1
|
Abreu CI, Mathur S, Petrov DA. Environmental memory alters the fitness effects of adaptive mutations in fluctuating environments. Nat Ecol Evol 2024:10.1038/s41559-024-02475-9. [PMID: 39020024 DOI: 10.1038/s41559-024-02475-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 06/11/2024] [Indexed: 07/19/2024]
Abstract
Evolution in a static laboratory environment often proceeds via large-effect beneficial mutations that may become maladaptive in other environments. Conversely, natural settings require populations to endure environmental fluctuations. A sensible assumption is that the fitness of a lineage in a fluctuating environment is the time average of its fitness over the sequence of static conditions it encounters. However, transitions between conditions may pose entirely new challenges, which could cause deviations from this time average. To test this, we tracked hundreds of thousands of barcoded yeast lineages evolving in static and fluctuating conditions and subsequently isolated 900 mutants for pooled fitness assays in 15 environments. Here we find that fitness in fluctuating environments indeed often deviates from the time average, leading to fitness non-additivity. Moreover, closer examination reveals that fitness in one component of a fluctuating environment is often strongly influenced by the previous component. We show that this environmental memory is especially common for mutants with high variance in fitness across tested environments. We use a simple mathematical model and whole-genome sequencing to propose mechanisms underlying this effect, including lag time evolution and sensing mutations. Our results show that environmental fluctuations impact fitness and suggest that variance in static environments can explain these impacts.
Collapse
Affiliation(s)
- Clare I Abreu
- Department of Biology, Stanford University, Stanford, CA, USA.
| | - Shaili Mathur
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA, USA.
| |
Collapse
|
2
|
Anderson A, Van der Mijnsbrugge A, Cameleyre X, Gorret N. From yeast screening for suitability as single cell protein to fed-batch cultures. Biotechnol Lett 2024:10.1007/s10529-024-03504-0. [PMID: 39002086 DOI: 10.1007/s10529-024-03504-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 05/06/2024] [Accepted: 05/28/2024] [Indexed: 07/15/2024]
Abstract
PURPOSE Fed-batch cultures have rarely been used in single cell protein (SCP) research. This work evaluated multiple yeast species for suitability as SCP cultivated using glucose- and sucrose-based substrate and performed in-depth studies of fed-batch SCP cultivation kinetics for selected yeasts, including determination of specific crude nitrogen-to-protein conversion factors. METHODS SCP was cultivated using fully synthetic media in flask batch or bioreactor fed-batch cultures. Crude nitrogen and nucleic acid content were determined using the Dumas method and fluorescence assay kits, respectively. RESULTS C. utilis compared favorably to other yeasts in flask batch cultures in terms of process yield (0.52 ± 0.01 gx gs-1) and crude nitrogen content (10.0 ± 0.5 and 9.9 ± 0.5%CDW for glucose and sucrose, respectively). This is the first time biomass composition data was reported for SCP cultivated in fed-batch mode. C. utilis crude nitrogen content was consistent across the tested conditions (protein content stabilized around 50%CDW in fed-batch), while that of the benchmark yeast S. cerevisiae was higher in batch cultures and at the beginning of fed-batch relative to the end (protein content decreased over time and stabilized around 43%CDW). Total nucleic acid content of the yeasts was similar (6.8%CDW and 6.3%CDW, for C. utilis and S. cerevisiae, respectively), with crude nitrogen-to-protein conversion factors of 4.97 and 5.80. CONCLUSION This study demonstrated the suitability of C. utilis as SCP, notably the robustness of its crude nitrogen content (as an indicator of protein content) across batch and fed-batch conditions, compared to that of the benchmark yeast S. cerevisiae.
Collapse
Affiliation(s)
| | | | - Xavier Cameleyre
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Nathalie Gorret
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| |
Collapse
|
3
|
Palomba E, Chiusano ML, Monticolo F, Langella MC, Sanchez M, Tirelli V, de Alteriis E, Iannaccone M, Termolino P, Capparelli R, Carteni F, Incerti G, Mazzoleni S. Extracellular Self-DNA Effects on Yeast Cell Cycle and Transcriptome during Batch Growth. Biomolecules 2024; 14:663. [PMID: 38927066 PMCID: PMC11201494 DOI: 10.3390/biom14060663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
The cell cycle and the transcriptome dynamics of yeast exposed to extracellular self-DNA during an aerobic batch culture on glucose have been investigated using cytofluorimetric and RNA-seq analyses. In parallel, the same study was conducted on yeast cells growing in the presence of (heterologous) nonself-DNA. The self-DNA treatment determined a reduction in the growth rate and a major elongation of the diauxic lag phase, as well as a significant delay in the achievement of the stationary phase. This was associated with significant changes in the cell cycle dynamics, with slower exit from the G0 phase, followed by an increased level of cell percentage in the S phase, during the cultivation. Comparatively, the exposure to heterologous DNA did not affect the growth curve and the cell cycle dynamics. The transcriptomic analysis showed that self-DNA exposure produced a generalized downregulation of transmembrane transport and an upregulation of genes associated with sulfur compounds and the pentose phosphate pathway. Instead, in the case of the nonself treatment, a clear response to nutrient deprivation was detected. Overall, the presented findings represent further insights into the complex functional mechanisms of self-DNA inhibition.
Collapse
Affiliation(s)
- Emanuela Palomba
- Institute of Biosciences and Bioresources CNR, Via Università 133, 80055 Portici, Italy; (E.P.); (P.T.)
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples “Federico II”, Via Università 100, 80055 Portici, Italy; (M.L.C.); (F.M.); (M.C.L.); (R.C.); (F.C.)
| | - Francesco Monticolo
- Department of Agricultural Sciences, University of Naples “Federico II”, Via Università 100, 80055 Portici, Italy; (M.L.C.); (F.M.); (M.C.L.); (R.C.); (F.C.)
- Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Maria Chiara Langella
- Department of Agricultural Sciences, University of Naples “Federico II”, Via Università 100, 80055 Portici, Italy; (M.L.C.); (F.M.); (M.C.L.); (R.C.); (F.C.)
| | - Massimo Sanchez
- Istituto Superiore di Sanità (ISS) Core Facilities, Viale Regina Elena 299, 00161 Rome, Italy; (M.S.); (V.T.)
| | - Valentina Tirelli
- Istituto Superiore di Sanità (ISS) Core Facilities, Viale Regina Elena 299, 00161 Rome, Italy; (M.S.); (V.T.)
| | - Elisabetta de Alteriis
- Department of Biology, University of Naples “Federico II”, Via Cinthia 26, 80126 Naples, Italy;
| | - Marco Iannaccone
- Laboratory of Bioproducts and Bioprocesses ENEA, Piazzale Enrico Fermi 1, 80055 Portici, Italy;
| | - Pasquale Termolino
- Institute of Biosciences and Bioresources CNR, Via Università 133, 80055 Portici, Italy; (E.P.); (P.T.)
| | - Rosanna Capparelli
- Department of Agricultural Sciences, University of Naples “Federico II”, Via Università 100, 80055 Portici, Italy; (M.L.C.); (F.M.); (M.C.L.); (R.C.); (F.C.)
| | - Fabrizio Carteni
- Department of Agricultural Sciences, University of Naples “Federico II”, Via Università 100, 80055 Portici, Italy; (M.L.C.); (F.M.); (M.C.L.); (R.C.); (F.C.)
| | - Guido Incerti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy;
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, University of Naples “Federico II”, Via Università 100, 80055 Portici, Italy; (M.L.C.); (F.M.); (M.C.L.); (R.C.); (F.C.)
| |
Collapse
|
4
|
Nguyen V, Li Y, Lu T. Emergence of Orchestrated and Dynamic Metabolism of Saccharomyces cerevisiae. ACS Synth Biol 2024; 13:1442-1453. [PMID: 38657170 PMCID: PMC11103795 DOI: 10.1021/acssynbio.3c00542] [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: 04/26/2024]
Abstract
Microbial metabolism is a fundamental cellular process that involves many biochemical events and is distinguished by its emergent properties. While the molecular details of individual reactions have been increasingly elucidated, it is not well understood how these reactions are quantitatively orchestrated to produce collective cellular behaviors. Here we developed a coarse-grained, systems, and dynamic mathematical framework, which integrates metabolic reactions with signal transduction and gene regulation to dissect the emergent metabolic traits of Saccharomyces cerevisiae. Our framework mechanistically captures a set of characteristic cellular behaviors, including the Crabtree effect, diauxic shift, diauxic lag time, and differential growth under nutrient-altered environments. It also allows modular expansion for zooming in on specific pathways for detailed metabolic profiles. This study provides a systems mathematical framework for yeast metabolic behaviors, providing insights into yeast physiology and metabolic engineering.
