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Duperray M, Delvenne M, François JM, Delvigne F, Capp JP. Genomic and metabolic instability during long-term fermentation of an industrial Saccharomyces cerevisiae strain engineered for C5 sugar utilization. Front Bioeng Biotechnol 2024; 12:1357671. [PMID: 38595997 PMCID: PMC11002265 DOI: 10.3389/fbioe.2024.1357671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/07/2024] [Indexed: 04/11/2024] Open
Abstract
The genetic stability and metabolic robustness of production strains is one of the key criteria for the production of bio-based products by microbial fermentation on an industrial scale. These criteria were here explored in an industrial ethanol-producer strain of Saccharomyces cerevisiae able to co-ferment D-xylose and L-arabinose with glucose through the chromosomal integration of several copies of pivotal genes for the use of these pentose (C5) sugars. Using batch sequential cultures in a controlled bioreactor that mimics long-term fermentation in an industrial setting, this strain was found to exhibit significant fluctuations in D-xylose and L-arabinose consumption as early as the 50th generation and beyond. These fluctuations seem not related to the few low-consumption C5 sugar clones that appeared throughout the sequential batch cultures at a frequency lower than 1.5% and that were due to the reduction in the number of copies of transgenes coding for C5 sugar assimilation enzymes. Also, subpopulations enriched with low or high RAD52 expression, whose expression level was reported to be proportional to homologous recombination rate did not exhibit defect in C5-sugar assimilation, arguing that other mechanisms may be responsible for copy number variation of transgenes. Overall, this work highlighted the existence of genetic and metabolic instabilities in an industrial yeast which, although modest in our conditions, could be more deleterious in harsher industrial conditions, leading to reduced production performance.
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Affiliation(s)
- Maëlle Duperray
- Toulouse Biotechnology Institute, INSA/University of Toulouse, CNRS, INRAE, Toulouse, France
| | - Mathéo Delvenne
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Jean Marie François
- Toulouse Biotechnology Institute, INSA/University of Toulouse, CNRS, INRAE, Toulouse, France
- Toulouse White Biotechnology, INSA, INRAE, CNRS, Toulouse, France
| | - Frank Delvigne
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Jean-Pascal Capp
- Toulouse Biotechnology Institute, INSA/University of Toulouse, CNRS, INRAE, Toulouse, France
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Wang R, Hu P, Wang F, Lyu J, Ou Y, Edderkaoui M, Zhang Y, Lewis MS, Pandol SJ, Zhau HE, Chung LWK. Spontaneous Fusion with Transformed Mesenchymal Stromal Cells Results in Complete Heterogeneity in Prostate Cancer Cells. Cancers (Basel) 2024; 16:951. [PMID: 38473313 PMCID: PMC10931070 DOI: 10.3390/cancers16050951] [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: 02/16/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Tumor cells gain advantages in growth and survival by acquiring genotypic and phenotypic heterogeneity. Interactions with bystander cells in the tumor microenvironment contribute to the progression of heterogeneity. We have shown that fusion between tumor and bystander cells is one form of interaction, and that tumor-bystander cell fusion has contrasting effects. By trapping fusion hybrids in the heterokaryon or synkaryon state, tumor-bystander cell fusion prevents the progression of heterogeneity. However, if trapping fails, fusion hybrids will resume replication to form derivative clones with diverse genomic makeups and behavioral phenotypes. To determine the characteristics of bystander cells that influence the fate of fusion hybrids, we co-cultured prostate mesenchymal stromal cell lines and their spontaneously transformed sublines with LNCaP as well as HPE-15 prostate cancer cells. Subclones derived from cancer-stromal fusion hybrids were examined for genotypic and phenotypic diversifications. Both stromal cell lines were capable of fusing with cancer cells, but only fusion hybrids with the transformed stromal subline generated large numbers of derivative subclones. Each subclone had distinct cell morphologies and growth behaviors and was detected with complete genomic hybridization. The health conditions of the bystander cell compartment play a crucial role in the progression of tumor cell heterogeneity.
