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Qiao K, Zhao T, Wang L, Zhang W, Meng W, Liu F, Gao X, Zhu J. Screening and identification of functional bacterial attachment genes in aerobic granular sludge. J Environ Sci (China) 2024; 141:205-214. [PMID: 38408821 DOI: 10.1016/j.jes.2023.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 02/28/2024]
Abstract
The screening and identification of attachment genes is important to exploring the formation mechanism of biofilms at the gene level. It is helpful to the development of key culture technologies for aerobic granular sludge (AGS). In this study, genome-wide sequencing and gene editing were employed for the first time to investigate the effects and functions of attachment genes in AGS. With the help of whole-genome analysis, ten attachment genes were screened from thirteen genes, and the efficiency of gene screening was greatly improved. Then, two attachment genes were selected as examples to further confirm the gene functions by constructing gene-knockout recombinant mutants of Stenotrophomonas maltophilia; when the two attachment genes were knocked out, the attachment potential was reduced by 50.67% and 43.93%, respectively. The results provide a new theoretical principle and efficient method for the development of AGS from the perspective of attachment genes.
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Affiliation(s)
- Kai Qiao
- School of Environment, Beijing Normal University, Beijing 100875, China; State Key Laboratory of Water Simulation, Beijing 100875, China
| | - Tingting Zhao
- School of Environment, Beijing Normal University, Beijing 100875, China; R & D Centre of Aerobic Granule Technology, Beijing 100875, China
| | - Lei Wang
- School of Environment, Beijing Normal University, Beijing 100875, China; R & D Centre of Aerobic Granule Technology, Beijing 100875, China
| | - Wei Zhang
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wei Meng
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Fan Liu
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xu Gao
- School of Environment, Beijing Normal University, Beijing 100875, China; State Key Laboratory of Water Simulation, Beijing 100875, China
| | - Jianrong Zhu
- School of Environment, Beijing Normal University, Beijing 100875, China; R & D Centre of Aerobic Granule Technology, Beijing 100875, China.
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2
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Schaible GA, Jay ZJ, Cliff J, Schulz F, Gauvin C, Goudeau D, Malmstrom RR, Ruff SE, Edgcomb V, Hatzenpichler R. Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells. PLoS Biol 2024; 22:e3002638. [PMID: 38990824 PMCID: PMC11239054 DOI: 10.1371/journal.pbio.3002638] [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: 12/18/2023] [Accepted: 04/24/2024] [Indexed: 07/13/2024] Open
Abstract
Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single-cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing 8 new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nanoscale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal noncanonical amino acid tagging (BONCAT), we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.
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Affiliation(s)
- George A. Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
| | - Zackary J. Jay
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
| | - John Cliff
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Colin Gauvin
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
| | - Danielle Goudeau
- Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Rex R. Malmstrom
- Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - S. Emil Ruff
- Ecosystems Center and Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - Virginia Edgcomb
- Woods Hole Oceanographic Institution, Falmouth, Massachusetts, United States of America
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, United States of America
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3
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Tang Z, Wang L, Xiong Z, Zhu Y, Zhang H. Process optimized for production of iturin A in biofilm reactor by Bacillus velezensis ND. Bioprocess Biosyst Eng 2024; 47:1095-1105. [PMID: 38847888 DOI: 10.1007/s00449-024-03038-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 05/23/2024] [Indexed: 06/29/2024]
Abstract
In this research, to provide an optimal growth medium for the production of iturin A, the concentrations of key amino acid precursors were optimized in shake flask cultures using the response surface method. The optimized medium were applied in a biofilm reactor for batch fermentation, resulting in enhanced production of iturin A. On this basis, a step-wise pH control strategy and a combined step-wise pH and temperature control strategy were introduced to further improve the production of iturin A. Finally, the fed-batch fermentation was performed based on combined step-wise pH and temperature control. The titer and productivity of iturin A reached 7.86 ± 0.23 g/L and 65.50 ± 1.92 mg/L/h, respectively, which were 37.65 and 65.20% higher than that before process optimization.
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Affiliation(s)
- Zhongmin Tang
- College of Life Sciences, Shihezi University, Xinjiang, People's Republic of China
| | - Leiming Wang
- College of Life Sciences, Shihezi University, Xinjiang, People's Republic of China
| | - Zhengjun Xiong
- Sel Biochem Xinjiang Co., Ltd, Xinjiang, People's Republic of China
| | - Yuxia Zhu
- Sel Biochem Xinjiang Co., Ltd, Xinjiang, People's Republic of China
| | - Huili Zhang
- College of Life Sciences, Shihezi University, Xinjiang, People's Republic of China.
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4
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Shapiro JA. A very brief note on why bacterial evolution has physiology. J Physiol 2024; 602:2395-2399. [PMID: 37641409 DOI: 10.1113/jp284409] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
The majority of bacteria live and evolve in surface biofilms. Both growth in biofilms and horizontal transfer of DNA are regulated by quorum-sensing pheromone signals. The common regulation of bacterial surface growth and DNA transfers illustrates how physiology contributes to bacterial evolution.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
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5
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Cunha-Ferreira IC, Vizzotto CS, Freitas MAM, Peixoto J, Carvalho LS, Tótola MR, Thompson FL, Krüger RH. Genomic and physiological characterization of Kitasatospora sp. nov., an actinobacterium with potential for biotechnological application isolated from Cerrado soil. Braz J Microbiol 2024; 55:1099-1115. [PMID: 38605254 PMCID: PMC11153394 DOI: 10.1007/s42770-024-01324-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 03/21/2024] [Indexed: 04/13/2024] Open
Abstract
An Actinobacteria - Kitasatospora sp. K002 - was isolated from the soil of Cerrado, a savanna-like Brazilian biome. Herein, we conducted a phylogenetic, phenotypic and physiological characterization, revealing its potential for biotechnological applications. Kitasatospora sp. K002 is an aerobic, non-motile, Gram-positive bacteria that forms grayish-white mycelium on solid cultures and submerged spores with vegetative mycelia on liquid cultures. The strain showed antibacterial activity against Bacillus subtilis, Pseudomonas aeruginosa and Escherichia coli. Genomic analysis indicated that Kitasatospora xanthocidica JCM 4862 is the closest strain to K002, with a dDDH of 32.8-37.8% and an ANI of 86.86% and the pangenome investigations identified a high number of rare genes. A total of 60 gene clusters of 22 different types were detected by AntiSMASH, and 22 gene clusters showed low similarity (< 10%) with known compounds, which suggests the potential production of novel bioactive compounds. In addition, phylogenetic analysis and morphophysiological characterization clearly distinguished Kitasatospora sp. K002 from other related species. Therefore, we propose that Kitasatospora sp. K002 should be recognized as a new species of the genus Kitasatospora - Kitasatospora brasiliensis sp. nov. (type strains = K002).
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Affiliation(s)
- I C Cunha-Ferreira
- Laboratory of Enzymology, Department of Cellular Biology, University of Brasília (UNB), Brasília, Brazil
| | - C S Vizzotto
- Laboratory of Environmental Sanitation, Department of Civil and Environmental Engineering, University of Brasília (UNB), Brasília, Brazil
| | - M A M Freitas
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - J Peixoto
- Laboratory of Enzymology, Department of Cellular Biology, University of Brasília (UNB), Brasília, Brazil
| | - L S Carvalho
- Laboratory of Enzymology, Department of Cellular Biology, University of Brasília (UNB), Brasília, Brazil
| | - M R Tótola
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Universidade Federal de Viçosa (UFV), Viçosa, Brazil
| | - F L Thompson
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - R H Krüger
- Laboratory of Enzymology, Department of Cellular Biology, University of Brasília (UNB), Brasília, Brazil.
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6
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Hoskisson PA, Barona-Gómez F, Rozen DE. Phenotypic heterogeneity in Streptomyces colonies. Curr Opin Microbiol 2024; 78:102448. [PMID: 38447313 DOI: 10.1016/j.mib.2024.102448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
Streptomyces are a large genus of multicellular bacteria best known for their prolific production of bioactive natural products. In addition, they play key roles in the mineralisation of insoluble resources, such as chitin and cellulose. Because of their multicellular mode of growth, colonies of interconnected hyphae extend over a large area that may experience different conditions in different parts of the colony. Here, we argue that within-colony phenotypic heterogeneity can allow colonies to simultaneously respond to divergent inputs from resources or competitors that are spatially and temporally dynamic. We discuss causal drivers of heterogeneity, including competitors, precursor availability, metabolic diversity and division of labour, that facilitate divergent phenotypes within Streptomyces colonies. We discuss the adaptive causes and consequences of within-colony heterogeneity, highlight current knowledge (gaps) and outline key questions for future studies.
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Affiliation(s)
- Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | | | - Daniel E Rozen
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, The Netherlands.
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7
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Glass DS, Bren A, Vaisbourd E, Mayo A, Alon U. A synthetic differentiation circuit in Escherichia coli for suppressing mutant takeover. Cell 2024; 187:931-944.e12. [PMID: 38320549 PMCID: PMC10882425 DOI: 10.1016/j.cell.2024.01.024] [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: 07/10/2023] [Revised: 11/27/2023] [Accepted: 01/16/2024] [Indexed: 02/08/2024]
Abstract
Differentiation is crucial for multicellularity. However, it is inherently susceptible to mutant cells that fail to differentiate. These mutants outcompete normal cells by excessive self-renewal. It remains unclear what mechanisms can resist such mutant expansion. Here, we demonstrate a solution by engineering a synthetic differentiation circuit in Escherichia coli that selects against these mutants via a biphasic fitness strategy. The circuit provides tunable production of synthetic analogs of stem, progenitor, and differentiated cells. It resists mutations by coupling differentiation to the production of an essential enzyme, thereby disadvantaging non-differentiating mutants. The circuit selected for and maintained a positive differentiation rate in long-term evolution. Surprisingly, this rate remained constant across vast changes in growth conditions. We found that transit-amplifying cells (fast-growing progenitors) underlie this environmental robustness. Our results provide insight into the stability of differentiation and demonstrate a powerful method for engineering evolutionarily stable multicellular consortia.
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Affiliation(s)
- David S Glass
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Anat Bren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elizabeth Vaisbourd
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Avi Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
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8
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Bingham EP, Ratcliff WC. A nonadaptive explanation for macroevolutionary patterns in the evolution of complex multicellularity. Proc Natl Acad Sci U S A 2024; 121:e2319840121. [PMID: 38315855 PMCID: PMC10873551 DOI: 10.1073/pnas.2319840121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
"Complex multicellularity," conventionally defined as large organisms with many specialized cell types, has evolved five times independently in eukaryotes, but never within prokaryotes. A number of hypotheses have been proposed to explain this phenomenon, most of which posit that eukaryotes evolved key traits (e.g., dynamic cytoskeletons, alternative mechanisms of gene regulation, or subcellular compartments) which were a necessary prerequisite for the evolution of complex multicellularity. Here, we propose an alternative, nonadaptive hypothesis for this broad macroevolutionary pattern. By binning cells into groups with finite genetic bottlenecks between generations, the evolution of multicellularity greatly reduces the effective population size (Ne) of cellular populations, increasing the role of genetic drift in evolutionary change. While both prokaryotes and eukaryotes experience this phenomenon, they have opposite responses to drift: eukaryotes tend to undergo genomic expansion, providing additional raw genetic material for subsequent multicellular innovation, while prokaryotes generally face genomic erosion. Taken together, we hypothesize that these idiosyncratic lineage-specific evolutionary dynamics play a fundamental role in the long-term divergent evolution of complex multicellularity across the tree of life.