Collapse
Affiliation(s)
- Viviana Nguyen
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Yifei Li
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Ting Lu
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- National Center for Supercomputing Applications, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
5
|
Azad A, Sheikh MN, Hai FI. A critical review of the mechanisms, factors, and performance of pervious concrete to remove contaminants from stormwater runoff. WATER RESEARCH 2024; 251:121101. [PMID: 38218072 DOI: 10.1016/j.watres.2024.121101] [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: 08/26/2023] [Revised: 12/01/2023] [Accepted: 01/01/2024] [Indexed: 01/15/2024]
Abstract
Stormwater can carry pollutants accumulated on impervious surfaces in urban areas into natural water bodies in absence of stormwater quality improvement devices. Pervious concrete (PC) pavement is one of the low-impact development practices introduced for urban flooding prevention and stormwater pollution reduction. PC removes various types of water contaminants. Mechanisms contributing to the water pollution removal capacity of PC can be categorized into three groups: physical, chemical, and biological. Properties of PC such as permeability, porosity, thickness, and adsorption capacity influence removal of all contaminants, although their impact might differ depending on the pollutant properties. Chemical mechanisms include precipitation, co-precipitation, ion and ligand exchange, complexation, diffusion, and sorption. Bulk organics and nutrients are removed primarily by biodegradation. Physical filtration is the primary mechanism to retain suspended solids, although biological activities may have a minor contribution. Release of calcium (Ca2+) and hydroxide (OH-) from hardened cement elevates the effluent pH, which is an environmental concern. However, the pH elevation is also the prime contributor to heavy metals and nutrients removal through precipitation. Specific cementitious materials (e.g., Pozzolans and nanoparticles) and carbonation curing approach are recommended to control effluent pH elevation. Complexation, diffusion, ion solubility, and stability constants are other mechanisms and parameters that influence heavy metal removal. Organic matter availability, electrostatic attraction, temperature, pH, contact time, specific surface area, and roughness of PC pores contribute to the pathogen removal process. Although PC has been found promising in removing various water pollutants, limited salinity removal can be achieved due to the inherent release of Ca2+and OH- from PC.
Collapse
Affiliation(s)
- Armin Azad
- Strategic Water Infrastructure Laboratory, School of Civil, Mining, Environmental and Architectural Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - M Neaz Sheikh
- School of Civil, Mining, Environmental and Architectural Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Faisal I Hai
- Strategic Water Infrastructure Laboratory, School of Civil, Mining, Environmental and Architectural Engineering, University of Wollongong, Wollongong, NSW 2522, Australia.
| |
Collapse
|
6
|
Höhmann S, Briol TA, Ihle N, Frick O, Schmid A, Bühler B. Glycolate as alternative carbon source for Escherichia coli. J Biotechnol 2024; 381:76-85. [PMID: 38190849 DOI: 10.1016/j.jbiotec.2024.01.001] [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: 10/04/2023] [Revised: 12/20/2023] [Accepted: 01/01/2024] [Indexed: 01/10/2024]
Abstract
The physiology of different Escherichia coli stains was analyzed for growth with glycolate as a potentially promising sustainable sole source of carbon and energy. Different E. coli strains showed large differences regarding lag phases after provision of glycolate. Whereas E. coli W showed fast adaptation, E. coli BW25113, JM101, and BL21 (DE3) needed extensive time for adaption (up to 30 generations) until the attainable µmax was reached, which, at 30 °C, amounted to 0.20-0.25 h-1 for all strains. The overexpression of genes encoding glycolate degradation did neither overcome the need for adaptation of E. coli BL21 (DE3) nor improve growth of E. coli W. Rather, high level expression of proteins involved in uptake and initial degradation steps had an adverse effect on growth. Overall, the results show a promising capacity of E. coli strains for growth on glycolate.
Collapse
Affiliation(s)
- Sonja Höhmann
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany; Department of Microbial Biotechnology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
| | - Tim Arik Briol
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany; Department of Microbial Biotechnology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
| | - Nadine Ihle
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
| | - Oliver Frick
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
| | - Andreas Schmid
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany; Department of Microbial Biotechnology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany.
| |
Collapse
|
7
|
Solari CA, Ortolá Martínez MC, Fernandez JM, Bates C, Cueto G, Valacco MP, Morales-Polanco F, Moreno S, Rossi S, Ashe MP, Portela P. Riboproteome remodeling during quiescence exit in Saccharomyces cerevisiae. iScience 2024; 27:108727. [PMID: 38235324 PMCID: PMC10792236 DOI: 10.1016/j.isci.2023.108727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/15/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
The quiescent state is the prevalent mode of cellular life in most cells. Saccharomyces cerevisiae is a useful model for studying the molecular basis of the cell cycle, quiescence, and aging. Previous studies indicate that heterogeneous ribosomes show a specialized translation function to adjust the cellular proteome upon a specific stimulus. Using nano LC-MS/MS, we identified 69 of the 79 ribosomal proteins (RPs) that constitute the eukaryotic 80S ribosome during quiescence. Our study shows that the riboproteome is composed of 444 accessory proteins comprising cellular functions such as translation, protein folding, amino acid and glucose metabolism, cellular responses to oxidative stress, and protein degradation. Furthermore, the stoichiometry of both RPs and accessory proteins on ribosome particles is different depending on growth conditions and among monosome and polysome fractions. Deficiency of different RPs resulted in defects of translational capacity, suggesting that ribosome composition can result in changes in translational activity during quiescence.
Collapse
Affiliation(s)
- Clara A. Solari
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - María Clara Ortolá Martínez
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Juan M. Fernandez
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Christian Bates
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Gerardo Cueto
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Instituto IEGEBA (CONICET-UBA), Buenos Aires, Argentina
| | - María Pía Valacco
- CEQUIBIEM- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Fabián Morales-Polanco
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Silvia Moreno
- CEQUIBIEM- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Silvia Rossi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Mark P. Ashe
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Paula Portela
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| |
Collapse
|
8
|
Bannenberg JW, Boeren S, Zwietering MH, Abee T, den Besten HMW. Insight in lag phase of Listeria monocytogenes during enrichment through proteomic and transcriptomic responses. Food Res Int 2024; 175:113609. [PMID: 38128973 DOI: 10.1016/j.foodres.2023.113609] [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: 06/06/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 12/23/2023]
Abstract
The dynamics of the enrichment-based detection procedure of the foodborne pathogen Listeria monocytogenes from food still remains poorly understood. This enrichment is crucial in the reliable detection of this pathogen and more insight into the recovery mechanism during this step is important to advance our understanding of lag phase behaviour during enrichment. In this study we combined transcriptomic and proteomic analyses to better understand the physiological processes within the lag phase of L. monocytogenes during enrichment. Upon transfer of BHI-cultured stationary phase L. monocytogenes cells to half-Fraser enrichment broth (HFB), motility-associated genes and proteins were downregulated, while expression of metal uptake transporters, resuscitation-promoting factors that stimulate growth from dormancy, antibiotic efflux pumps and oxidative stress proteins were upregulated. Next to this, when cells with a heat stress history were cultured in enrichment broth, proteins necessary for recovery were upregulated with functions in DNA-damage repair, protein refolding, cell-wall repair, and zinc transport. Proteomic results pointed to possible factors that support shortening the lag duration, including the addition of 10 µM zinc and the addition of spent HFB containing presumed concentrations of resuscitation-promoting factors. However, these interventions did not lead to biologically relevant reduction of lag phase. Also, when cells were enriched in spent HFB, final cell concentrations were similar to enrichments in fresh HFB, indicating that the enrichment broth seems not to lack critical substrates. Concludingly, this study gives insight into the proteomic changes in the lag phase during enrichment and shows that supplementation of HFB is not the best strategy to optimize the current enrichment method.
Collapse
Affiliation(s)
- Jasper W Bannenberg
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, The Netherlands
| | - Marcel H Zwietering
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Tjakko Abee
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Heidy M W den Besten
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
| |
Collapse
|
9
|
Torello Pianale L, Caputo F, Olsson L. Four ways of implementing robustness quantification in strain characterisation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:195. [PMID: 38115067 PMCID: PMC10729505 DOI: 10.1186/s13068-023-02445-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND In industrial bioprocesses, microorganisms are generally selected based on performance, whereas robustness, i.e., the ability of a system to maintain a stable performance, has been overlooked due to the challenges in its quantification and implementation into routine experimental procedures. This work presents four ways of implementing robustness quantification during strain characterisation. One Saccharomyces cerevisiae laboratory strain (CEN.PK113-7D) and two industrial strains (Ethanol Red and PE2) grown in seven different lignocellulosic hydrolysates were assessed for growth-related functions (specific growth rate, product yields, etc.) and eight intracellular parameters (using fluorescent biosensors). RESULTS Using flasks and high-throughput experimental setups, robustness was quantified in relation to: (i) stability of growth functions in response to the seven hydrolysates; (ii) stability of growth functions across different strains to establish the impact of perturbations on yeast metabolism; (iii) stability of intracellular parameters over time; (iv) stability of intracellular parameters within a cell population to indirectly quantify population heterogeneity. Ethanol Red was the best-performing strain under all tested conditions, achieving the highest growth function robustness. PE2 displayed the highest population heterogeneity. Moreover, the intracellular environment varied in response to non-woody or woody lignocellulosic hydrolysates, manifesting increased oxidative stress and unfolded protein response, respectively. CONCLUSIONS Robustness quantification is a powerful tool for strain characterisation as it offers novel information on physiological and biochemical parameters. Owing to the flexibility of the robustness quantification method, its implementation was successfully validated at single-cell as well as high-throughput levels, showcasing its versatility and potential for several applications.