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Affiliation(s)
- Ruoxiang Wang
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (P.H.); (F.W.); (J.L.); (M.E.); (S.J.P.); (H.E.Z.); (L.W.K.C.)
| | - Peizhen Hu
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (P.H.); (F.W.); (J.L.); (M.E.); (S.J.P.); (H.E.Z.); (L.W.K.C.)
| | - Fubo Wang
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (P.H.); (F.W.); (J.L.); (M.E.); (S.J.P.); (H.E.Z.); (L.W.K.C.)
| | - Ji Lyu
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (P.H.); (F.W.); (J.L.); (M.E.); (S.J.P.); (H.E.Z.); (L.W.K.C.)
| | - Yan Ou
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (Y.O.); (Y.Z.)
| | - Mouad Edderkaoui
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (P.H.); (F.W.); (J.L.); (M.E.); (S.J.P.); (H.E.Z.); (L.W.K.C.)
| | - Yi Zhang
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (Y.O.); (Y.Z.)
| | - Michael S. Lewis
- Department of Medicine and Pathology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA;
| | - Stephen J. Pandol
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (P.H.); (F.W.); (J.L.); (M.E.); (S.J.P.); (H.E.Z.); (L.W.K.C.)
| | - Haiyen E. Zhau
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (P.H.); (F.W.); (J.L.); (M.E.); (S.J.P.); (H.E.Z.); (L.W.K.C.)
| | - Leland W. K. Chung
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (P.H.); (F.W.); (J.L.); (M.E.); (S.J.P.); (H.E.Z.); (L.W.K.C.)
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Capp J. Interplay between genetic, epigenetic, and gene expression variability: Considering complexity in evolvability. Evol Appl 2021; 14:893-901. [PMID: 33897810 PMCID: PMC8061278 DOI: 10.1111/eva.13204] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 12/11/2022] Open
Abstract
Genetic variability, epigenetic variability, and gene expression variability (noise) are generally considered independently in their relationship with phenotypic variation. However, they appear to be intrinsically interconnected and influence it in combination. The study of the interplay between genetic and epigenetic variability has the longest history. This article rather considers the introduction of gene expression variability in its relationships with the two others and reviews for the first time experimental evidences over the four relationships connected to gene expression noise. They show how introducing this third source of variability complicates the way of thinking evolvability and the emergence of biological novelty. Finally, cancer cells are proposed to be an ideal model to decipher the dynamic interplay between genetic, epigenetic, and gene expression variability when one of them is either experimentally increased or therapeutically targeted. This interplay is also discussed in an evolutionary perspective in the context of cancer cell drug resistance.
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Affiliation(s)
- Jean‐Pascal Capp
- Toulouse Biotechnology InstituteINSACNRSINRAEUniversity of ToulouseToulouseFrance
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Kuwahara H, Gao X. Stable maintenance of hidden switches as a strategy to increase the gene expression stability. NATURE COMPUTATIONAL SCIENCE 2021; 1:62-70. [PMID: 38217152 DOI: 10.1038/s43588-020-00001-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 11/02/2020] [Indexed: 01/15/2024]
Abstract
In response to severe genetic and environmental perturbations, wild-type organisms can express hidden alternative phenotypes adaptive to such adverse conditions. While our theoretical understanding of the population-level fitness advantage and evolution of phenotypic switching under variable environments has grown, the mechanism by which these organisms maintain phenotypic switching capabilities under static environments remains to be elucidated. Here, using computational simulations, we analyzed the evolution of gene circuits under natural selection and found that different strategies evolved to increase the gene expression stability near the optimum level. In a population comprising bistable individuals, a strategy of maintaining bistability and raising the potential barrier separating the bistable regimes was consistently taken. Our results serve as evidence that hidden bistable switches can be stably maintained during environmental stasis-an essential property enabling the timely release of adaptive alternatives with small genetic changes in the event of substantial perturbations.
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Affiliation(s)
- Hiroyuki Kuwahara
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Liu J, François JM, Capp JP. Gene Expression Noise Produces Cell-to-Cell Heterogeneity in Eukaryotic Homologous Recombination Rate. Front Genet 2019; 10:475. [PMID: 31164905 PMCID: PMC6536703 DOI: 10.3389/fgene.2019.00475] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 05/03/2019] [Indexed: 11/13/2022] Open
Abstract
Variation in gene expression among genetically identical individual cells (called gene expression noise) directly contributes to phenotypic diversity. Whether such variation can impact genome stability and lead to variation in genotype remains poorly explored. We addressed this question by investigating whether noise in the expression of genes affecting homologous recombination (HR) activity either directly (RAD52) or indirectly (RAD27) confers cell-to-cell heterogeneity in HR rate in Saccharomyces cerevisiae. Using cell sorting to isolate subpopulations with various expression levels, we show that spontaneous HR rate is highly heterogeneous from cell-to-cell in clonal populations depending on the cellular amount of proteins affecting HR activity. Phleomycin-induced HR is even more heterogeneous, showing that RAD27 expression variation strongly affects the rate of recombination from cell-to-cell. Strong variations in HR rate between subpopulations are not correlated to strong changes in cell cycle stage. Moreover, this heterogeneity occurs even when simultaneously sorting cells at equal expression level of another gene involved in DNA damage response (BMH1) that is upregulated by DNA damage, showing that the initiating DNA damage is not responsible for the observed heterogeneity in HR rate. Thus gene expression noise seems mainly responsible for this phenomenon. Finally, HR rate non-linearly scales with Rad27 levels showing that total amount of HR cannot be explained solely by the time- or population-averaged Rad27 expression. Altogether, our data reveal interplay between heterogeneity at the gene expression and genetic levels in the production of phenotypic diversity with evolutionary consequences from microbial to cancer cell populations.