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Affiliation(s)
- Emma P. Bingham
- School of Physics, Georgia Institute of Technology, Atlanta, GA30332
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA30332
| | - William C. Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30332
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9
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Ye Y, Ghrayeb M, Miercke S, Arif S, Müller S, Mascher T, Chai L, Zaburdaev V. Residual cells and nutrient availability guide wound healing in bacterial biofilms. SOFT MATTER 2024; 20:1047-1060. [PMID: 38205608 DOI: 10.1039/d3sm01032e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Biofilms are multicellular heterogeneous bacterial communities characterized by social-like division of labor, and remarkable robustness with respect to external stresses. Increasingly often an analogy between biofilms and arguably more complex eukaryotic tissues is being drawn. One illustrative example of where this analogy can be practically useful is the process of wound healing. While it has been extensively studied in eukaryotic tissues, the mechanism of wound healing in biofilms is virtually unexplored. Combining experiments in Bacillus subtilis bacteria, a model organism for biofilm formation, and a lattice-based theoretical model of biofilm growth, we studied how biofilms recover after macroscopic damage. We suggest that nutrient gradients and the abundance of proliferating cells are key factors augmenting wound closure. Accordingly, in the model, cell quiescence, nutrient fluxes, and biomass represented by cells and self-secreted extracellular matrix are necessary to qualitatively recapitulate the experimental results for damage repair. One of the surprising experimental findings is that residual cells, persisting in a damaged area after removal of a part of the biofilm, prominently affect the healing process. Taken together, our results outline the important roles of nutrient gradients and residual cells on biomass regrowth on macroscopic scales of the whole biofilm. The proposed combined experiment-simulation framework opens the way to further investigate the possible relation between wound healing, cell signaling and cell phenotype alternation in the local microenvironment of the wound.
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Affiliation(s)
- Yusong Ye
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Mnar Ghrayeb
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Sania Arif
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | - Susann Müller
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | | | - Liraz Chai
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vasily Zaburdaev
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
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10
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Augustijn HE, Roseboom AM, Medema MH, van Wezel GP. Harnessing regulatory networks in Actinobacteria for natural product discovery. J Ind Microbiol Biotechnol 2024; 51:kuae011. [PMID: 38569653 PMCID: PMC10996143 DOI: 10.1093/jimb/kuae011] [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: 01/22/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024]
Abstract
Microbes typically live in complex habitats where they need to rapidly adapt to continuously changing growth conditions. To do so, they produce an astonishing array of natural products with diverse structures and functions. Actinobacteria stand out for their prolific production of bioactive molecules, including antibiotics, anticancer agents, antifungals, and immunosuppressants. Attention has been directed especially towards the identification of the compounds they produce and the mining of the large diversity of biosynthetic gene clusters (BGCs) in their genomes. However, the current return on investment in random screening for bioactive compounds is low, while it is hard to predict which of the millions of BGCs should be prioritized. Moreover, many of the BGCs for yet undiscovered natural products are silent or cryptic under laboratory growth conditions. To identify ways to prioritize and activate these BGCs, knowledge regarding the way their expression is controlled is crucial. Intricate regulatory networks control global gene expression in Actinobacteria, governed by a staggering number of up to 1000 transcription factors per strain. This review highlights recent advances in experimental and computational methods for characterizing and predicting transcription factor binding sites and their applications to guide natural product discovery. We propose that regulation-guided genome mining approaches will open new avenues toward eliciting the expression of BGCs, as well as prioritizing subsets of BGCs for expression using synthetic biology approaches. ONE-SENTENCE SUMMARY This review provides insights into advances in experimental and computational methods aimed at predicting transcription factor binding sites and their applications to guide natural product discovery.
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Affiliation(s)
- Hannah E Augustijn
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Anna M Roseboom
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- Netherlands Institute for Ecology (NIOO-KNAW), Wageningen, The Netherlands
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11
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Khosakueng M, Taweechaisupapong S, Boonyanugomol W, Prapatpong P, Wongkaewkhiaw S, Kanthawong S. Cymbopogon citratus L. essential oil as a potential anti-biofilm agent active against antibiotic-resistant bacteria isolated from chronic rhinosinusitis patients. BIOFOULING 2024; 40:26-39. [PMID: 38286789 DOI: 10.1080/08927014.2024.2305387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/07/2024] [Indexed: 01/31/2024]
Abstract
Chronic rhinosinusitis (CRS) is long-term inflammation of the sinuses that can be caused by infection due to antibiotic-resistant bacteria. Biofilm developed by microbes is postulated to cause antibiotic treatment failure. Thus, the anti-biofilm activities of seven Thai herbal essential oils (EOs) against antibiotic-resistant bacteria isolated from CRS patients was investigated. Lemongrass (Cymbopogon citratus L.) EO showed the most effective antibiofilm activity against Klebsiella pneumoniae, Pseudomonas aeruginosa and Staphylococcus epidermidis grown as biofilm. GC-MS analysis found that myrcene was the major bioactive compound. Pretreatment with lemongrass EO significantly inhibited biofilm formation of all bacterial strains in more than 50% of cases. Furthermore, confocal microscopy analysis revealed the biofilm-disrupting activity of lemongrass EO against the biofilm matrix of all these bacterial species and also increased P. aeruginosa swarming motility with no toxicity to human cells. These results suggest that lemongrass EO has promising clinical applications as an anti-biofilm agent for CRS patients.
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Affiliation(s)
- Mintra Khosakueng
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | | | - Wongwarut Boonyanugomol
- Department of Medical Science, Amnatcharoen Campus, Mahidol University, Amnatcharoen, Thailand
| | - Pornpan Prapatpong
- Department of Public Health, Amnatcharoen Campus, Mahidol University, Amnatcharoen, Thailand
| | - Saharut Wongkaewkhiaw
- School of Dentistry, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Sakawrat Kanthawong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
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12
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Zhu S, Sun X, Li Y, Feng X, Gao B. The common origin and degenerative evolution of flagella in Actinobacteria. mBio 2023; 14:e0252623. [PMID: 38019005 PMCID: PMC10746217 DOI: 10.1128/mbio.02526-23] [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: 09/20/2023] [Accepted: 10/19/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Flagellar motility plays an important role in the environmental adaptation of bacteria and is found in more than 50% of known bacterial species. However, this important characteristic is sparsely distributed within members of the phylum Actinobacteria, which constitutes one of the largest bacterial groups. It is unclear why this important fitness organelle is absent in most actinobacterial species and the origin of flagellar genes in other species. Here, we present detailed analyses of the evolution of flagellar genes in Actinobacteria, in conjunction with the ecological distribution and cell biological features of major actinobacterial lineages, and the co-evolution of signal transduction systems. The results presented in addition to clarifying the puzzle of sporadic distribution of flagellar motility in Actinobacteria, also provide important insights into the evolution of major lineages within this phylum.
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Affiliation(s)
- Siqi Zhu
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, Hainan, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xian Sun
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, Hainan, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
| | - Yuqian Li
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, Hainan, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
| | - Xueyin Feng
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, Hainan, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Beile Gao
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, Hainan, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
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13
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Yin L, Zheng Z, Li Y, Li X, Cheng D, Dong C, Liu Y, Zhao J. PatU3 plays a central role in coordinating cell division and differentiation in pattern formation of filamentous cyanobacterium Nostoc sp. PCC 7120. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2896-2909. [PMID: 37505430 DOI: 10.1007/s11427-023-2380-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/31/2023] [Indexed: 07/29/2023]
Abstract
Spatial periodic signal for cell differentiation in some multicellular organisms is generated according to Turing's principle for pattern formation. How a dividing cell responds to the signal of differentiation is addressed with the filamentous cyanobacterium Nostoc sp. PCC 7120, which forms the patterned distribution of heterocysts. We show that differentiation of a dividing cell was delayed until its division was completed and only one daughter cell became heterocyst. A mutant of patU3, which encodes an inhibitor of heterocyst formation, showed no such delay and formed heterocyst pairs from the daughter cells of cell division or dumbbell-shaped heterocysts from the cells undergoing cytokinesis. The patA mutant, which forms heterocysts only at the filament ends, restored intercalary heterocysts by a single nucleotide mutation of patU3, and double mutants of patU3/patA and patU3/hetF had the phenotypes of the patU3 mutant. We provide evidence that HetF, which can degrade PatU3, is recruited to cell divisome through its C-terminal domain. A HetF mutant with its N-terminal peptidase domain but lacking the C-terminal domain could not prevent the formation of heterocyst pairs, suggesting that the divisome recruitment of HetF is needed to sequester HetF for the delay of differentiation in dividing cells. Our study demonstrates that PatU3 plays a key role in cell-division coupled control of differentiation.
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Affiliation(s)
- Lei Yin
- State Key Laboratory of Protein and Plant Genetic Engineering, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhenggao Zheng
- State Key Laboratory of Protein and Plant Genetic Engineering, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yilin Li
- State Key Laboratory of Protein and Plant Genetic Engineering, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Xiying Li
- State Key Laboratory of Protein and Plant Genetic Engineering, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Dan Cheng
- State Key Laboratory of Protein and Plant Genetic Engineering, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Chunxia Dong
- State Key Laboratory of Protein and Plant Genetic Engineering, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yixuan Liu
- National Teaching Center for Experimental Biology, School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Jindong Zhao
- State Key Laboratory of Protein and Plant Genetic Engineering, School of Life Sciences, Peking University, Beijing, 100871, China.
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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14
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Schaible GA, Jay ZJ, Cliff J, Schulz F, Gauvin C, Goudeau D, Malmstrom RR, Emil Ruff S, Edgcomb V, Hatzenpichler R. Multicellular magnetotactic bacterial consortia are metabolically differentiated and not clonal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.568837. [PMID: 38076927 PMCID: PMC10705294 DOI: 10.1101/2023.11.27.568837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing eight new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nano-scale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal non-canonical amino acid tagging (BONCAT) we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.
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Affiliation(s)
- George A. Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717
| | - Zackary J. Jay
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717
| | - John Cliff
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720
| | - Colin Gauvin
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717
| | - Danielle Goudeau
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720
| | - Rex R. Malmstrom
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720
| | - S. Emil Ruff
- Ecosystems Center and Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543
| | | | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717
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15
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Bingham EP, Ratcliff WC. A non-adaptive explanation for macroevolutionary patterns in the evolution of complex multicellularity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.11.566713. [PMID: 38014282 PMCID: PMC10680650 DOI: 10.1101/2023.11.11.566713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
"Complex multicellularity", conventionally defined as large organisms with many specialized cell types, has evolved five times independently in eukaryotes, but never within prokaryotes. A number hypotheses have been proposed to explain this phenomenon, most of which posit that eukaryotes evolved key traits (e.g., dynamic cytoskeletons, alternative mechanisms of gene regulation, or subcellular compartments) which were a necessary prerequisite for the evolution of complex multicellularity. Here we propose an alternative, non-adaptive hypothesis for this broad macroevolutionary pattern. By binning cells into groups with finite genetic bottlenecks between generations, the evolution of multicellularity greatly reduces the effective population size (Ne) of cellular populations, increasing the role of genetic drift in evolutionary change. While both prokaryotes and eukaryotes experience this phenomenon, they have opposite responses to drift: mutational biases in eukaryotes tend to drive genomic expansion, providing additional raw genetic material for subsequent multicellular innovation, while prokaryotes generally face genomic erosion. These effects become more severe as organisms evolve larger size and more stringent genetic bottlenecks between generations- both of which are hallmarks of complex multicellularity. Taken together, we hypothesize that it is these idiosyncratic lineage-specific mutational biases, rather than cell-biological innovations within eukaryotes, that underpins the long-term divergent evolution of complex multicellularity across the tree of life.