Collapse
Affiliation(s)
- Luca Torello Pianale
- Industrial Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Fabio Caputo
- Industrial Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Lisbeth Olsson
- Industrial Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
| |
Collapse
|
10
|
Lane BR, Anderson HM, Dicko AH, Fulcher MR, Kinkel LL. Temporal variability in nutrient use among Streptomyces suggests dynamic niche partitioning. Environ Microbiol 2023; 25:3527-3535. [PMID: 37669222 DOI: 10.1111/1462-2920.16498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/02/2023] [Indexed: 09/07/2023]
Abstract
Soil bacteria spend significant periods in dormant or semi-dormant states that are interrupted by resource pulses which can lead to periods of rapid growth and intense nutrient competition. Microbial populations have evolved diverse strategies to circumvent competitive interactions and facilitate coexistence. Here, we show that nutrient use of soilborne Streptomyces is temporally partitioned during experimental resource pulses, leading to reduced niche overlap, and potential coexistence. Streptomyces grew rapidly on the majority of distinct 95 carbon sources but varied in which individual resources were utilized in the first 24 h. Only a handful of carbon sources (19 out of 95) were consistently utilized (>95% of isolates) most rapidly in the first 24 h. These consistently utilized carbon sources also generated the majority of biomass accumulated by isolates. Our results shed new light on a novel mechanism microbes may employ to alleviate competitive interactions by temporally partitioning the consumption of carbon resources. As competitive interactions have been proposed to drive the suppression of disease-causing microbes in agronomic soils, our findings may hold widespread implications for soil management for plant health.
Collapse
Affiliation(s)
- Brett R Lane
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Hannah M Anderson
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Amadou H Dicko
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
- Faculty of Agronomy and Animal Sciences, University of Segou, Ségou, Mali
| | - Michael R Fulcher
- USDA Agricultural Research Service, Foreign Disease-Weed Science Research, Frederick, Maryland, USA
| | - Linda L Kinkel
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| |
Collapse
|
11
|
Silva CR, Flávia da Silva Rovida A, Gabriele Martins J, Nathane Nunes de Freitas P, Ricardo Olchanheski L, Grange L, Alvim Veiga Pileggi S, Pileggi M. Bacterial adaptation to rhizosphere soil is independent of the selective pressure exerted by the herbicide saflufenacil, through the modulation of catalase and glutathione S-transferase. PLoS One 2023; 18:e0292967. [PMID: 37963158 PMCID: PMC10645333 DOI: 10.1371/journal.pone.0292967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 10/03/2023] [Indexed: 11/16/2023] Open
Abstract
Herbicides cause oxidative stress in nontarget microorganisms, which may exhibit adaptive responses to substances they have not previously encountered. Nevertheless, it is unclear whether these characteristics occur in bacteria isolated from agricultural soil. Two possible adaptation strategies of Stenotrophomonas sp. CMA26 was evaluated in agricultural soil in Brazil, which is considered stressful due to the intense use of pesticides. The study focused on degradation and antioxidant enzymes in response to the herbicide Heat, which was absent at the isolation site. The results indicated that higher concentrations of herbicide led to more intense stress conditions during the initial periods of growth. This was evidenced by elevated levels of malondialdehyde and peroxide, as well as a significant reduction in growth. Our data show that herbicide degradation is a selection-dependent process, as none of the 35 isolates from the same environment in our collection were able to degrade the herbicide. The stress was controlled by changes in the enzymatic modulation of catalase activity in response to peroxide and glutathione S-transferase activity in response to malondialdehyde, especially at higher herbicide concentrations. This modulation pattern is related to the bacterial growth phases and herbicide concentration, with a specific recovery response observed during the mid phase for higher herbicide concentrations. The metabolic systems that contributed to tolerance did not depend on the specific prior selection of saflufenacil. Instead, they were related to general stress responses, regardless of the stress-generating substance. This system may have evolved in response to reactive oxygen species, regardless of the substance that caused oxidative stress, by modulating of the activities of various antioxidant enzymes. Bacterial communities possessing these plastic tolerance mechanisms can survive without necessarily degrading herbicides. However, their presence can lead to changes in biodiversity, compromise the functionality of agricultural soils, and contribute to environmental contamination through drift.
Collapse
Affiliation(s)
- Caroline Rosa Silva
- Department of Biological and Health Sciences, Department of Structural, Molecular and Genetic Biology, State University of Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | | | - Juliane Gabriele Martins
- Department of Biological and Health Sciences, Department of Structural, Molecular and Genetic Biology, State University of Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | | | - Luiz Ricardo Olchanheski
- Department of Biological and Health Sciences, Department of Structural, Molecular and Genetic Biology, State University of Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Luciana Grange
- Department of Agricultural Sciences, Federal University of Paraná—Palotina Sector, Palotina, Brazil
| | - Sônia Alvim Veiga Pileggi
- Department of Biological and Health Sciences, Department of Structural, Molecular and Genetic Biology, State University of Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Marcos Pileggi
- Department of Biological and Health Sciences, Department of Structural, Molecular and Genetic Biology, State University of Ponta Grossa, Ponta Grossa, Paraná, Brazil
| |
Collapse
|
12
|
Abreu CI, Mathur S, Petrov DA. Strong environmental memory revealed by experimental evolution in static and fluctuating environments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557739. [PMID: 37745585 PMCID: PMC10515930 DOI: 10.1101/2023.09.14.557739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Evolution in a static environment, such as a laboratory setting with constant and uniform conditions, often proceeds via large-effect beneficial mutations that may become maladaptive in other environments. Conversely, natural settings require populations to endure environmental fluctuations. A sensible assumption is that the fitness of a lineage in a fluctuating environment is the time-average of its fitness over the sequence of static conditions it encounters. However, transitions between conditions may pose entirely new challenges, which could cause deviations from this time-average. To test this, we tracked hundreds of thousands of barcoded yeast lineages evolving in static and fluctuating conditions and subsequently isolated 900 mutants for pooled fitness assays in 15 environments. We find that fitness in fluctuating environments indeed often deviates from the expectation based on static components, leading to fitness non-additivity. Moreover, closer examination reveals that fitness in one component of a fluctuating environment is often strongly influenced by the previous component. We show that this environmental memory is especially common for mutants with high variance in fitness across tested environments, even if the components of the focal fluctuating environment are excluded from this variance. We employ a simple mathematical model and whole-genome sequencing to propose mechanisms underlying this effect, including lag time evolution and sensing mutations. Our results demonstrate that environmental fluctuations have large impacts on fitness and suggest that variance in static environments can explain these impacts.
Collapse
Affiliation(s)
- Clare I. Abreu
- Department of Biology, Stanford University; Stanford CA, USA
| | - Shaili Mathur
- Department of Biology, Stanford University; Stanford CA, USA
| | | |
Collapse
|
13
|
Ahmad M, Prensky H, Balestrieri J, ElNaggar S, Gomez-Simmonds A, Uhlemann AC, Traxler B, Singh A, Lopatkin AJ. Tradeoff between lag time and growth rate drives the plasmid acquisition cost. Nat Commun 2023; 14:2343. [PMID: 37095096 PMCID: PMC10126158 DOI: 10.1038/s41467-023-38022-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
Conjugative plasmids drive genetic diversity and evolution in microbial populations. Despite their prevalence, plasmids can impose long-term fitness costs on their hosts, altering population structure, growth dynamics, and evolutionary outcomes. In addition to long-term fitness costs, acquiring a new plasmid introduces an immediate, short-term perturbation to the cell. However, due to the transient nature of this plasmid acquisition cost, a quantitative understanding of its physiological manifestations, overall magnitudes, and population-level implications, remains unclear. To address this, here we track growth of single colonies immediately following plasmid acquisition. We find that plasmid acquisition costs are primarily driven by changes in lag time, rather than growth rate, for nearly 60 conditions covering diverse plasmids, selection environments, and clinical strains/species. Surprisingly, for a costly plasmid, clones exhibiting longer lag times also achieve faster recovery growth rates, suggesting an evolutionary tradeoff. Modeling and experiments demonstrate that this tradeoff leads to counterintuitive ecological dynamics, whereby intermediate-cost plasmids outcompete both their low and high-cost counterparts. These results suggest that, unlike fitness costs, plasmid acquisition dynamics are not uniformly driven by minimizing growth disadvantages. Moreover, a lag/growth tradeoff has clear implications in predicting the ecological outcomes and intervention strategies of bacteria undergoing conjugation.
