liquid Phase Condensates in Bacteria. Mol Cell 2020; 79:293-303.e4. [PMID: 32679076 DOI: 10.1016/j.molcel.2020.06.034] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 04/08/2020] [Accepted: 06/22/2020] [Indexed: 12/18/2022]
Abstract
Liquid-liquid phase-separated (LLPS) states are key to compartmentalizing components in the absence of membranes; however, it is unclear whether LLPS condensates are actively and specifically organized in the subcellular space and by which mechanisms. Here, we address this question by focusing on the ParABS DNA segregation system, composed of a centromeric-like sequence (parS), a DNA-binding protein (ParB), and a motor (ParA). We show that parS and ParB associate to form nanometer-sized, round condensates. ParB molecules diffuse rapidly within the nucleoid volume but display confined motions when trapped inside ParB condensates. Single ParB molecules are able to rapidly diffuse between different condensates, and nucleation is strongly favored by parS. Notably, the ParA motor is required to prevent the fusion of ParB condensates. These results describe a novel active mechanism that splits, segregates, and localizes non-canonical LLPS condensates in the subcellular space.
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Affiliation(s)
- Baptiste Guilhas
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090 Montpellier, France
| | - Jean-Charles Walter
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS, Montpellier, France
| | - Jerome Rech
- LMGM, CBI, CNRS, Université de Toulouse, UPS, Toulouse, France
| | - Gabriel David
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS, Montpellier, France
| | - Nils Ole Walliser
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS, Montpellier, France
| | - John Palmeri
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS, Montpellier, France
| | | | - Andrea Parmeggiani
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS, Montpellier, France; LPHI, CNRS, Université de Montpellier, Montpellier, France
| | - Jean-Yves Bouet
- LMGM, CBI, CNRS, Université de Toulouse, UPS, Toulouse, France
| | - Antoine Le Gall
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090 Montpellier, France.
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090 Montpellier, France.
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50
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Bergkessel M. Regulation of protein biosynthetic activity during growth arrest. Curr Opin Microbiol 2020; 57:62-69. [PMID: 32858411 DOI: 10.1016/j.mib.2020.07.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 07/18/2020] [Accepted: 07/20/2020] [Indexed: 01/10/2023]
Abstract
Heterotrophic bacteria grow and divide rapidly when resources are abundant. Yet resources are finite, and environments fluctuate, so bacteria need strategies to survive when nutrients become scarce. In fact, many bacteria spend most of their time in such conditions of nutrient limitation, and hence they need to optimise gene regulation and protein biosynthesis during growth arrest. An optimal strategy in these conditions must mitigate the challenges and risks of making new proteins, while the cell is severely limited for energy and substrates. Recently, ribosome abundance and activity were measured in these conditions, revealing very low amounts of new protein synthesis, which is nevertheless vital for survival. The underlying mechanisms are only now starting to be explored. Improving our understanding of the regulation of protein production during bacterial growth arrest could have important implications for a wide range of challenges, including the identification of new targets for antibiotic development.
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Affiliation(s)
- Megan Bergkessel
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK.
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