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Affiliation(s)
- Emma P Bingham
- School of Physics, Georgia Institute of Technology. Atlanta, Georgia 30332, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology. Atlanta, Georgia 30332, USA
| | - William C Ratcliff
- School of Biology, Georgia Institute of Technology. Atlanta, Georgia 30332, USA
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16
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Velázquez-Suárez C, Springstein BL, Nieves-Morión M, Helbig AO, Kieninger AK, Maldener I, Nürnberg DJ, Stucken K, Luque I, Dagan T, Herrero A. SepT, a novel protein specific to multicellular cyanobacteria, influences peptidoglycan growth and septal nanopore formation in Anabaena sp. PCC 7120. mBio 2023; 14:e0098323. [PMID: 37650636 PMCID: PMC10653889 DOI: 10.1128/mbio.00983-23] [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: 04/20/2023] [Accepted: 06/27/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE Multicellular organization is a requirement for the development of complex organisms, and filamentous cyanobacteria such as Anabaena represent a paradigmatic case of bacterial multicellularity. The Anabaena filament can include hundreds of communicated cells that exchange nutrients and regulators and, depending on environmental conditions, can include different cell types specialized in distinct biological functions. Hence, the specific features of the Anabaena filament and how they are propagated during cell division represent outstanding biological issues. Here, we studied SepT, a novel coiled-coil-rich protein of Anabaena that is located in the intercellular septa and influences the formation of the septal specialized structures that allow communication between neighboring cells along the filament, a fundamental trait for the performance of Anabaena as a multicellular organism.
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Affiliation(s)
| | | | - Mercedes Nieves-Morión
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - Andreas O. Helbig
- AG Proteomics & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Ann-Katrin Kieninger
- Department of Microbiology/Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Iris Maldener
- Department of Microbiology/Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Dennis J. Nürnberg
- Institute of Experimental Physics and Dahlem Centre of Plant Sciences, Free University of Berlin, Berlin, Germany
| | - Karina Stucken
- Department of Food Engineering, Universidad de La Serena, La Serena, Chile
| | - Ignacio Luque
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Antonia Herrero
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
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17
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Zohravi E, Moreno N, Ellero M. Computational mesoscale framework for biological clustering and fractal aggregation. SOFT MATTER 2023; 19:7399-7411. [PMID: 37743687 DOI: 10.1039/d3sm01090b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Hierarchical clustering due to diffusion and reaction is a widespread occurrence in natural phenomena, displaying fractal behavior with non-integer size scaling. The study of this phenomenon has garnered interest in both biological systems such as morphogenesis and blood clotting, and synthetic systems such as colloids and polymers. The modeling of biological clustering can be difficult, as it can occur on a variety of scales and involve multiple mechanisms, necessitating the use of various methods to capture its behavior. Here, we propose a novel framework, the generalized-mesoscale-clustering (GMC), for the study of complex hierarchical clustering phenomena in biological systems. The GMC framework incorporates the effects of hydrodynamic interactions, bonding, and surface tension, and allows for the analysis of both static and dynamic states of cluster development. The framework is applied to a range of biological clustering mechanisms, with a focus on blood-related clustering from fibrin network formation to platelet aggregation. Our study highlights the importance of a comprehensive characterization of the structural properties of the cluster, including fractal dimension, pore-scale diffusion, initiation time, and consolidation time, in fully understanding the behavior of biological clustering systems. The GMC framework also provides the potential to investigate the temporal evolution and mechanical properties of the clusters by tracking bond density and including hydrodynamic interactions.
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Affiliation(s)
- Elnaz Zohravi
- Basque Center for Applied Mathematics (BCAM), Alameda de Mazarredo 14, Bilbao 48009, Spain.
| | - Nicolas Moreno
- Basque Center for Applied Mathematics (BCAM), Alameda de Mazarredo 14, Bilbao 48009, Spain.
| | - Marco Ellero
- Basque Center for Applied Mathematics (BCAM), Alameda de Mazarredo 14, Bilbao 48009, Spain.
- IKERBASQUE, Basque Foundation for Science, Calle de Maria Diaz de Haro 3, 48013, Bilbao, Spain
- Zienkiewicz Center for Computational Engineering (ZCCE), Swansea University, Bay Campus, Swansea SA1 8EN, UK
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18
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Kalia VC, Patel SKS, Lee JK. Bacterial biofilm inhibitors: An overview. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 264:115389. [PMID: 37634478 DOI: 10.1016/j.ecoenv.2023.115389] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/05/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023]
Abstract
Bacteria that cause infectious diseases adopt biofilms as one of their most prevalent lifestyles. Biofilms enable bacteria to tolerate environmental stress and evade antibacterial agents. This bacterial defense mechanism has rendered the use of antibiotics ineffective for the treatment of infectious diseases. However, many highly drug-resistant microbes have rapidly emerged owing to such treatments. Different signaling mechanisms regulate bacterial biofilm formation, including cyclic dinucleotide (c-di-GMP), small non-coding RNAs, and quorum sensing (QS). A cell density-dependent phenomenon, QS is associated with c-di-GMP (a global messenger), which regulates gene expression related to adhesion, extracellular matrix production, the transition from the planktonic to biofilm stage, stability, pathogenicity, virulence, and acquisition of nutrients. The article aims to provide information on inhibiting biofilm formation and disintegrating mature/preformed biofilms. This treatment enables antimicrobials to target the free-living/exposed bacterial cells at lower concentrations than those needed to treat bacteria within the biofilm. Therefore, a complementary action of antibiofilm and antimicrobial agents can be a robust strategic approach to dealing with infectious diseases. Taken together, these molecules have broad implications for human health.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
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19
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Mattioli R, Ilari A, Colotti B, Mosca L, Fazi F, Colotti G. Doxorubicin and other anthracyclines in cancers: Activity, chemoresistance and its overcoming. Mol Aspects Med 2023; 93:101205. [PMID: 37515939 DOI: 10.1016/j.mam.2023.101205] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/31/2023]
Abstract
Anthracyclines have been important and effective treatments against a number of cancers since their discovery. However, their use in therapy has been complicated by severe side effects and toxicity that occur during or after treatment, including cardiotoxicity. The mode of action of anthracyclines is complex, with several mechanisms proposed. It is possible that their high toxicity is due to the large set of processes involved in anthracycline action. The development of resistance is a major barrier to successful treatment when using anthracyclines. This resistance is based on a series of mechanisms that have been studied and addressed in recent years. This work provides an overview of the anthracyclines used in cancer therapy. It discusses their mechanisms of activity, toxicity, and chemoresistance, as well as the approaches used to improve their activity, decrease their toxicity, and overcome resistance.
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Affiliation(s)
- Roberto Mattioli
- Dept. Biochemical Sciences A. Rossi Fanelli, Sapienza University of Rome, Rome, Italy
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology, Italian National Research Council IBPM-CNR, Rome, Italy
| | - Beatrice Colotti
- Dept. Biochemical Sciences A. Rossi Fanelli, Sapienza University of Rome, Rome, Italy
| | - Luciana Mosca
- Dept. Biochemical Sciences A. Rossi Fanelli, Sapienza University of Rome, Rome, Italy
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopaedic Sciences, Section of Histology and Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology, Italian National Research Council IBPM-CNR, Rome, Italy.
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20
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van Gestel J, Wagner A, Ackermann M. Pleiotropic hubs drive bacterial surface competition through parallel changes in colony composition and expansion. PLoS Biol 2023; 21:e3002338. [PMID: 37844064 PMCID: PMC10578586 DOI: 10.1371/journal.pbio.3002338] [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: 03/22/2023] [Accepted: 09/18/2023] [Indexed: 10/18/2023] Open
Abstract
Bacteria commonly adhere to surfaces where they compete for both space and resources. Despite the importance of surface growth, it remains largely elusive how bacteria evolve on surfaces. We previously performed an evolution experiment where we evolved distinct Bacilli populations under a selective regime that favored colony spreading. In just a few weeks, colonies of Bacillus subtilis showed strongly advanced expansion rates, increasing their radius 2.5-fold relative to that of the ancestor. Here, we investigate what drives their rapid evolution by performing a uniquely detailed analysis of the evolutionary changes in colony development. We find mutations in diverse global regulators, RicT, RNAse Y, and LexA, with strikingly similar pleiotropic effects: They lower the rate of sporulation and simultaneously facilitate colony expansion by either reducing extracellular polysaccharide production or by promoting filamentous growth. Combining both high-throughput flow cytometry and gene expression profiling, we show that regulatory mutations lead to highly reproducible and parallel changes in global gene expression, affecting approximately 45% of all genes. This parallelism results from the coordinated manner by which regulators change activity both during colony development-in the transition from vegetative growth to dormancy-and over evolutionary time. This coordinated activity can however also break down, leading to evolutionary divergence. Altogether, we show how global regulators function as major pleiotropic hubs that drive rapid surface adaptation by mediating parallel changes in both colony composition and expansion, thereby massively reshaping gene expression.
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Affiliation(s)
- Jordi van Gestel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
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21
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McWilliam KR. Cell-cell communication in African trypanosomes. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001388. [PMID: 37643128 PMCID: PMC10482365 DOI: 10.1099/mic.0.001388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
Years of research have shown us that unicellular organisms do not exist entirely in isolation, but rather that they are capable of an altogether far more sociable way of living. Single cells produce, receive and interpret signals, coordinating and changing their behaviour according to the information received. Although this cell-cell communication has long been considered the norm in the bacterial world, an increasing body of knowledge is demonstrating that single-celled eukaryotic parasites also maintain active social lives. This communication can drive parasite development, facilitate the invasion of new niches and, ultimately, influence infection outcome. In this review, I present the evidence for cell-cell communication during the life cycle of the African trypanosomes, from their mammalian hosts to their insect vectors, and reflect on the many remaining unanswered questions in this fascinating field.