Collapse
Affiliation(s)
- Mehrose Ahmad
- Department of Biology, Barnard College, New York, NY, 10027, USA
| | - Hannah Prensky
- Department of Biology, Barnard College, New York, NY, 10027, USA
| | | | - Shahd ElNaggar
- Department of Biology, Barnard College, New York, NY, 10027, USA
| | - Angela Gomez-Simmonds
- Department of Medicine, Division of Infectious Diseases, Columbia University Medical Center, New York, NY, 10032, USA
| | - Anne-Catrin Uhlemann
- Department of Medicine, Division of Infectious Diseases, Columbia University Medical Center, New York, NY, 10032, USA
| | - Beth Traxler
- Department Microbiology, University of Washington, Seattle, WA, 98195, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, 19717, USA
| | - Allison J Lopatkin
- Department of Biology, Barnard College, New York, NY, 10027, USA.
- Department Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, 10027, USA.
- Data Science Institute, Columbia University, New York, NY, 10027, USA.
- Department of Chemical Engineering, University of Rochester, Rochester, NY, 14627, USA.
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14627, USA.
| |
Collapse
|
14
|
van Kasteren S, Rozen DE. Using click chemistry to study microbial ecology and evolution. ISME COMMUNICATIONS 2023; 3:9. [PMID: 36721064 PMCID: PMC9889756 DOI: 10.1038/s43705-022-00205-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/16/2022] [Accepted: 11/23/2022] [Indexed: 02/01/2023]
Abstract
Technological advances have largely driven the revolution in our understanding of the structure and function of microbial communities. Culturing, long the primary tool to probe microbial life, was supplanted by sequencing and other -omics approaches, which allowed detailed quantitative insights into species composition, metabolic potential, transcriptional activity, secretory responses and more. Although the ability to characterize "who's there" has never been easier or cheaper, it remains technically challenging and expensive to understand what the diverse species and strains that comprise microbial communities are doing in situ, and how these behaviors change through time. Our aim in this brief review is to introduce a developing toolkit based on click chemistry that can accelerate and reduce the expense of functional analyses of the ecology and evolution of microbial communities. After first outlining the history of technological development in this field, we will discuss key applications to date using diverse labels, including BONCAT, and then end with a selective (biased) view of areas where click-chemistry and BONCAT-based approaches stand to have a significant impact on our understanding of microbial communities.
Collapse
Affiliation(s)
- Sander van Kasteren
- Leiden Institute of Chemistry and The Institute of Chemical Immunology, Leiden University, Einsteinweg 55, Leiden, 2300 RA, The Netherlands.
| | - Daniel E Rozen
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2300 RA, The Netherlands.
| |
Collapse
|
15
|
Chandra HB, Shome A, Sahoo R, Apoorva S, Bhure SK, Mahawar M. Periplasmic methionine sulfoxide reductase (MsrP)-a secondary factor in stress survival and virulence of Salmonella Typhimurium. FEMS Microbiol Lett 2023; 370:fnad063. [PMID: 37403401 PMCID: PMC10653988 DOI: 10.1093/femsle/fnad063] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/06/2023] Open
Abstract
Among others, methionine residues are highly susceptible to host-generated oxidants. Repair of oxidized methionine (Met-SO) residues to methionine (Met) by methionine sulfoxide reductases (Msrs) play a chief role in stress survival of bacterial pathogens, including Salmonella Typhimurium. Periplasmic proteins, involved in many important cellular functions, are highly susceptible to host-generated oxidants. According to location in cell, two types of Msrs, cytoplasmic and periplasmic are present in S. Typhimurium. Owing to its localization, periplasmic Msr (MsrP) might play a crucial role in defending the host-generated oxidants. Here, we have assessed the role of MsrP in combating oxidative stress and colonization of S. Typhimurium. ΔmsrP (mutant strain) grew normally in in-vitro media. In comparison to S. Typhimurium (wild type), mutant strain showed mild hypersensitivity to HOCl and chloramine-T (ChT). Following exposure to HOCl, mutant strain showed almost similar protein carbonyl levels (a marker of protein oxidation) as compared to S. Typhimurium strain. Additionally, ΔmsrP strain showed higher susceptibility to neutrophils than the parent strain. Further, the mutant strain showed very mild defects in survival in mice spleen and liver as compared to wild-type strain. In a nutshell, our results indicate that MsrP plays only a secondary role in combating oxidative stress and colonization of S. Typhimurium.
Collapse
Affiliation(s)
- Hari Balaji Chandra
- Division of Biochemistry, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| | - Arijit Shome
- Division of Biochemistry, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| | - Raj Sahoo
- Division of Biochemistry, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| | - S Apoorva
- Division of Biochemistry, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| | - Sanjeev Kumar Bhure
- Division of Biochemistry, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| | - Manish Mahawar
- Division of Biochemistry, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| |
Collapse
|
16
|
Classifying Interactions in a Synthetic Bacterial Community Is Hindered by Inhibitory Growth Medium. mSystems 2022; 7:e0023922. [PMID: 36197097 PMCID: PMC9600862 DOI: 10.1128/msystems.00239-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Predicting the fate of a microbial community and its member species relies on understanding the nature of their interactions. However, designing simple assays that distinguish between interaction types can be challenging. Here, we performed spent medium assays based on the predictions of a mathematical model to decipher the interactions among four bacterial species: Agrobacterium tumefaciens, Comamonas testosteroni, Microbacterium saperdae, and Ochrobactrum anthropi. While most experimental results matched model predictions, the behavior of C. testosteroni did not: its lag phase was reduced in the pure spent media of A. tumefaciens and M. saperdae but prolonged again when we replenished our growth medium. Further experiments showed that the growth medium actually delayed the growth of C. testosteroni, leading us to suspect that A. tumefaciens and M. saperdae could alleviate this inhibitory effect. There was, however, no evidence supporting such "cross-detoxification," and instead, we identified metabolites secreted by A. tumefaciens and M. saperdae that were then consumed or "cross-fed" by C. testosteroni, shortening its lag phase. Our results highlight that even simple, defined growth media can have inhibitory effects on some species and that such negative effects need to be included in our models. Based on this, we present new guidelines to correctly distinguish between different interaction types such as cross-detoxification and cross-feeding. IMPORTANCE Communities of microbes colonize virtually every place on earth. Ultimately, we strive to predict and control how these communities behave, for example, if they reside in our guts and make us sick. But precise control is impossible unless we can identify exactly how their member species interact with one another. To find a systematic way to measure interactions, we started very simply with a small community of four bacterial species and carefully designed experiments based on a mathematical model. This first attempt accurately mapped out interactions for all species except one. By digging deeper, we understood that our method failed for that species as it was suffering in the growth medium that we chose. A revised model that considered that growth media can be harmful could then make more accurate predictions. What we have learned with these four species can now be applied to decipher interactions in larger communities.
Collapse
|
17
|
Novel species of parasitic green microalgae Coccomyxa veronica sp. nov. infects Anadara broughtonii from the Sea of Japan. Symbiosis 2022. [DOI: 10.1007/s13199-022-00877-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
18
|
de Siqueira VM, da Silva BGM, Passos JCDS, Pinto AP, da Rocha JBT, Alberto-Silva C, Costa MS. (MeOPhSe)2, a synthetic organic selenium compound, inhibits virulence factors of Candida krusei: Adherence to cervical epithelial cells and biofilm formation. J Trace Elem Med Biol 2022; 73:127019. [PMID: 35709560 DOI: 10.1016/j.jtemb.2022.127019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 02/26/2022] [Accepted: 06/07/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Systemic candidiasis is produced by Candida albicans or non-albicans Candida species, opportunistic fungi that produce both superficial and invasive infections. Despite the availability of a wide range of antifungal agents for the treatment of candidiasis, failure of therapy is observed frequently, which opens new avenues in the field of alternative therapeutic strategies. METHODS The effects of p,p'-methoxyl-diphenyl diselenide [(MeOPhSe)2], a synthetic organic selenium (organochalcogen) compound, were investigated on virulence factors of C. krusei and compared with its antifungal effects on the virulence factors related to adhesion to cervical epithelial cell surfaces with C. albicans. RESULTS (MeOPhSe)2, a compound non-toxic in epithelial (HeLa) and fibroblastic (Vero) cells, inhibited the growth in a dose-dependent manner and changed the kinetics parameters of C. krusei and, most importantly, extending the duration of lag phase of growth, inhibiting biofilm formation, and changing the structure of biofilm. Also, (MeOPhSe)2 reduced C. albicans and C. krusei adherence to cervical epithelial cells, an important factor for the early stage of the Candida-host interaction. The reduction was 37.24 ± 2.7 % in C. krusei (p = 0.00153) and 32.84 ± 3.2 % in C. albicans (p = 0.0072) at 20 µM (MeOPhSe)2, and the effect is in a concentration-dependent manner. Surprisingly, the antifungal potential on adhesion was similar between both species, indicating the potential of (MeOPhSe)2 as a promising antifungal drug against different Candida infections. CONCLUSION Overall, we demonstrated the potential of (MeOPhSe)2 as an effective antifungal drug against the virulence factors of Candida species.