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Affiliation(s)
- K. R. McWilliam
- Institute for Immunology and Infection Research, School of Biological Sciences, King’s Buildings, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
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22
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Liu S, Wang P, Wang C, Chen J, Wang X, Hu B, Shan X. Disparate toxicity mechanisms of parabens with different alkyl chain length in freshwater biofilms: Ecological hazards associated with antibiotic resistome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163168. [PMID: 37003345 DOI: 10.1016/j.scitotenv.2023.163168] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/15/2023] [Accepted: 03/26/2023] [Indexed: 06/01/2023]
Abstract
As emerging organic pollutants, parabens are of global concern because of their ubiquitous presence and adverse effects. However, few researchers have addressed the relationship between parabens' structural features and toxicity mechanisms. This study conducted theoretical calculations and laboratory exposure experiments to uncover the toxic effects and mechanisms of parabens with different alkyl chains in freshwater biofilms. The result demonstrated that parabens' hydrophobicity and lethality increased with their alkyl-chain length, whereas the possibility of chemical reactions and reactive sites were unchanged despite the alkyl-chain length alteration. Due to the hydrophobicity variation, parabens with different alkyl-chain presented different distribution patterns in cells of freshwater biofilms and consequently induced distinct toxic effects and led to diverse cell death modes. The butylparaben with longer alkyl-chain preferred to stay in the membrane and altered membrane permeability by non-covalent interaction with phospholipid, which caused cell necrosis. The methylparaben with shorter alkyl-chain preferred to enter into the cytoplasm and influence mazE gene expression by chemically reacting with biomacromolecules, thereby triggering apoptosis. The different cell death patterns induced by parabens contributed to different ecological hazards associated with antibiotic resistome. Compared with butylparaben, methylparaben was more likely to spread ARGs among microbial communities despite its lower lethality.
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Affiliation(s)
- Sheng Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; School of Civil Engineering, Shandong University, Jinan 250061, China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China.
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Bin Hu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Xiaorong Shan
- Sid and Reva Dewberry Dept. of Civil, Environmental, & Infrastructure Engineering, George Mason University, Fairfax, VA, USA
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23
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Premetis GE, Georgakis ND, Stathi A, Labrou NE. Metaviromics analysis of marine biofilm reveals a glycoside hydrolase endolysin with high specificity towards Acinetobacter baumannii. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140918. [PMID: 37150474 DOI: 10.1016/j.bbapap.2023.140918] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/09/2023]
Abstract
Multidrug-resistant (MDR) bacteria are a growing threat to the public health. Among them, the Gram-negative Acinetobacter baumannii is considered today as the most dangerous MDR pathogen. Phage-derived endolysins are peptidoglycan (PG) hydrolytic enzymes that can function as effective tools in the fight against MDR bacteria. In the present work, the viral diversity of a marine environmental sample (biofilm), formed near an industrial zone, was mined for the identification of a putative endolysin (AbLys2) that belongs to the glycoside hydrolase family 24 (GH24, EC 3.2.1.17). The coding sequence of AbLys2 was cloned and expressed in E. coli. The lytic activity and specificity of the recombinant enzyme were evaluated against suspensions of a range of Gram-positive and Gram-negative human pathogens using turbidity assays. AbLys2 displayed enhanced selectivity towards A. baumannii cells, compared to other bacteria. Kinetics analysis was carried out to characterize the dependence of its lytic activity on pH and showed that the enzyme exhibits its maximal activity at pH 5.5. Thermostability analysis showed that AbLys2 displays melting temperature Tm 47.1 °C. Florescence microscopy and cell viability assays established that AbLys2 is active towards live cultures of A. baumannii cells with an inhibitory concentration IC50 3.41 ± 0.09 μM. Molecular modeling allowed the prediction of important amino acid residues involved in catalysis. The results of the present study suggest that AbLys2 provides efficient lytic and antimicrobial activity towards A. baumannii cells and therefore is a promising new antimicrobial against this pathogen.
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Affiliation(s)
- Georgios E Premetis
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 -Athens, Greece
| | - Nikolaos D Georgakis
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 -Athens, Greece
| | - Angeliki Stathi
- Department of Microbiology, "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 -Athens, Greece.
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24
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Chavhan Y, Dey S, Lind PA. Bacteria evolve macroscopic multicellularity by the genetic assimilation of phenotypically plastic cell clustering. Nat Commun 2023; 14:3555. [PMID: 37322016 PMCID: PMC10272148 DOI: 10.1038/s41467-023-39320-9] [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: 09/20/2022] [Accepted: 06/05/2023] [Indexed: 06/17/2023] Open
Abstract
The evolutionary transition from unicellularity to multicellularity was a key innovation in the history of life. Experimental evolution is an important tool to study the formation of undifferentiated cellular clusters, the likely first step of this transition. Although multicellularity first evolved in bacteria, previous experimental evolution research has primarily used eukaryotes. Moreover, it focuses on mutationally driven (and not environmentally induced) phenotypes. Here we show that both Gram-negative and Gram-positive bacteria exhibit phenotypically plastic (i.e., environmentally induced) cell clustering. Under high salinity, they form elongated clusters of ~ 2 cm. However, under habitual salinity, the clusters disintegrate and grow planktonically. We used experimental evolution with Escherichia coli to show that such clustering can be assimilated genetically: the evolved bacteria inherently grow as macroscopic multicellular clusters, even without environmental induction. Highly parallel mutations in genes linked to cell wall assembly formed the genomic basis of assimilated multicellularity. While the wildtype also showed cell shape plasticity across high versus low salinity, it was either assimilated or reversed after evolution. Interestingly, a single mutation could genetically assimilate multicellularity by modulating plasticity at multiple levels of organization. Taken together, we show that phenotypic plasticity can prime bacteria for evolving undifferentiated macroscopic multicellularity.
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Affiliation(s)
- Yashraj Chavhan
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
| | - Sutirth Dey
- Indian Institute of Science Education and Research (IISER) Pune, Pune, India
| | - Peter A Lind
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.
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25
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Barona-Gómez F, Chevrette MG, Hoskisson PA. On the evolution of natural product biosynthesis. Adv Microb Physiol 2023; 83:309-349. [PMID: 37507161 DOI: 10.1016/bs.ampbs.2023.05.001] [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: 07/30/2023]
Abstract
Natural products are the raw material for drug discovery programmes. Bioactive natural products are used extensively in medicine and agriculture and have found utility as antibiotics, immunosuppressives, anti-cancer drugs and anthelminthics. Remarkably, the natural role and what mechanisms drive evolution of these molecules is relatively poorly understood. The exponential increase in genome and chemical data in recent years, coupled with technical advances in bioinformatics and genetics have enabled progress to be made in understanding the evolution of biosynthetic gene clusters and the products of their enzymatic machinery. Here we discuss the diversity of natural products, incorporating the mechanisms that govern evolution of metabolic pathways and how this can be applied to biosynthetic gene clusters. We build on the nomenclature of natural products in terms of primary, integrated, secondary and specialised metabolism and place this within an ecology-evolutionary-developmental biology framework. This eco-evo-devo framework we believe will help to clarify the nature and use of the term specialised metabolites in the future.
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Affiliation(s)
| | - Marc G Chevrette
- Department of Microbiology and Cell Sciences, University of Florida, Museum Drive, Gainesville, FL, United States; University of Florida Genetics Institute, University of Florida, Mowry Road, Gainesville, FL, United States
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Cathedral Street, Glasgow, United Kingdom.
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26
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Tang SK, Zhi XY, Zhang Y, Makarova KS, Liu BB, Zheng GS, Zhang ZP, Zheng HJ, Wolf YI, Zhao YR, Jiang SH, Chen XM, Li EY, Zhang T, Chen PR, Feng YZ, Xiang MX, Lin ZQ, Shi JH, Chang C, Zhang X, Li R, Lou K, Wang Y, Chang L, Yin M, Yang LL, Gao HY, Zhang ZK, Tao TS, Guan TW, He FC, Lu YH, Cui HL, Koonin EV, Zhao GP, Xu P. Cellular differentiation into hyphae and spores in halophilic archaea. Nat Commun 2023; 14:1827. [PMID: 37005419 PMCID: PMC10067837 DOI: 10.1038/s41467-023-37389-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/14/2023] [Indexed: 04/04/2023] Open
Abstract
Several groups of bacteria have complex life cycles involving cellular differentiation and multicellular structures. For example, actinobacteria of the genus Streptomyces form multicellular vegetative hyphae, aerial hyphae, and spores. However, similar life cycles have not yet been described for archaea. Here, we show that several haloarchaea of the family Halobacteriaceae display a life cycle resembling that of Streptomyces bacteria. Strain YIM 93972 (isolated from a salt marsh) undergoes cellular differentiation into mycelia and spores. Other closely related strains are also able to form mycelia, and comparative genomic analyses point to gene signatures (apparent gain or loss of certain genes) that are shared by members of this clade within the Halobacteriaceae. Genomic, transcriptomic and proteomic analyses of non-differentiating mutants suggest that a Cdc48-family ATPase might be involved in cellular differentiation in strain YIM 93972. Additionally, a gene encoding a putative oligopeptide transporter from YIM 93972 can restore the ability to form hyphae in a Streptomyces coelicolor mutant that carries a deletion in a homologous gene cluster (bldKA-bldKE), suggesting functional equivalence. We propose strain YIM 93972 as representative of a new species in a new genus within the family Halobacteriaceae, for which the name Actinoarchaeum halophilum gen. nov., sp. nov. is herewith proposed. Our demonstration of a complex life cycle in a group of haloarchaea adds a new dimension to our understanding of the biological diversity and environmental adaptation of archaea.
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Affiliation(s)
- Shu-Kun Tang
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Bing-Bing Liu
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, China
| | - Guo-Song Zheng
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhen-Peng Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Hua-Jun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 201203, China
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Yu-Rong Zhao
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Song-Hao Jiang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China
| | - Xi-Ming Chen
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - En-Yuan Li
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Tao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Pei-Ru Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China
| | - Yu-Zhou Feng
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Ming-Xian Xiang
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Zhi-Qian Lin
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Jia-Hui Shi
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China
| | - Cheng Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Xue Zhang
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, China
| | - Rui Li
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Kai Lou
- Xinjiang Institute of Microbiology, Xinjiang Academy of Agricultural Science, Urumqi, 830091, China
| | - Yun Wang
- Xinjiang Institute of Microbiology, Xinjiang Academy of Agricultural Science, Urumqi, 830091, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Min Yin
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Ling-Ling Yang
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Hui-Ying Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Zhong-Kai Zhang
- Biotechnology and Genetic Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Tian-Shen Tao
- Department of Microbiology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, China
| | - Tong-Wei Guan
- College of Food and Biological Engineering, Xihua University, Chengdu, 610039, China
| | - Fu-Chu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Yin-Hua Lu
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA.
| | - Guo-Ping Zhao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200032, China.
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China.
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China.
- Department of Microbiology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, China.
- Guizhou University, School of Medicine, Guiyang, 550025, China.
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China.
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27
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Sinha S, Callow BW, Farfel AP, Roy S, Chen S, Rajendran S, Buschhaus JM, Luker KE, Ghosh P, Luker GD. A Multiomic Analysis Reveals How Breast Cancers Disseminated to the Bone Marrow Acquire Aggressive Phenotypes through Tumor-Stroma Tunnels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.18.533175. [PMID: 36993616 PMCID: PMC10055300 DOI: 10.1101/2023.03.18.533175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Estrogen receptor-positive (ER+) breast cancer commonly disseminates to bone marrow, where interactions with mesenchymal stromal cells (MSCs) shape disease trajectory. We modeled these interactions with tumor-MSC co-cultures and used an integrated transcriptome-proteome-network- analyses workflow to identify a comprehensive catalog of contact-induced changes. Induced genes and proteins in cancer cells, some borrowed and others tumor-intrinsic, were not recapitulated merely by conditioned media from MSCs. Protein-protein interaction networks revealed the rich connectome between 'borrowed' and 'intrinsic' components. Bioinformatic approaches prioritized one of the 'borrowed' components, CCDC88A /GIV, a multi-modular metastasis-related protein which has recently been implicated in driving one of the hallmarks of cancers, i.e., growth signaling autonomy. MSCs transferred GIV protein to ER+ breast cancer cells (that lack GIV) through tunnelling nanotubes via connexin (Cx)43-facilitated intercellular transport. Reinstating GIV alone in GIV-negative breast cancer cells reproduced ∼20% of both the 'borrowed' and the 'intrinsic' gene induction patterns from contact co-cultures; conferred resistance to anti-estrogen drugs; and enhanced tumor dissemination. Findings provide a multiomic insight into MSC→tumor cell intercellular transport and validate how transport of one such candidate, GIV, from the haves (MSCs) to have-nots (ER+ breast cancer) orchestrates aggressive disease states.
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28
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Cytoplasmic contractile injection systems mediate cell death in Streptomyces. Nat Microbiol 2023; 8:711-726. [PMID: 36894633 PMCID: PMC10066040 DOI: 10.1038/s41564-023-01341-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 02/10/2023] [Indexed: 03/11/2023]
Abstract
Contractile injection systems (CIS) are bacteriophage tail-like structures that mediate bacterial cell-cell interactions. While CIS are highly abundant across diverse bacterial phyla, representative gene clusters in Gram-positive organisms remain poorly studied. Here we characterize a CIS in the Gram-positive multicellular model organism Streptomyces coelicolor and show that, in contrast to most other CIS, S. coelicolor CIS (CISSc) mediate cell death in response to stress and impact cellular development. CISSc are expressed in the cytoplasm of vegetative hyphae and are not released into the medium. Our cryo-electron microscopy structure enabled the engineering of non-contractile and fluorescently tagged CISSc assemblies. Cryo-electron tomography showed that CISSc contraction is linked to reduced cellular integrity. Fluorescence light microscopy furthermore revealed that functional CISSc mediate cell death upon encountering different types of stress. The absence of functional CISSc had an impact on hyphal differentiation and secondary metabolite production. Finally, we identified three putative effector proteins, which when absent, phenocopied other CISSc mutants. Our results provide new functional insights into CIS in Gram-positive organisms and a framework for studying novel intracellular roles, including regulated cell death and life-cycle progression in multicellular bacteria.
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29
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Colizzi ES, van Dijk B, Merks RMH, Rozen DE, Vroomans RMA. Evolution of genome fragility enables microbial division of labor. Mol Syst Biol 2023; 19:e11353. [PMID: 36727665 PMCID: PMC9996244 DOI: 10.15252/msb.202211353] [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: 09/14/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 02/03/2023] Open
Abstract
Division of labor can evolve when social groups benefit from the functional specialization of its members. Recently, a novel means of coordinating the division of labor was found in the antibiotic-producing bacterium Streptomyces coelicolor, where specialized cells are generated through large-scale genomic re-organization. We investigate how the evolution of a genome architecture enables such mutation-driven division of labor, using a multiscale computational model of bacterial evolution. In this model, bacterial behavior-antibiotic production or replication-is determined by the structure and composition of their genome, which encodes antibiotics, growth-promoting genes, and fragile genomic loci that can induce chromosomal deletions. We find that a genomic organization evolves, which partitions growth-promoting genes and antibiotic-coding genes into distinct parts of the genome, separated by fragile genomic loci. Mutations caused by these fragile sites mostly delete growth-promoting genes, generating sterile, and antibiotic-producing mutants from weakly-producing progenitors, in agreement with experimental observations. This division of labor enhances the competition between colonies by promoting antibiotic diversity. These results show that genomic organization can co-evolve with genomic instabilities to enable reproductive division of labor.
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Affiliation(s)
- Enrico Sandro Colizzi
- Mathematical Institute, Leiden University, Leiden, The Netherlands.,Origins Center, Leiden, The Netherlands.,Sainsbury Laboratory, Cambridge University, Cambridge, UK
| | - Bram van Dijk
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Roeland M H Merks
- Mathematical Institute, Leiden University, Leiden, The Netherlands.,Origins Center, Leiden, The Netherlands.,Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Daniel E Rozen
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Renske M A Vroomans
- Origins Center, Leiden, The Netherlands.,Sainsbury Laboratory, Cambridge University, Cambridge, UK.,Informatic Institute, University of Amsterdam, Amsterdam, The Netherlands
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30
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Tang S, Pichugin Y, Hammerschmidt K. An environmentally induced multicellular life cycle of a unicellular cyanobacterium. Curr Biol 2023; 33:764-769.e5. [PMID: 36854263 DOI: 10.1016/j.cub.2023.01.069] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/19/2022] [Accepted: 01/04/2023] [Indexed: 03/02/2023]
Abstract
Understanding the evolutionary transition to multicellularity is a key problem in biology.1,2,3,4 Nevertheless, the ecological conditions driving such transitions are not well understood. The first known transition to multicellularity occurred 2.5 billion years ago in cyanobacteria,5,6,7 and today's cyanobacteria are characterized by enormous morphological diversity. They range from unicellular species; unicellular cyanobacteria with packet-like phenotypes, e.g., tetrads; and simple filamentous species to highly differentiated filamentous species.8,9,10 The cyanobacterium Cyanothece sp. ATCC 51142, an isolate from the intertidal zone of the U.S. Gulf Coast,11 was classified as a unicellular species.12 We report a facultative life cycle of Cyanothece sp. in which multicellular filaments alternate with unicellular stages. In a series of experiments, we identified salinity and population density as environmental factors triggering the phenotypic switch between the two morphologies. Then, we used numerical models to test hypotheses regarding the nature of the environmental cues and the mechanisms underlying filament dissolution. While the results predict that the observed response is likely caused by an excreted compound in the medium, we cannot fully exclude changes in nutrient availability (as in Tuomi et al.13 and Matz and Jürgens14). The best-fit modeling results show a nonlinear effect of the compound, which is characteristic of density-dependent sensing systems.15,16 Furthermore, filament fragmentation is predicted to occur by connection cleavage rather than cell death of each alternating cell, which is supported by fluorescent and scanning electron microscopy results. The switch between unicellular and multicellular morphology constitutes an environmentally dependent life cycle that is likely an important step en route to permanent multicellularity.
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Affiliation(s)
- Si Tang
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Yuriy Pichugin
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany.
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31
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Zhang L, Willemse J, Yagüe P, de Waal E, Claessen D, van Wezel GP. The SepF-like proteins SflA and SflB prevent ectopic localization of FtsZ and DivIVA during sporulation of Streptomyces coelicolor. Biochem Biophys Res Commun 2023; 645:79-87. [PMID: 36680940 DOI: 10.1016/j.bbrc.2023.01.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023]
Abstract
Bacterial cytokinesis starts with the polymerization of the tubulin-like FtsZ, which forms the cell division scaffold. SepF aligns FtsZ polymers and also acts as a membrane anchor for the Z-ring. While in most bacteria cell division takes place at midcell, during sporulation of Streptomyces many septa are laid down almost simultaneously in multinucleoid aerial hyphae. The genomes of streptomycetes encode two additional SepF paralogs, SflA and SflB, which can interact with SepF. Here we show that the sporogenic aerial hyphae of sflA and sflB mutants of Streptomyces coelicolor frequently branch, a phenomenon never seen in the wild-type strain. The branching coincided with ectopic localization of DivIVA along the lateral wall of sporulating aerial hyphae. Constitutive expression of SflA and SflB largely inhibited hyphal growth, further correlating SflAB activity to that of DivIVA. SflAB localized in foci prior to and after the time of sporulation-specific cell division, while SepF co-localized with active septum synthesis. Foci of FtsZ and DivIVA frequently persisted between adjacent spores in spore chains of sflA and sflB mutants, at sites occupied by SflAB in wild-type cells. Taken together, our data show that SflA and SflB play an important role in the control of growth and cell division during Streptomyces development.
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Affiliation(s)
- Le Zhang
- Department of Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, Leiden, 2300, AB, the Netherlands
| | - Joost Willemse
- Department of Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, Leiden, 2300, AB, the Netherlands
| | - Paula Yagüe
- Departamento de Biología Funcional e IUOPA, Área de Microbiología, Facultad de Medicina, Universidad de Oviedo, Oviedo, 33006, Spain
| | - Ellen de Waal
- Department of Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, Leiden, 2300, AB, the Netherlands
| | - Dennis Claessen
- Department of Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, Leiden, 2300, AB, the Netherlands
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, Leiden, 2300, AB, the Netherlands.
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32
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Salimimarand M, Rizzacasa MA. Synthesis of isochromanone containing natural products from myxobacteria. Org Biomol Chem 2023; 21:1341-1355. [PMID: 36655696 DOI: 10.1039/d2ob01926d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
This review details the biological activity, biosynthesis and synthesis of isochromanone metabolites isolated from myxobacteria. Strategies towards the synthesis of the isochomanone and oxazole fragments of these natural products are highlighted.
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Affiliation(s)
- Mina Salimimarand
- School of Chemistry, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, Australia.
| | - Mark A Rizzacasa
- School of Chemistry, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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33
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Tychonema sp. BBK16 Characterisation: Lifestyle, Phylogeny and Related Phages. Viruses 2023; 15:v15020442. [PMID: 36851656 PMCID: PMC9958718 DOI: 10.3390/v15020442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
Cyanobacterial expansion is harmful to the environment, the ecology of Lake Baikal and the economy of nearby regions and can be dangerous to people and animals. Since 2011, the process of colonisation of the lake with potentially toxic cyanobacteria belonging to the genus Tychonema has continued. An understanding of the mechanism of successful expansion of Tychonema requires scrutiny of biological and genomic features. Tychonema sp. BBK16 was isolated from the coastal zone of Lake Baikal. The morphology of BBK16 biofilm was studied with light, scanning electron and confocal microscopy. The biofilm is based on filaments of cyanobacteria, which are intertwined like felt; there are also dense fascicles of rope-like twisted filaments that impart heterogeneity to the surface of the biofilm. Genome sequencing, intergenomic comparisons and phylogenetic analyses indicated that Tychonema sp. BBK16 represent a new species related to planktic cyanobacterium Tychonema bourrellyi, isolated from Alpine lentic freshwater. Genome investigation revealed the genes possibly responsible for the mixotrophic lifestyle. The presence of CRISPR-Cas and restriction modification defence mechanisms allowed to suggest the existence of phages infecting Tychonema sp. BBK16. Analysis of CRISPR spacers and prophage-derived regions allowed to suggest related cyanophages. Genomic analysis supported the assumption that mobile elements and horizontal transfer participate in shaping the Tychonema sp. BBK16 genome. The findings of the current research suggest that the aptitude of Tychonema sp. BBK16 for biofilm formation and, possibly, its mixotrophic lifestyle provide adaptation advantages that lead to the successful expansion of this cyanobacterium in the Baikal's conditions of freshwater lake environments.