Collapse
Affiliation(s)
- Victor Mendes de Siqueira
- Instituto de Pesquisa e Desenvolvimento - IP&D, Universidade do Vale do Paraíba - UNIVAP, Av. Shishima Hifumi, São José dos Campos, SP 2911, Brazil
| | - Bruna Graziele Marques da Silva
- Instituto de Pesquisa e Desenvolvimento - IP&D, Universidade do Vale do Paraíba - UNIVAP, Av. Shishima Hifumi, São José dos Campos, SP 2911, Brazil
| | - Juliene Cristina da Silva Passos
- Instituto de Pesquisa e Desenvolvimento - IP&D, Universidade do Vale do Paraíba - UNIVAP, Av. Shishima Hifumi, São José dos Campos, SP 2911, Brazil
| | - Ana Paula Pinto
- Instituto de Pesquisa e Desenvolvimento - IP&D, Universidade do Vale do Paraíba - UNIVAP, Av. Shishima Hifumi, São José dos Campos, SP 2911, Brazil
| | | | - Carlos Alberto-Silva
- Natural and Humanities Sciences Center, Experimental Morphophysiology Laboratory Federal University of ABC (UFABC), Rua Arcturus, no 03, Bloco Delta, São Bernardo do Campo, SP 09606-070, Brazil
| | - Maricilia Silva Costa
- Instituto de Pesquisa e Desenvolvimento - IP&D, Universidade do Vale do Paraíba - UNIVAP, Av. Shishima Hifumi, São José dos Campos, SP 2911, Brazil.
| |
Collapse
|
19
|
A Feedback Control Strategy for a Fed-Batch Monoclonal Antibody Production Process Utilising Infrequent and Irregular Sampled Measurements. Processes (Basel) 2022. [DOI: 10.3390/pr10081448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The ability to take non-invasive Raman measurements presents a unique opportunity to use one Raman probe across multiple vessels in parallel, reducing costs but making measurements infrequent. Under these conditions, infrequent and irregular feedback signals can result in poor closed-loop control performance. This study addressed the issue of infrequent and irregular Raman measurements using a linear dynamic model developed from interpolated data to predict more frequent measurements of the controlled variable. The simulated monoclonal antibody production was sampled hourly with white noise added to the simulated glucose concentration to replicate real Raman measurements. The hourly samples were interpolated into 15 min intervals and a linear dynamic model was developed to predict the glucose concentration at 15 min intervals. These predicted values were then used in a feedback control loop by using model predictive control or a conventional proportional and integral controller to control the glucose concentration at 15 min sampling intervals. For setpoint tracking, the model predictive control reduced the integral of absolute errors to 14,600 from 15,900 (with a 1 h sampling time) or 8.2% reduction. With adaptive model predictive control, the integral of absolute errors was reduced from 14,500 (1 h sampling time) to 14,200 for setpoint tracking and from 13,500 (1 h sampling time) to 13,300 for disturbance rejection. A final comparison demonstrated that the proposed method can also cope with random variations in the sampling time.
Collapse
|
20
|
Bloxham B, Lee H, Gore J. Diauxic lags explain unexpected coexistence in multi-resource environments. Mol Syst Biol 2022; 18:e10630. [PMID: 35507445 PMCID: PMC9067609 DOI: 10.15252/msb.202110630] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 11/09/2022] Open
Abstract
How the coexistence of species is affected by the presence of multiple resources is a major question in microbial ecology. We experimentally demonstrate that differences in diauxic lags, which occur as species deplete their own environments and adapt their metabolisms, allow slow-growing microbes to stably coexist with faster-growing species in multi-resource environments despite being excluded in single-resource environments. In our focal example, an Acinetobacter species (Aci2) competitively excludes Pseudomonas aurantiaca (Pa) on alanine and on glutamate. However, they coexist on the combination of both resources. Experiments reveal that Aci2 grows faster but Pa has shorter diauxic lags. We establish a tradeoff between Aci2's fast growth and Pa's short lags as their mechanism for coexistence. We model this tradeoff to accurately predict how environmental changes affect community composition. We extend our work by surveying a large set of competitions and observe coexistence nearly four times as frequently when the slow-grower is the fast-switcher. Our work illustrates a simple mechanism, based entirely on supplied-resource growth dynamics, for the emergence of multi-resource coexistence.
Collapse
Affiliation(s)
- Blox Bloxham
- Physics of Living SystemsDepartment of PhysicsMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Hyunseok Lee
- Physics of Living SystemsDepartment of PhysicsMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Jeff Gore
- Physics of Living SystemsDepartment of PhysicsMassachusetts Institute of TechnologyCambridgeMAUSA
| |
Collapse
|
21
|
da Silva BGM, Pinto AP, Passos JCDS, da Rocha JBT, Alberto-Silva C, Costa MS. Diphenyl diselenide suppresses key virulence factors of Candida krusei, a neglected fungal pathogen. BIOFOULING 2022; 38:427-440. [PMID: 35670068 DOI: 10.1080/08927014.2022.2084388] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 05/17/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Candida krusei is a candidiasis etiological agent of relevance in the clinical setting because of its intrinsic resistance to fluconazole. Also, it has opened up new paths in the area of alternative therapeutic techniques. This project demonstrated the effects of diphenyl diselenide (PhSe)2 and p-cloro diphenyl diselenide (pCl-PhSe)2, two organochalcogen compounds, on relevant virulence factors for the early stage of the C. krusei host interaction and infection process. Both compounds inhibited adherence of C. krusei to both polystyrene surfaces and cervical epithelial cells and biofilm formation; the structure of the biofilm was also changed in a dose-dependent manner. In addition, both compounds inhibited C. krusei growth, but (PhSe)2 significantly increased the time duration of the lag phase and delayed the start of the exponential phase in growth kinetics. (PhSe)2 has more potential antifungal activity than (pCl-PhSe)2 in inhibiting the adherence to epithelial cells, biofilm formation, and growth of C. krusei.
Collapse
Affiliation(s)
| | - Ana Paula Pinto
- Instituto de Pesquisa e Desenvolvimento-IP&D, Universidade do Vale do Paraíba, São José dos Campos, São Paulo, Brazil
| | | | - João Batista Teixeira da Rocha
- Departamento de Química, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, São Paulo, Brazil
| | - Carlos Alberto-Silva
- Experimental Morphophysiology Laboratory, Natural and Humanities Sciences Center (CCNH), Federal University of ABC-UFABC, São Paulo, Brazil
| | - Maricilia Silva Costa
- Instituto de Pesquisa e Desenvolvimento-IP&D, Universidade do Vale do Paraíba, São José dos Campos, São Paulo, Brazil
| |
Collapse
|
22
|
Antifungal and Aflatoxin-Reducing Activity of β-Glucan Isolated from Pichia norvegensis Grown on Tofu Wastewater. Foods 2021; 10:foods10112619. [PMID: 34828900 PMCID: PMC8618602 DOI: 10.3390/foods10112619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/17/2021] [Accepted: 10/19/2021] [Indexed: 12/02/2022] Open
Abstract
Yeast can be isolated from tofu wastewater and the cell wall in the form of β-glucan can act as a natural decontaminant agent. This study aimed to isolate and characterize native yeast from tofu wastewater, which can be extracted to obtain β-glucan and then identify the yeast and its β-glucan activity regarding antifungal ability against Aspergillus flavus and aflatoxin-reducing activity towards aflatoxin B1 (AFB1) and B2 (AFB2). Tofu wastewater native yeast was molecularly identified, and the growth observed based on optical density for 96 h and the pH also measured. β-glucan was extracted from native yeast cell walls with the acid-base method and then the inhibition activity towards A. flavus was tested using the well diffusion method and microscopic observation. AFB1 and AFB2 reduction were identified using HPLC LC-MS/MS. The results showed that the native yeast isolated was Pichia norvegensis with a β-glucan yield of 6.59%. Pichia norvegensis and its β-glucan showed an inhibition zone against Aspergillus flavus of 11.33 ± 4.93 and 7.33 ± 3.51 mm, respectively. Total aflatoxin-reducing activity was also shown by Pichia norvegensis of 26.85 ± 2.87%, and β-glucan of 27.30 ± 1.49%, while AFB1- and AFB2-reducing activity by Pichia norvegensis was 36.97 ± 3.07% and 27.13 ± 1.69%, and β-glucan was 27.13 ± 1.69% and 32.59 ± 4.20%, respectively.