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Vanreppelen G, Wuyts J, Van Dijck P, Vandecruys P. Sources of Antifungal Drugs. J Fungi (Basel) 2023; 9:jof9020171. [PMID: 36836286 PMCID: PMC9965926 DOI: 10.3390/jof9020171] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/22/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Due to their eukaryotic heritage, the differences between a fungal pathogen's molecular makeup and its human host are small. Therefore, the discovery and subsequent development of novel antifungal drugs are extremely challenging. Nevertheless, since the 1940s, researchers have successfully uncovered potent candidates from natural or synthetic sources. Analogs and novel formulations of these drugs enhanced the pharmacological parameters and improved overall drug efficiency. These compounds ultimately became the founding members of novel drug classes and were successfully applied in clinical settings, offering valuable and efficient treatment of mycosis for decades. Currently, only five different antifungal drug classes exist, all characterized by a unique mode of action; these are polyenes, pyrimidine analogs, azoles, allylamines, and echinocandins. The latter, being the latest addition to the antifungal armamentarium, was introduced over two decades ago. As a result of this limited arsenal, antifungal resistance development has exponentially increased and, with it, a growing healthcare crisis. In this review, we discuss the original sources of antifungal compounds, either natural or synthetic. Additionally, we summarize the existing drug classes, potential novel candidates in the clinical pipeline, and emerging non-traditional treatment options.
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35
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Khushboo, Singhvi N, Gupta V, Dhaka N, Dubey KK. Draft genome sequence of Streptomyces sp. KD18, isolated from industrial soil. 3 Biotech 2023; 13:34. [PMID: 36619820 PMCID: PMC9810780 DOI: 10.1007/s13205-022-03453-3] [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: 10/21/2022] [Accepted: 12/24/2022] [Indexed: 01/05/2023] Open
Abstract
The present study scrutinizes the presence of Streptomyces strains in the soil sample collected from industrial area of Bahadurgarh (Haryana) India. The morphological approach manifested the isolated strain belong to Streptomyces species and named as Streptomyces sp. KD18. Sequencing of Streptomyces sp. KD18 genome was performed by Illumina Nextseq500 platform. 65 contigs were generated via SPAdes v3.11.1 and harboured genome size of 7.2 Mb. AntiSMASH server revealed the presence of 25 biosynthetic gene clusters in KD18 genome where BGC of lipstatin was of more interest from industrial and pharmaceutical purpose. The draft genome sequence represented via ANI values claimed that the KD18 strain belongs to Streptomyces toxytricini and finally named as S. toxytricini KD18. The LC-MS analysis of the extracted metabolite confirmed the production of lipstatin. The genome sequence data have been deposited to NCBI under the accession number of GCA_014748315.1. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03453-3.
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Affiliation(s)
- Khushboo
- Department of Biotechnology, Central University of Haryana, Mahendergarh, 123031 India
| | - Nirjara Singhvi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, Uttarakhand 248007 India
| | - Vipin Gupta
- Ministry of Environment, Forest and Climate Change, Integrated Regional Office, Dehradun, Uttarakhand 248001 India
| | - Namrata Dhaka
- Department of Biotechnology, Central University of Haryana, Mahendergarh, 123031 India
| | - Kashyap Kumar Dubey
- Bioprocess Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
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Yagüe P, Willemse J, Xiao X, Zhang L, Manteca A, van Wezel GP. FtsZ phosphorylation pleiotropically affects Z-ladder formation, antibiotic production, and morphogenesis in Streptomyces coelicolor. Antonie Van Leeuwenhoek 2023; 116:1-19. [PMID: 36383329 PMCID: PMC9823044 DOI: 10.1007/s10482-022-01778-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 08/27/2022] [Indexed: 11/17/2022]
Abstract
The GTPase FtsZ forms the cell division scaffold in bacteria, which mediates the recruitment of the other components of the divisome. Streptomycetes undergo two different forms of cell division. Septa without detectable peptidoglycan divide the highly compartmentalised young hyphae during early vegetative growth, and cross-walls are formed that dissect the hyphae into long multinucleoid compartments in the substrate mycelium, while ladders of septa are formed in the aerial hyphae that lead to chains of uninucleoid spores. In a previous study, we analysed the phosphoproteome of Streptomyces coelicolor and showed that FtsZ is phosphorylated at Ser 317 and Ser389. Substituting Ser-Ser for either Glu-Glu (mimicking phosphorylation) or Ala-Ala (mimicking non-phosphorylation) hinted at changes in antibiotic production. Here we analyse development, colony morphology, spore resistance, and antibiotic production in FtsZ knockout mutants expressing FtsZ alleles mimicking Ser319 and Ser387 phosphorylation and non-phosphorylation: AA (no phosphorylation), AE, EA (mixed), and EE (double phosphorylation). The FtsZ-eGFP AE, EA and EE alleles were not able to form observable FtsZ-eGFP ladders when they were expressed in the S. coelicolor wild-type strain, whereas the AA allele could form apparently normal eGFP Z-ladders. The FtsZ mutant expressing the FtsZ EE or EA or AE alleles is able to sporulate indicating that the mutant alleles are able to form functional Z-rings leading to sporulation when the wild-type FtsZ gene is absent. The four mutants were pleiotropically affected in colony morphogenesis, antibiotic production, substrate mycelium differentiation and sporulation (sporulation timing and spore resistance) which may be an indirect result of the effect in sporulation Z-ladder formation. Each mutant showed a distinctive phenotype in antibiotic production, single colony morphology, and sporulation (sporulation timing and spore resistance) indicating that the different FtsZ phosphomimetic alleles led to different phenotypes. Taken together, our data provide evidence for a pleiotropic effect of FtsZ phosphorylation in colony morphology, antibiotic production, and sporulation.
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Affiliation(s)
- Paula Yagüe
- grid.5132.50000 0001 2312 1970Department of Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, 2300 AB Leiden, The Netherlands
| | - Joost Willemse
- grid.5132.50000 0001 2312 1970Department of Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, 2300 AB Leiden, The Netherlands
| | - Xiansha Xiao
- grid.5132.50000 0001 2312 1970Department of Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, 2300 AB Leiden, The Netherlands
| | - Le Zhang
- grid.5132.50000 0001 2312 1970Department of Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, 2300 AB Leiden, The Netherlands
| | - Angel Manteca
- grid.10863.3c0000 0001 2164 6351Departamento de Biología Funcional e IUOPA, Área de Microbiología, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Gilles P. van Wezel
- grid.5132.50000 0001 2312 1970Department of Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, 2300 AB Leiden, The Netherlands
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Aguilera A, Distéfano A, Jauzein C, Correa-Aragunde N, Martinez D, Martin MV, Sueldo DJ. Do photosynthetic cells communicate with each other during cell death? From cyanobacteria to vascular plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7219-7242. [PMID: 36179088 DOI: 10.1093/jxb/erac363] [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: 02/19/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
As in metazoans, life in oxygenic photosynthetic organisms relies on the accurate regulation of cell death. During development and in response to the environment, photosynthetic cells activate and execute cell death pathways that culminate in the death of a specific group of cells, a process known as regulated cell death (RCD). RCD control is instrumental, as its misregulation can lead to growth penalties and even the death of the entire organism. Intracellular molecules released during cell demise may act as 'survival' or 'death' signals and control the propagation of cell death to surrounding cells, even in unicellular organisms. This review explores different signals involved in cell-cell communication and systemic signalling in photosynthetic organisms, in particular Ca2+, reactive oxygen species, lipid derivates, nitric oxide, and eATP. We discuss their possible mode-of-action as either 'survival' or 'death' molecules and their potential role in determining cell fate in neighbouring cells. By comparing the knowledge available across the taxonomic spectrum of this coherent phylogenetic group, from cyanobacteria to vascular plants, we aim at contributing to the identification of conserved mechanisms that control cell death propagation in oxygenic photosynthetic organisms.
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Affiliation(s)
- Anabella Aguilera
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 39231 Kalmar, Sweden
| | - Ayelén Distéfano
- Instituto de Investigaciones Biológicas-CONICET, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Cécile Jauzein
- Ifremer, Centre de Brest, DYNECO-Pelagos, F-29280 Plouzané, France
| | - Natalia Correa-Aragunde
- Instituto de Investigaciones Biológicas-CONICET, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Dana Martinez
- Instituto de Fisiología Vegetal (INFIVE-CONICET), Universidad Nacional de La Plata, 1900 La Plata, Argentina
| | - María Victoria Martin
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), Fundación para Investigaciones Biológicas Aplicadas (FIBA), Universidad Nacional de Mar del Plata,7600 Mar del Plata, Argentina
| | - Daniela J Sueldo
- Norwegian University of Science and Technology, 7491 Trondheim, Norway
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Overcoming Antibiotic Resistance with Novel Paradigms of Antibiotic Selection. Microorganisms 2022; 10:microorganisms10122383. [PMID: 36557636 PMCID: PMC9781420 DOI: 10.3390/microorganisms10122383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
Conventional antimicrobial susceptibility tests, including phenotypic and genotypic methods, are insufficiently accurate and frequently fail to identify effective antibiotics. These methods predominantly select therapies based on the antibiotic response of only the lead bacterial pathogen within pure bacterial culture. However, this neglects the fact that, in the majority of human infections, the lead bacterial pathogens are present as a part of multispecies communities that modulate the response of these lead pathogens to antibiotics and that multiple pathogens can contribute to the infection simultaneously. This discrepancy is a major cause of the failure of antimicrobial susceptibility tests to detect antibiotics that are effective in vivo. This review article provides a comprehensive overview of the factors that are missed by conventional antimicrobial susceptibility tests and it explains how accounting for these methods can aid the development of novel diagnostic approaches.
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39
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Oda AH, Tamura M, Kaneko K, Ohta K, Hatakeyama TS. Autotoxin-mediated latecomer killing in yeast communities. PLoS Biol 2022; 20:e3001844. [PMID: 36342925 PMCID: PMC9639812 DOI: 10.1371/journal.pbio.3001844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 09/22/2022] [Indexed: 11/09/2022] Open
Abstract
Cellular adaptation to stressful environments such as starvation is essential to the survival of microbial communities, but the uniform response of the cell community may lead to entire cell death or severe damage to their fitness. Here, we demonstrate an elaborate response of the yeast community against glucose depletion, in which the first adapted cells kill the latecomer cells. During glucose depletion, yeast cells release autotoxins, such as leucic acid and L-2keto-3methylvalerate, which can even kill the clonal cells of the ones producing them. Although these autotoxins were likely to induce mass suicide, some cells differentiated to adapt to the autotoxins without genetic changes. If nondifferentiated latecomers tried to invade the habitat, autotoxins damaged or killed the latecomers, but the differentiated cells could selectively survive. Phylogenetically distant fission and budding yeast shared this behavior using the same autotoxins, suggesting that latecomer killing may be the universal system of intercellular communication, which may be relevant to the evolutional transition from unicellular to multicellular organisms.
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Affiliation(s)
- Arisa H. Oda
- Department of Basic Science, University of Tokyo, Tokyo, Japan
- * E-mail: (AHO); (TSH)
| | - Miki Tamura
- Department of Basic Science, University of Tokyo, Tokyo, Japan
| | - Kunihiko Kaneko
- Department of Basic Science, University of Tokyo, Tokyo, Japan
- Research Center for Complex Systems Biology, Universal Biology Institute, University of Tokyo, Tokyo, Japan
- The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Kunihiro Ohta
- Department of Basic Science, University of Tokyo, Tokyo, Japan
- Research Center for Complex Systems Biology, Universal Biology Institute, University of Tokyo, Tokyo, Japan
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40
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Romeu MJ, Lima M, Gomes LC, de Jong ED, Morais J, Vasconcelos V, Pereira MFR, Soares OSGP, Sjollema J, Mergulhão FJ. The Use of 3D Optical Coherence Tomography to Analyze the Architecture of Cyanobacterial Biofilms Formed on a Carbon Nanotube Composite. Polymers (Basel) 2022; 14:polym14204410. [PMID: 36297988 PMCID: PMC9607013 DOI: 10.3390/polym14204410] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
The development of environmentally friendly antifouling strategies for marine applications is of paramount importance, and the fabrication of innovative nanocomposite coatings is a promising approach. Moreover, since Optical Coherence Tomography (OCT) is a powerful imaging technique in biofilm science, the improvement of its analytical power is required to better evaluate the biofilm structure under different scenarios. In this study, the effect of carbon nanotube (CNT)-modified surfaces in cyanobacterial biofilm development was assessed over a long-term assay under controlled hydrodynamic conditions. Their impact on the cyanobacterial biofilm architecture was evaluated by novel parameters obtained from three-dimensional (3D) OCT analysis, such as the contour coefficient, total biofilm volume, biovolume, volume of non-connected pores, and the average size of non-connected pores. The results showed that CNTs incorporated into a commercially used epoxy resin (CNT composite) had a higher antifouling effect at the biofilm maturation stage compared to pristine epoxy resin. Along with a delay in biofilm development, a decrease in biofilm wet weight, thickness, and biovolume was also achieved with the CNT composite compared to epoxy resin and glass (control surfaces). Additionally, biofilms developed on the CNT composite were smoother and presented a lower porosity and a strictly packed structure when compared with those formed on the control surfaces. The novel biofilm parameters obtained from 3D OCT imaging are extremely important when evaluating the biofilm architecture and behavior under different scenarios beyond marine applications.
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Affiliation(s)
- Maria J. Romeu
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Marta Lima
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Luciana C. Gomes
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Ed. D. de Jong
- Department of Biomedical Engineering, University of Groningen, University Medical Centre Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - João Morais
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Vítor Vasconcelos
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Manuel F. R. Pereira
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- LSRE–LCM—Laboratory of Separation and Reaction Engineering–Laboratory of Catalysis and Materials, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Olívia S. G. P. Soares
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- LSRE–LCM—Laboratory of Separation and Reaction Engineering–Laboratory of Catalysis and Materials, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Jelmer Sjollema
- Department of Biomedical Engineering, University of Groningen, University Medical Centre Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Filipe J. Mergulhão
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- Correspondence: ; Tel.: +351-225081668
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41
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Hydrodynamic conditions affect the proteomic profile of marine biofilms formed by filamentous cyanobacterium. NPJ Biofilms Microbiomes 2022; 8:80. [PMID: 36253388 PMCID: PMC9576798 DOI: 10.1038/s41522-022-00340-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 09/23/2022] [Indexed: 11/08/2022] Open
Abstract
Proteomic studies on cyanobacterial biofilms can be an effective approach to unravel metabolic pathways involved in biofilm formation and, consequently, obtain more efficient biofouling control strategies. Biofilm development by the filamentous cyanobacterium Toxifilum sp. LEGE 06021 was evaluated on different surfaces, glass and perspex, and at two significant shear rates for marine environments (4 s-1 and 40 s-1). Higher biofilm development was observed at 4 s-1. Overall, about 1877 proteins were identified, and differences in proteome were more noticeable between hydrodynamic conditions than those found between surfaces. Twenty Differentially Expressed Proteins (DEPs) were found between 4 s-1 vs. 40 s-1. On glass, some of these DEPs include phage tail proteins, a carotenoid protein, cyanophynase glutathione-dependent formaldehyde dehydrogenase, and the MoaD/ThiS family protein, while on perspex, DEPs include transketolase, dihydroxy-acid dehydratase, iron ABC transporter substrate-binding protein and protein NusG. This study contributes to developing a standardized protocol for proteomic analysis of filamentous cyanobacterial biofilms. This kind of proteomic analysis can also be useful for different research fields, given the broad spectrum of promising secondary metabolites and added-value compounds produced by cyanobacteria, as well as for the development of new antibiofilm strategies.
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42
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Mizuno K, Maree M, Nagamura T, Koga A, Hirayama S, Furukawa S, Tanaka K, Morikawa K. Novel multicellular prokaryote discovered next to an underground stream. eLife 2022; 11:71920. [PMID: 36217817 PMCID: PMC9555858 DOI: 10.7554/elife.71920] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
A diversity of prokaryotes currently exhibit multicellularity with different generation mechanisms in a variety of contexts of ecology on Earth. In the present study, we report a new type of multicellular bacterium, HS-3, isolated from an underground stream. HS-3 self-organizes its filamentous cells into a layer-structured colony with the properties of a nematic liquid crystal. After maturation, the colony starts to form a semi-closed sphere accommodating clusters of coccobacillus daughter cells and selectively releases them upon contact with water. This is the first report that shows that a liquid-crystal status of cells can support the prokaryotic multicellular behavior. Importantly, the observed behavior of HS-3 suggests that the recurrent intermittent exposure of colonies to water flow in the cave might have been the ecological context that cultivated the evolutionary transition from unicellular to multicellular life. This is the new extant model that underpins theories regarding a role of ecological context in the emergence of multicellularity.
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Affiliation(s)
- Kouhei Mizuno
- Division of International Affairs, Headquaters, National Institute of Technology, Tokyo, Japan.,Department of Creative Engineering, National Institute of Technology, Kitakyushu, Japan
| | - Mais Maree
- Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Toshihiko Nagamura
- Department of Creative Engineering, National Institute of Technology, Kitakyushu, Japan
| | - Akihiro Koga
- Department of Creative Engineering, National Institute of Technology, Kitakyushu, Japan
| | - Satoru Hirayama
- Department of Food Bioscience and Biotechnology, College of Bioresource Sciences, Nihon University, Fujisawa, Japan.,Division of Microbiology and Infectious Diseases, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Soichi Furukawa
- Department of Food Bioscience and Biotechnology, College of Bioresource Sciences, Nihon University, Fujisawa, Japan
| | - Kenji Tanaka
- Department of Biological and Environmental Chemistry, School of Humanity-Oriented Science and Engineering, Kindai University, Iizuka, Japan
| | - Kazuya Morikawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
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43
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Tetz V, Tetz G. Novel prokaryotic system employing previously unknown nucleic acids-based receptors. Microb Cell Fact 2022; 21:202. [PMID: 36195904 PMCID: PMC9531389 DOI: 10.1186/s12934-022-01923-0] [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: 08/24/2022] [Accepted: 09/16/2022] [Indexed: 12/26/2022] Open
Abstract
The present study describes a previously unknown universal system that orchestrates the interaction of bacteria with the environment, named the Teazeled receptor system (TR-system). The identical system was recently discovered within eukaryotes. The system includes DNA- and RNA-based molecules named "TezRs", that form receptor's network located outside the membrane, as well as reverse transcriptases and integrases. TR-system takes part in the control of all major aspects of bacterial behavior, such as intra cellular communication, growth, biofilm formation and dispersal, utilization of nutrients including xenobiotics, virulence, chemo- and magnetoreception, response to external factors (e.g., temperature, UV, light and gas content), mutation events, phage-host interaction, and DNA recombination activity. Additionally, it supervises the function of other receptor-mediated signaling pathways. Importantly, the TR-system is responsible for the formation and maintenance of cell memory to preceding cellular events, as well the ability to "forget" preceding events. Transcriptome and biochemical analysis revealed that the loss of different TezRs instigates significant alterations in gene expression and proteins synthesis.
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Affiliation(s)
- Victor Tetz
- Human Microbiology Institute, New York, NY, 10013, USA
| | - George Tetz
- Human Microbiology Institute, New York, NY, 10013, USA.
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44
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Pérez J, Contreras-Moreno FJ, Muñoz-Dorado J, Moraleda-Muñoz A. Development versus predation: Transcriptomic changes during the lifecycle of Myxococcus xanthus. Front Microbiol 2022; 13:1004476. [PMID: 36225384 PMCID: PMC9548883 DOI: 10.3389/fmicb.2022.1004476] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Myxococcus xanthus is a multicellular bacterium with a complex lifecycle. It is a soil-dwelling predator that preys on a wide variety of microorganisms by using a group and collaborative epibiotic strategy. In the absence of nutrients this myxobacterium enters in a unique developmental program by using sophisticated and complex regulatory systems where more than 1,400 genes are transcriptional regulated to guide the community to aggregate into macroscopic fruiting bodies filled of environmentally resistant myxospores. Herein, we analyze the predatosome of M. xanthus, that is, the transcriptomic changes that the predator undergoes when encounters a prey. This study has been carried out using as a prey Sinorhizobium meliloti, a nitrogen fixing bacteria very important for the fertility of soils. The transcriptional changes include upregulation of genes that help the cells to detect, kill, lyse, and consume the prey, but also downregulation of genes not required for the predatory process. Our results have shown that, as expected, many genes encoding hydrolytic enzymes and enzymes involved in biosynthesis of secondary metabolites increase their expression levels. Moreover, it has been found that the predator modifies its lipid composition and overproduces siderophores to take up iron. Comparison with developmental transcriptome reveals that M. xanthus downregulates the expression of a significant number of genes coding for regulatory elements, many of which have been demonstrated to be key elements during development. This study shows for the first time a global view of the M. xanthus lifecycle from a transcriptome perspective.
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45
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Nyongesa S, Weber PM, Bernet È, Pulido F, Nieves C, Nieckarz M, Delaby M, Viehboeck T, Krause N, Rivera-Millot A, Nakamura A, Vischer NOE, vanNieuwenhze M, Brun YV, Cava F, Bulgheresi S, Veyrier FJ. Evolution of longitudinal division in multicellular bacteria of the Neisseriaceae family. Nat Commun 2022; 13:4853. [PMID: 35995772 PMCID: PMC9395523 DOI: 10.1038/s41467-022-32260-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Rod-shaped bacteria typically elongate and divide by transverse fission. However, several bacterial species can form rod-shaped cells that divide longitudinally. Here, we study the evolution of cell shape and division mode within the family Neisseriaceae, which includes Gram-negative coccoid and rod-shaped species. In particular, bacteria of the genera Alysiella, Simonsiella and Conchiformibius, which can be found in the oral cavity of mammals, are multicellular and divide longitudinally. We use comparative genomics and ultrastructural microscopy to infer that longitudinal division within Neisseriaceae evolved from a rod-shaped ancestor. In multicellular longitudinally-dividing species, neighbouring cells within multicellular filaments are attached by their lateral peptidoglycan. In these bacteria, peptidoglycan insertion does not appear concentric, i.e. from the cell periphery to its centre, but as a medial sheet guillotining each cell. Finally, we identify genes and alleles associated with multicellularity and longitudinal division, including the acquisition of amidase-encoding gene amiC2, and amino acid changes in proteins including MreB and FtsA. Introduction of amiC2 and allelic substitution of mreB in a rod-shaped species that divides by transverse fission results in shorter cells with longer septa. Our work sheds light on the evolution of multicellularity and longitudinal division in bacteria, and suggests that members of the Neisseriaceae family may be good models to study these processes due to their morphological plasticity and genetic tractability. Rod-shaped bacteria typically elongate and divide by transverse fission, but a few species are known to divide longitudinally. Here, the authors use genomic, phylogenetic and microscopy techniques to shed light on the evolution of cell shape, multicellularity and division mode within the family Neisseriaceae.