Collapse
|
23
|
A CRISPR Interference Screen of Essential Genes Reveals that Proteasome Regulation Dictates Acetic Acid Tolerance in Saccharomyces cerevisiae. mSystems 2021; 6:e0041821. [PMID: 34313457 PMCID: PMC8407339 DOI: 10.1128/msystems.00418-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
CRISPR interference (CRISPRi) is a powerful tool to study cellular physiology under different growth conditions, and this technology provides a means for screening changed expression of essential genes. In this study, a Saccharomyces cerevisiae CRISPRi library was screened for growth in medium supplemented with acetic acid. Acetic acid is a growth inhibitor challenging the use of yeast for the industrial conversion of lignocellulosic biomasses. Tolerance to acetic acid that is released during biomass hydrolysis is crucial for cell factories to be used in biorefineries. The CRISPRi library screened consists of >9,000 strains, where >98% of all essential and respiratory growth-essential genes were targeted with multiple guide RNAs (gRNAs). The screen was performed using the high-throughput, high-resolution Scan-o-matic platform, where each strain is analyzed separately. Our study identified that CRISPRi targeting of genes involved in vesicle formation or organelle transport processes led to severe growth inhibition during acetic acid stress, emphasizing the importance of these intracellular membrane structures in maintaining cell vitality. In contrast, strains in which genes encoding subunits of the 19S regulatory particle of the 26S proteasome were downregulated had increased tolerance to acetic acid, which we hypothesize is due to ATP salvage through an increased abundance of the 20S core particle that performs ATP-independent protein degradation. This is the first study where high-resolution CRISPRi library screening paves the way to understanding and bioengineering the robustness of yeast against acetic acid stress. IMPORTANCE Acetic acid is inhibitory to the growth of the yeast Saccharomyces cerevisiae, causing ATP starvation and oxidative stress, which leads to the suboptimal production of fuels and chemicals from lignocellulosic biomass. In this study, where each strain of a CRISPRi library was characterized individually, many essential and respiratory growth-essential genes that regulate tolerance to acetic acid were identified, providing a new understanding of the stress response of yeast and new targets for the bioengineering of industrial yeast. Our findings on the fine-tuning of the expression of proteasomal genes leading to increased tolerance to acetic acid suggest that this could be a novel strategy for increasing stress tolerance, leading to improved strains for the production of biobased chemicals.
Collapse
|
24
|
Hazan R, Schoemann M, Klutstein M. Endurance of extremely prolonged nutrient prevention across kingdoms of life. iScience 2021; 24:102745. [PMID: 34258566 PMCID: PMC8258982 DOI: 10.1016/j.isci.2021.102745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Numerous observations demonstrate that microorganisms can survive very long periods of nutrient deprivation and starvation. Moreover, it is evident that prolonged periods of starvation are a feature of many habitats, and many cells in all kingdoms of life are found in prolonged starvation conditions. Bacteria exhibit a range of responses to long-term starvation. These include genetic adaptations such as the long-term stationary phase and the growth advantage in stationary phase phenotypes characterized by mutations in stress-signaling genes and elevated mutation rates. Here, we suggest using the term "endurance of prolonged nutrient prevention" (EPNP phase), to describe this phase, which was also recently described in eukaryotes. Here, we review this literature and describe the current knowledge about the adaptations to very long-term starvation conditions in bacteria and eukaryotes, its conceptual and structural conservation across all kingdoms of life, and point out possible directions that merit further research.
Collapse
Affiliation(s)
- Ronen Hazan
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 9112001, Israel
| | - Miriam Schoemann
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 9112001, Israel
| | - Michael Klutstein
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 9112001, Israel
| |
Collapse
|
25
|
Kim HJ, Jeong H, Lee SJ. Visualization and Quantification of Genetically Adapted Microbial Cells During Preculture. Front Microbiol 2021; 12:693464. [PMID: 34335520 PMCID: PMC8317463 DOI: 10.3389/fmicb.2021.693464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
As culture history is known to affect the length of the lag phase and microbial cell growth, precultures are often grown in the same medium as the main culture for physiological adaptation and to reduce a prolonged lag time in some microbial cells. To understand the adaptation process of microbial cells during transfer from Luria-Bertani medium to minimal medium, we used the growth of Escherichia coli BL21(DE3) in succinate minimal medium as a model system. We observed that only one or two sequential transfers from minimal medium to fresh minimal medium accelerated the growth rate of BL21(DE3) cells. In addition, the number of large colonies (diameter ≥0.1 cm) on succinate agar increased with the number of transfers. Genome and transcript analyses showed that the C-to-T point mutation in large colony cells converted the inactive promoter of kgtP (known to encode α-ketoglutarate permease) to the active form, allowing efficient uptake of exogenous succinate. Moreover, we visualized the occurrence of genetically adapted cells with better fitness in real time and quantified the number of those cells in the microbial population during transfer to the same medium. Fluorescence microscopy showed the occurrence and increase of adapted mutant cells, which contain intracellular KgtP-fused green fluorescent proteins, as a result of the C-to-T mutation in the promoter of a fused kgtP-sfgfp during transfer to fresh medium. Flow cytometry revealed that the proportion of mutant cells increased from 1.75% (first transfer) to 12.16% (second transfer) and finally 70.79% (third transfer), explaining the shortened lag time and accelerated growth rate of BL21(DE3) cells during adaptation to the minimal medium. This study provides new insights into the genetic heterogeneity of microbial populations that aids microbial adaptability in new environments.
Collapse
Affiliation(s)
- Hyun Ju Kim
- Department of Systems Biotechnology, Institute of Microbiomics, Chung-Ang University, Anseong, South Korea
| | - Haeyoung Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology, Institute of Microbiomics, Chung-Ang University, Anseong, South Korea
| |
Collapse
|
26
|
Identification of Oxygen-Independent Pathways for Pyridine Nucleotide and Coenzyme A Synthesis in Anaerobic Fungi by Expression of Candidate Genes in Yeast. mBio 2021; 12:e0096721. [PMID: 34154398 PMCID: PMC8262920 DOI: 10.1128/mbio.00967-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Neocallimastigomycetes are unique examples of strictly anaerobic eukaryotes. This study investigates how these anaerobic fungi bypass reactions involved in synthesis of pyridine nucleotide cofactors and coenzyme A that, in canonical fungal pathways, require molecular oxygen. Analysis of Neocallimastigomycetes proteomes identified a candidate l-aspartate-decarboxylase (AdcA) and l-aspartate oxidase (NadB) and quinolinate synthase (NadA), constituting putative oxygen-independent bypasses for coenzyme A synthesis and pyridine nucleotide cofactor synthesis. The corresponding gene sequences indicated acquisition by ancient horizontal gene transfer (HGT) events involving bacterial donors. To test whether these enzymes suffice to bypass corresponding oxygen-requiring reactions, they were introduced into fms1Δ and bna2Δ Saccharomyces cerevisiae strains. Expression of nadA and nadB from Piromyces finnis and adcA from Neocallimastix californiae conferred cofactor prototrophy under aerobic and anaerobic conditions. This study simulates how HGT can drive eukaryotic adaptation to anaerobiosis and provides a basis for elimination of auxotrophic requirements in anaerobic industrial applications of yeasts and fungi. IMPORTANCE NAD (NAD+) and coenzyme A (CoA) are central metabolic cofactors whose canonical biosynthesis pathways in fungi require oxygen. Anaerobic gut fungi of the Neocallimastigomycota phylum are unique eukaryotic organisms that adapted to anoxic environments. Analysis of Neocallimastigomycota genomes revealed that these fungi might have developed oxygen-independent biosynthetic pathways for NAD+ and CoA biosynthesis, likely acquired through horizontal gene transfer (HGT) from prokaryotic donors. We confirmed functionality of these putative pathways under anaerobic conditions by heterologous expression in the yeast Saccharomyces cerevisiae. This approach, combined with sequence comparison, offers experimental insight on whether HGT events were required and/or sufficient for acquiring new traits. Moreover, our results demonstrate an engineering strategy for enabling S. cerevisiae to grow anaerobically in the absence of the precursor molecules pantothenate and nicotinate, thereby contributing to alleviate oxygen requirements and to move closer to prototrophic anaerobic growth of this industrially relevant yeast.