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Affiliation(s)
- Sammy Nyongesa
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, QC, H7V 1B7, Canada
| | - Philipp M Weber
- Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, University of Vienna, Vienna, Djerassiplatz 1, 1030, Vienna, Austria.,University of Vienna, Vienna Doctoral School of Ecology and Evolution, Vienna, Austria
| | - Ève Bernet
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, QC, H7V 1B7, Canada
| | - Francisco Pulido
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, QC, H7V 1B7, Canada
| | - Cecilia Nieves
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, QC, H7V 1B7, Canada
| | - Marta Nieckarz
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, SE-90187, Sweden
| | - Marie Delaby
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC, Canada
| | - Tobias Viehboeck
- Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, University of Vienna, Vienna, Djerassiplatz 1, 1030, Vienna, Austria.,University of Vienna, Vienna Doctoral School of Ecology and Evolution, Vienna, Austria.,Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, , University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Nicole Krause
- Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, University of Vienna, Vienna, Djerassiplatz 1, 1030, Vienna, Austria.,University of Vienna, Vienna Doctoral School of Ecology and Evolution, Vienna, Austria
| | - Alex Rivera-Millot
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, QC, H7V 1B7, Canada
| | - Arnaldo Nakamura
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, QC, H7V 1B7, Canada
| | - Norbert O E Vischer
- Bacterial Cell Biology & Physiology, Swammerdam Institute of Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098, Amsterdam, the Netherlands
| | | | - Yves V Brun
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC, Canada
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, SE-90187, Sweden
| | - Silvia Bulgheresi
- Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, University of Vienna, Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Frédéric J Veyrier
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, QC, H7V 1B7, Canada.
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46
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To Die or Not to Die—Regulated Cell Death and Survival in Cyanobacteria. Microorganisms 2022; 10:microorganisms10081657. [PMID: 36014075 PMCID: PMC9415839 DOI: 10.3390/microorganisms10081657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/06/2022] [Accepted: 08/12/2022] [Indexed: 11/24/2022] Open
Abstract
Regulated cell death (RCD) is central to the development, integrity, and functionality of multicellular organisms. In the last decade, evidence has accumulated that RCD is a universal phenomenon in all life domains. Cyanobacteria are of specific interest due to their importance in aquatic and terrestrial habitats and their role as primary producers in global nutrient cycling. Current knowledge on cyanobacterial RCD is based mainly on biochemical and morphological observations, often by methods directly transferred from vertebrate research and with limited understanding of the molecular genetic basis. However, the metabolism of different cyanobacteria groups relies on photosynthesis and nitrogen fixation, whereas mitochondria are the central executioner of cell death in vertebrates. Moreover, cyanobacteria chosen as biological models in RCD studies are mainly colonial or filamentous multicellular organisms. On the other hand, unicellular cyanobacteria have regulated programs of cellular survival (RCS) such as chlorosis and post-chlorosis resuscitation. The co-existence of different genetically regulated programs in cyanobacterial populations may have been a top engine in life diversification. Development of cyanobacteria-specific methods for identification and characterization of RCD and wider use of single-cell analysis combined with intelligent image-based cell sorting and metagenomics would shed more light on the underlying molecular mechanisms and help us to address the complex colonial interactions during these events. In this review, we focus on the functional implications of RCD in cyanobacterial communities.
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47
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Diegmiller R, Nunley H, Shvartsman SY, Imran Alsous J. Quantitative models for building and growing fated small cell networks. Interface Focus 2022; 12:20210082. [PMID: 35865502 PMCID: PMC9184967 DOI: 10.1098/rsfs.2021.0082] [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: 11/01/2021] [Accepted: 03/31/2022] [Indexed: 02/07/2023] Open
Abstract
Small cell clusters exhibit numerous phenomena typically associated with complex systems, such as division of labour and programmed cell death. A conserved class of such clusters occurs during oogenesis in the form of germline cysts that give rise to oocytes. Germline cysts form through cell divisions with incomplete cytokinesis, leaving cells intimately connected through intercellular bridges that facilitate cyst generation, cell fate determination and collective growth dynamics. Using the well-characterized Drosophila melanogaster female germline cyst as a foundation, we present mathematical models rooted in the dynamics of cell cycle proteins and their interactions to explain the generation of germline cell lineage trees (CLTs) and highlight the diversity of observed CLT sizes and topologies across species. We analyse competing models of symmetry breaking in CLTs to rationalize the observed dynamics and robustness of oocyte fate specification, and highlight remaining gaps in knowledge. We also explore how CLT topology affects cell cycle dynamics and synchronization and highlight mechanisms of intercellular coupling that underlie the observed collective growth patterns during oogenesis. Throughout, we point to similarities across organisms that warrant further investigation and comment on the extent to which experimental and theoretical findings made in model systems extend to other species.
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Affiliation(s)
- Rocky Diegmiller
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Hayden Nunley
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Stanislav Y. Shvartsman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA,Department of Molecular Biology, Princeton University, Princeton, NJ, USA,Flatiron Institute, Simons Foundation, New York, NY, USA
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48
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Schwartzman JA, Ebrahimi A, Chadwick G, Sato Y, Roller BRK, Orphan VJ, Cordero OX. Bacterial growth in multicellular aggregates leads to the emergence of complex life cycles. Curr Biol 2022; 32:3059-3069.e7. [PMID: 35777363 PMCID: PMC9496226 DOI: 10.1016/j.cub.2022.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/03/2022] [Accepted: 06/07/2022] [Indexed: 01/12/2023]
Abstract
Facultative multicellular behaviors expand the metabolic capacity and physiological resilience of bacteria. Despite their ubiquity in nature, we lack an understanding of how these behaviors emerge from cellular-scale phenomena. Here, we show how the coupling between growth and resource gradient formation leads to the emergence of multicellular lifecycles in a marine bacterium. Under otherwise carbon-limited growth conditions, Vibrio splendidus 12B01 forms clonal multicellular groups to collectively harvest carbon from soluble polymers of the brown-algal polysaccharide alginate. As they grow, groups phenotypically differentiate into two spatially distinct sub-populations: a static "shell" surrounding a motile, carbon-storing "core." Differentiation of these two sub-populations coincides with the formation of a gradient in nitrogen-source availability within clusters. Additionally, we find that populations of cells containing a high proportion of carbon-storing individuals propagate and form new clusters more readily on alginate than do populations with few carbon-storing cells. Together, these results suggest that local metabolic activity and differential partitioning of resources leads to the emergence of reproductive cycles in a facultatively multicellular bacterium.
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Affiliation(s)
- Julia A Schwartzman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Ali Ebrahimi
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Grayson Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yuya Sato
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Benjamin R K Roller
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Center for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, Vienna 1030, Austria; Department of Environmental Systems Sciences, ETH Zürich, Universitätsstrasse 16, Zürich 8092, Switzerland; Department of Environmental Microbiology, Eawag, Ueberlandstrasse 133, Dübendorf 8600, Switzerland
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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49
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Revealing bacterial cell biology using cryo-electron tomography. Curr Opin Struct Biol 2022; 75:102419. [PMID: 35820259 DOI: 10.1016/j.sbi.2022.102419] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022]
Abstract
Visualizing macromolecules inside bacteria at a high spatial resolution has remained a challenge owing to their small size and limited resolution of optical microscopy techniques. Recent advances in cryo-electron tomography (cryo-ET) imaging methods have revealed the spatial and temporal assemblies of many macromolecules involved in different cellular processes in bacteria at a resolution of a few nanometers in their native milieu. Specifically, the application of cryo-focused ion beam (cryo-FIB) milling to thin bacterial specimens makes them amenable for high-resolution cryo-ET data collection. In this review, we highlight recent research in three emerging areas of bacterial cell biology that have benefited from the cryo-FIB-ET technology - cytoskeletal filament assembly, intracellular organelles, and multicellularity.
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50
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Volland JM, Gonzalez-Rizzo S, Gros O, Tyml T, Ivanova N, Schulz F, Goudeau D, Elisabeth NH, Nath N, Udwary D, Malmstrom RR, Guidi-Rontani C, Bolte-Kluge S, Davies KM, Jean MR, Mansot JL, Mouncey NJ, Angert ER, Woyke T, Date SV. A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles. Science 2022; 376:1453-1458. [PMID: 35737788 DOI: 10.1126/science.abb3634] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cells of most bacterial species are around 2 micrometers in length, with some of the largest specimens reaching 750 micrometers. Using fluorescence, x-ray, and electron microscopy in conjunction with genome sequencing, we characterized Candidatus (Ca.) Thiomargarita magnifica, a bacterium that has an average cell length greater than 9000 micrometers and is visible to the naked eye. These cells grow orders of magnitude over theoretical limits for bacterial cell size, display unprecedented polyploidy of more than half a million copies of a very large genome, and undergo a dimorphic life cycle with asymmetric segregation of chromosomes into daughter cells. These features, along with compartmentalization of genomic material and ribosomes in translationally active organelles bound by bioenergetic membranes, indicate gain of complexity in the Thiomargarita lineage and challenge traditional concepts of bacterial cells.
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Affiliation(s)
- Jean-Marie Volland
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Laboratory for Research in Complex Systems, Menlo Park, CA, USA
| | - Silvina Gonzalez-Rizzo
- Institut de Systématique, Evolution, Biodiversité, Université des Antilles, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Campus de Fouillole, Pointe-à-Pitre, France
| | - Olivier Gros
- Institut de Systématique, Evolution, Biodiversité, Université des Antilles, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Campus de Fouillole, Pointe-à-Pitre, France.,Centre Commun de Caractérisation des Matériaux des Antilles et de la Guyane, Université des Antilles, UFR des Sciences Exactes et Naturelles, Pointe-à-Pitre, Guadeloupe, France
| | - Tomáš Tyml
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Laboratory for Research in Complex Systems, Menlo Park, CA, USA
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Danielle Goudeau
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nathalie H Elisabeth
- Department of Energy Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nandita Nath
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Daniel Udwary
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chantal Guidi-Rontani
- Institut de Systématique, Evolution, Biodiversité CNRS UMR 7205, Museum National d'Histoire Naturelle, Paris, France
| | - Susanne Bolte-Kluge
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS FRE3631, Institut de Biologie Paris Seine, Paris, France
| | - Karen M Davies
- Department of Energy Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, USA
| | - Maïtena R Jean
- Institut de Systématique, Evolution, Biodiversité, Université des Antilles, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Campus de Fouillole, Pointe-à-Pitre, France
| | - Jean-Louis Mansot
- Centre Commun de Caractérisation des Matériaux des Antilles et de la Guyane, Université des Antilles, UFR des Sciences Exactes et Naturelles, Pointe-à-Pitre, Guadeloupe, France
| | - Nigel J Mouncey
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Esther R Angert
- Cornell University, College of Agriculture and Life Sciences, Department of Microbiology, Ithaca, NY, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Laboratory for Research in Complex Systems, Menlo Park, CA, USA.,University of California Merced, School of Natural Sciences, Merced, CA, USA
| | - Shailesh V Date
- Laboratory for Research in Complex Systems, Menlo Park, CA, USA.,University of California San Francisco, San Francisco, CA, USA.,San Francisco State University, San Francisco, CA, USA
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