Collapse
|
27
|
Abstract
Hsp70 proteins are among the most ubiquitous chaperones and play important roles in maintaining proteostasis and resisting environmental stress. Multiple copies of Hsp70s are widely present in eukaryotic cells with redundant and divergent functions, but they have been less well investigated in prokaryotes. Myxococcus xanthus DK1622 is annotated as having many hsp70 genes. In this study, we performed a bioinformatic analysis of Hsp70 proteins and investigated the functions of six hsp70 genes in DK1622, including two genes that encode proteins with the conserved PRK00290 domain (MXAN_3192 and MXAN_6671) and four genes that encode proteins with the cl35085 or cd10170 domain. We found that only MXAN_3192 is essential for cell survival and heat shock induction. MXAN_3192, compared with the other hsp70 genes, has a high transcriptional level, far exceeding that of any other hsp70 gene, which, however, is not the reason for its essentiality. Deletion of MXAN_6671 (sglK) led to multiple deficiencies in development, social motility, and oxidative resistance, while deletion of each of the other four hsp70 genes decreased sporulation and oxidative resistance. MXAN_3192 or sglK, but not the other genes, restored the growth deficiency of the E. colidnaK mutant. Our results demonstrated that the PRK00290 proteins play a central role in the complex cellular functions of M. xanthus, while the other diverse Hsp70 superfamily homologues probably evolved as helpers with some unknown specific functions. IMPORTANCE Hsp70 proteins are highly conserved chaperones that occur in all kingdoms of life. Multiple copies of Hsp70s are often present in genome-sequenced prokaryotes, especially taxa with complex life cycles, such as myxobacteria. We investigated the functions of six hsp70 genes in Myxococcus xanthus DK1622 and demonstrated that the two Hsp70 proteins with the PRK00290 domain play a central role in complex cellular functions in M. xanthus, while other Hsp70 proteins probably evolved as helpers with some unknown specific functions.
Collapse
|
28
|
Functional Genomic and Biochemical Analysis Reveals Pleiotropic Effect of Congo Red on Aspergillus fumigatus. mBio 2021; 12:mBio.00863-21. [PMID: 34006660 PMCID: PMC8262895 DOI: 10.1128/mbio.00863-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Inhibition of fungal growth by Congo red (CR) has been putatively associated with specific binding to β-1,3-glucans, which blocks cell wall polysaccharide synthesis. In this study, we searched for transcription factors (TFs) that regulate the response to CR and interrogated their regulon. During the investigation of the susceptibility to CR of the TF mutant library, several CR-resistant and -hypersensitive mutants were discovered and further studied. Abnormal distorted swollen conidia called Quasimodo cells were seen in the presence of CR. Quasimodo cells in the resistant mutants were larger than the ones in the sensitive and parental strains; consequently, the conidia of the resistant mutants absorbed more CR than the germinating conidia of the sensitive or parental strains. Accordingly, this higher absorption rate by Quasimodo cells resulted in the removal of CR from the culture medium, allowing a subset of conidia to germinate and grow. In contrast, all resting conidia of the sensitive mutants and the parental strain were killed. This result indicated that the heterogeneity of the conidial population is essential to promote the survival of Aspergillus fumigatus in the presence of CR. Moreover, amorphous surface cell wall polysaccharides such as galactosaminogalactan control the influx of CR inside the cells and, accordingly, resistance to the drug. Finally, long-term incubation with CR led to the discovery of a new CR-induced growth effect, called drug-induced growth stimulation (DIGS), since the growth of one of them could be stimulated after recovery from CR stress.
Collapse
|
29
|
Ruiz J, de Celis M, Martín-Santamaría M, Benito-Vázquez I, Pontes A, Lanza VF, Sampaio JP, Santos A, Belda I. Global distribution of IRC7 alleles in Saccharomyces cerevisiae populations: a genomic and phenotypic survey within the wine clade. Environ Microbiol 2021; 23:3182-3195. [PMID: 33973343 DOI: 10.1111/1462-2920.15540] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 03/23/2021] [Accepted: 04/19/2021] [Indexed: 11/28/2022]
Abstract
The adaptation to the different biotic and abiotic factors of wine fermentation has led to the accumulation of numerous genomic hallmarks in Saccharomyces cerevisiae wine strains. IRC7, a gene encoding a cysteine-S-β-lyase enzyme related volatile thiols production in wines, has two alleles: a full-length allele (IRC7F ) and a mutated one (IRC7S ), harbouring a 38 bp-deletion. Interestingly, IRC7S -encoding a less active enzyme - appears widespread amongst wine populations. Studying the global distribution of the IRC7S allele in different yeast lineages, we confirmed its high prevalence in the Wine clade and demonstrated a minority presence in other domesticated clades (Wine-PDM, Beer and Bread) while it is completely missing in wild clades. Here, we show that IRC7S -homozygous (HS) strains exhibited both fitness and competitive advantages compared with IRC7F -homozygous (HF) strains. There are some pieces of evidence of the direct contribution of the IRC7S allele to the outstanding behaviour of HS strains (i.e., improved response to oxidative stress conditions and higher tolerance to high copper levels); however, we also identified a set of sequence variants with significant co-occurrence patterns with the IRC7S allele, which can be co-contributing to the fitness and competitive advantages of HS strains in wine fermentations.
Collapse
Affiliation(s)
- Javier Ruiz
- Department of Genetics, Physiology and Microbiology. Unit of Microbiology. Biology Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - Miguel de Celis
- Department of Genetics, Physiology and Microbiology. Unit of Microbiology. Biology Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - María Martín-Santamaría
- Department of Genetics, Physiology and Microbiology. Unit of Microbiology. Biology Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - Iván Benito-Vázquez
- Department of Genetics, Physiology and Microbiology. Unit of Microbiology. Biology Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - Ana Pontes
- Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal
| | - Val F Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Madrid, 28034, Spain
| | - José Paulo Sampaio
- Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal
| | - Antonio Santos
- Department of Genetics, Physiology and Microbiology. Unit of Microbiology. Biology Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - Ignacio Belda
- Department of Genetics, Physiology and Microbiology. Unit of Microbiology. Biology Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| |
Collapse
|
30
|
Boulton C. Provocation: all yeast cells are born equal, but some grow to be more equal than others. JOURNAL OF THE INSTITUTE OF BREWING 2021. [DOI: 10.1002/jib.647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
31
|
Lahue C, Madden AA, Dunn RR, Smukowski Heil C. History and Domestication of Saccharomyces cerevisiae in Bread Baking. Front Genet 2020; 11:584718. [PMID: 33262788 PMCID: PMC7686800 DOI: 10.3389/fgene.2020.584718] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/13/2020] [Indexed: 11/30/2022] Open
Abstract
The yeast Saccharomyces cerevisiae has been instrumental in the fermentation of foods and beverages for millennia. In addition to fermentations like wine, beer, cider, sake, and bread, S. cerevisiae has been isolated from environments ranging from soil and trees, to human clinical isolates. Each of these environments has unique selection pressures that S. cerevisiae must adapt to. Bread dough, for example, requires S. cerevisiae to efficiently utilize the complex sugar maltose; tolerate osmotic stress due to the semi-solid state of dough, high salt, and high sugar content of some doughs; withstand various processing conditions, including freezing and drying; and produce desirable aromas and flavors. In this review, we explore the history of bread that gave rise to modern commercial baking yeast, and the genetic and genomic changes that accompanied this. We illustrate the genetic and phenotypic variation that has been documented in baking strains and wild strains, and how this variation might be used for baking strain improvement. While we continue to improve our understanding of how baking strains have adapted to bread dough, we conclude by highlighting some of the remaining open questions in the field.
Collapse
Affiliation(s)
- Caitlin Lahue
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
| | - Anne A. Madden
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Caiti Smukowski Heil
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| |
Collapse
|
32
|
Kavatalkar V, Saini S, Bhat PJ. Role of Noise-Induced Cellular Variability in Saccharomyces cerevisiae During Metabolic Adaptation: Causes, Consequences and Ramifications. J Indian Inst Sci 2020. [DOI: 10.1007/s41745-020-00180-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
33
|
Sukmawati D, Shabrina A, Indrayanti R, Kurniati TH, Nurjayadi M, Hidayat I, Al Husna SN, Ratnaningtyas NI, El Enshasy H, Dailin DJ, Hesham AEL. Antifungal Mechanism of Rhodotorula mucilaginosa and Aureobasidium sp. nov. Isolated from Cerbera manghas L. against the Growth of Destructive Molds in Post Harvested Apples. Recent Pat Food Nutr Agric 2020; 11:219-228. [PMID: 32324527 DOI: 10.2174/2212798411666200423101159] [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: 08/06/2019] [Revised: 01/23/2020] [Accepted: 02/10/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Apples often experience postharvest damage due to being attacked by mold organisms. Several groups of molds such as Aspergillus sp., Penicilium expansum, Botrytis cinerea, and Venturia sp. can cause a serious postharvest disease exhibited as watery regions where areas of blue-green tufts of spores develop. Current methods using fungicides to control pathogenic fungi can cause resistance if applied in the long term. An alternative procedure using yeast as a biological agent has been found. OBJECTIVE The aim of this study is to screen potential yeast, which has the ability to inhibit the growth of Aspergillus brasielensis (isolate A1) and Aspergillus flavus section flavi (isolate A17) isolated from apple fruits. METHODS Antagonism test using YMA dual culture medium using in vitro assays and ITS rDNA identification were performed. RESULTS The result showed that 3 out of 19 yeast isolated from Cerbera manghas L, T1, T3 and T4, demonstrated the potential ability as a biocontrol agent. ITS rDNA identification demonstrated that T1 has a similarity to Rhodotorula mucilaginosa while T3 and T4 were identified as Aureobasidium sp. nov. The 3 isolates exhibited the ability to reduce the growth of A. brasiliensis sensu lato better than dithane 0.3% with a Disease Incidence (DI) of 100% and a Disease Severity (DS) value of 45%. Only isolate T1 and T3 were able to reduce decay symptoms in apples inoculated with A. flavus sensu lato (with DO and DS were 100% and 25%, respectively) compared to dithane pesticides 0.3%. CONCLUSION This study indicated that competition between nutrients occurs between pathogenic molds and under-yeast in vitro and in vivo conditions. However, further studies in the future might be able to elucidate the 'killer' activity and interaction with the pathogen cells and the bio-product production using Rhodotorula mucilaginosa and Aureoubasidium namibiae strains to control postharvest diseases.
Collapse
Affiliation(s)
- Dalia Sukmawati
- Biology Department, 9th Floor Hasyim Ashari Building, Faculty of Mathematics and Natural Sciences, Universitas Negeri Jakarta, Jakarta, Indonesia
| | - Andisa Shabrina
- Biology Department, 9th Floor Hasyim Ashari Building, Faculty of Mathematics and Natural Sciences, Universitas Negeri Jakarta, Jakarta, Indonesia
| | - Reni Indrayanti
- Biology Department, 9th Floor Hasyim Ashari Building, Faculty of Mathematics and Natural Sciences, Universitas Negeri Jakarta, Jakarta, Indonesia
| | - Tri Handayani Kurniati
- Biology Department, 9th Floor Hasyim Ashari Building, Faculty of Mathematics and Natural Sciences, Universitas Negeri Jakarta, Jakarta, Indonesia
| | - Muktiningsih Nurjayadi
- Education of Chemistry Department, 8th Floor Hasyim Ashari Building, Faculty of Mathematics and Natural Sciences, Universitas Negeri Jakarta, Jakarta, Indonesia
| | - Iman Hidayat
- Research Centre for Biology, Indonesian Institute of Sciences-LIPI Jl, Raya Jakarta-Bogor KM 46, Cibinong, 16911, West Java, Indonesia
| | - Shabrina Nida Al Husna
- Department of Microbiology, School of Life Sciences and Technology, Institut Teknologi Bandung, Indonesia
| | - Nuniek Ina Ratnaningtyas
- Biology Faculty, Jenderal Soedirman University, Jl. Dr. Suparno 63, Grendeng, Purwokerto, Jawa Tengah, 53122, Indonesia
| | - Hesham El Enshasy
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), 81130 UTM, Skudai, Malaysia
| | - Daniel Joe Dailin
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), 81130 UTM, Skudai, Malaysia
| | - Abd El-Latif Hesham
- Genetics Department, Faculty of Agriculture, Beni-Suef University, Beni-Suef, Egypt
| |
Collapse
|
34
|
Hamill PG, Stevenson A, McMullan PE, Williams JP, Lewis ADR, S S, Stevenson KE, Farnsworth KD, Khroustalyova G, Takemoto JY, Quinn JP, Rapoport A, Hallsworth JE. Microbial lag phase can be indicative of, or independent from, cellular stress. Sci Rep 2020; 10:5948. [PMID: 32246056 PMCID: PMC7125082 DOI: 10.1038/s41598-020-62552-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/16/2020] [Indexed: 01/01/2023] Open
Abstract
Measures of microbial growth, used as indicators of cellular stress, are sometimes quantified at a single time-point. In reality, these measurements are compound representations of length of lag, exponential growth-rate, and other factors. Here, we investigate whether length of lag phase can act as a proxy for stress, using a number of model systems (Aspergillus penicillioides; Bacillus subtilis; Escherichia coli; Eurotium amstelodami, E. echinulatum, E. halophilicum, and E. repens; Mrakia frigida; Saccharomyces cerevisiae; Xerochrysium xerophilum; Xeromyces bisporus) exposed to mechanistically distinct types of cellular stress including low water activity, other solute-induced stresses, and dehydration-rehydration cycles. Lag phase was neither proportional to germination rate for X. bisporus (FRR3443) in glycerol-supplemented media (r2 = 0.012), nor to exponential growth-rates for other microbes. In some cases, growth-rates varied greatly with stressor concentration even when lag remained constant. By contrast, there were strong correlations for B. subtilis in media supplemented with polyethylene-glycol 6000 or 600 (r2 = 0.925 and 0.961), and for other microbial species. We also analysed data from independent studies of food-spoilage fungi under glycerol stress (Aspergillus aculeatinus and A. sclerotiicarbonarius); mesophilic/psychrotolerant bacteria under diverse, solute-induced stresses (Brochothrix thermosphacta, Enterococcus faecalis, Pseudomonas fluorescens, Salmonella typhimurium, Staphylococcus aureus); and fungal enzymes under acid-stress (Terfezia claveryi lipoxygenase and Agaricus bisporus tyrosinase). These datasets also exhibited diversity, with some strong- and moderate correlations between length of lag and exponential growth-rates; and sometimes none. In conclusion, lag phase is not a reliable measure of stress because length of lag and growth-rate inhibition are sometimes highly correlated, and sometimes not at all.
Collapse
Affiliation(s)
- Philip G Hamill
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland
| | - Andrew Stevenson
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland
| | - Phillip E McMullan
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland
| | - James P Williams
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland
| | - Abiann D R Lewis
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland
| | - Sudharsan S
- Department of Chemistry, PGP College of Arts and Science, NH-7, Karur Main Road, Paramathi, Namakkal, Tamil Nadu, 637 207, India
| | - Kath E Stevenson
- Special Collections and Archives, McClay Library, Queen's University Belfast, 10 College Park Avenue, Belfast, BT7 1LP, Northern Ireland
| | - Keith D Farnsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland
| | - Galina Khroustalyova
- Laboratory of Cell Biology, Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Str., 1-537, LV-1004, Riga, Latvia
| | - Jon Y Takemoto
- Utah State University, Department of Biology, 5305 Old Main Hill, Logan, UT, 84322, USA
| | - John P Quinn
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland
| | - Alexander Rapoport
- Laboratory of Cell Biology, Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Str., 1-537, LV-1004, Riga, Latvia
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland.
| |
Collapse
|
35
|
Utama GL, Irena F, Lembong E, Kayaputri IL, Tensiska T, Balia RL. The Utilization of Vegetable and Fruit Wastes for Saccharomyces cerevisieae Cell Wall Based β-Glucan Production with Antioxidant Activity. ACTA UNIVERSITATIS AGRICULTURAE ET SILVICULTURAE MENDELIANAE BRUNENSIS 2020. [DOI: 10.11118/actaun202068010119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
36
|
Sheng DH, Wang YX, Qiu M, Zhao JY, Yue XJ, Li YZ. Functional Division Between the RecA1 and RecA2 Proteins in Myxococcus xanthus. Front Microbiol 2020; 11:140. [PMID: 32117159 PMCID: PMC7029660 DOI: 10.3389/fmicb.2020.00140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/21/2020] [Indexed: 12/18/2022] Open
Abstract
Myxococcus xanthus DK1622 has two RecA genes, recA1 (MXAN_1441) and recA2 (MXAN_1388), with unknown functional differentiation. Herein, we showed that both recA genes were induced by ultraviolet (UV) irradiation but that the induction of recA1 was more delayed than that of recA2. Deletion of recA1 did not affect the growth but significantly decreased the UV-radiation survival, homologous recombination (HR) ability, and induction of LexA-dependent SOS genes. In contrast, the deletion of recA2 markedly prolonged the lag phase of bacterial growth and increased the sensitivity to DNA damage caused by hydrogen peroxide but did not change the UV-radiation resistance or SOS gene inducibility. Protein activity analysis demonstrated that RecA1, but not RecA2, catalyzed DNA strand exchange (DSE) and LexA autocleavage in vitro. Transcriptomic analysis indicated that RecA2 has evolved mainly to regulate gene expression for cellular transportation and antioxidation. This is the first report of functional divergence of duplicated bacterial recA genes. The results highlight the evolutionary strategy of M. xanthus cells for DNA HR and genome sophistication.
Collapse
Affiliation(s)
- Duo-Hong Sheng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yi-Xue Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Miao Qiu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jin-Yi Zhao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Xin-Jing Yue
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| |
Collapse
|