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Affiliation(s)
- Jian Liu
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Institut National des Sciences Appliquées de Toulouse, UMR CNRS 5504, UMR INRA 792, Université de Toulouse, Toulouse, France
| | - Jean-Marie François
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Institut National des Sciences Appliquées de Toulouse, UMR CNRS 5504, UMR INRA 792, Université de Toulouse, Toulouse, France
| | - Jean-Pascal Capp
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Institut National des Sciences Appliquées de Toulouse, UMR CNRS 5504, UMR INRA 792, Université de Toulouse, Toulouse, France
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Abstract
Gene regulatory network that determines the cellular functions exhibits stochastic fluctuations, or "noise," in different layers. Noise has begun to be appreciated for many previously unrecognized functions in important cellular activities. In fact, molecular noise is unavoidable in both microbial and eukaryotic cells, the feedback system is established evolutionally to reduce noise or optimize the noise for cellular homeostasis. The small noncoding RNAs, particularly, microNRAs, post-transcriptionally and negatively regulate gene expressions. MicroRNAs function as a novel layer to buffer noise level, and stabilize mRNA and protein level to maintain normal cellular function. Furthermore, the changing of microRNA expression levels may increase the stochastic fluctuation leading to abnormal cellular function, even diseases.
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Affiliation(s)
- Wei Wu
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California in San Francisco, 600 16th Street Mission Bay/Genentech Hall, Room N212, San Francisco, CA, 94143, USA.
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Damodaran SP, Eberhard S, Boitard L, Rodriguez JG, Wang Y, Bremond N, Baudry J, Bibette J, Wollman FA. A millifluidic study of cell-to-cell heterogeneity in growth-rate and cell-division capability in populations of isogenic cells of Chlamydomonas reinhardtii. PLoS One 2015; 10:e0118987. [PMID: 25760649 PMCID: PMC4356620 DOI: 10.1371/journal.pone.0118987] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 01/08/2015] [Indexed: 12/31/2022] Open
Abstract
To address possible cell-to-cell heterogeneity in growth dynamics of isogenic cell populations of Chlamydomonas reinhardtii, we developed a millifluidic drop-based device that not only allows the analysis of populations grown from single cells over periods of a week, but is also able to sort and collect drops of interest, containing viable and healthy cells, which can be used for further experimentation. In this study, we used isogenic algal cells that were first synchronized in mixotrophic growth conditions. We show that these synchronized cells, when placed in droplets and kept in mixotrophic growth conditions, exhibit mostly homogeneous growth statistics, but with two distinct subpopulations: a major population with a short doubling-time (fast-growers) and a significant subpopulation of slowly dividing cells (slow-growers). These observations suggest that algal cells from an isogenic population may be present in either of two states, a state of restricted division and a state of active division. When isogenic cells were allowed to propagate for about 1000 generations on solid agar plates, they displayed an increased heterogeneity in their growth dynamics. Although we could still identify the original populations of slow- and fast-growers, drops inoculated with a single progenitor cell now displayed a wider diversity of doubling-times. Moreover, populations dividing with the same growth-rate often reached different cell numbers in stationary phase, suggesting that the progenitor cells differed in the number of cell divisions they could undertake. We discuss possible explanations for these cell-to-cell heterogeneities in growth dynamics, such as mutations, differential aging or stochastic variations in metabolites and macromolecules yielding molecular switches, in the light of single-cell heterogeneities that have been reported among isogenic populations of other eu- and prokaryotes.
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Affiliation(s)
- Shima P. Damodaran
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
| | - Stephan Eberhard
- Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, UMR CNRS/UPMC 7141, Paris, France
| | - Laurent Boitard
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
| | - Jairo Garnica Rodriguez
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
| | - Yuxing Wang
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
- Optical Science & Engineering Research Center, Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | - Nicolas Bremond
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
| | - Jean Baudry
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
| | - Jérôme Bibette
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
- * E-mail: (JB); (FAW)
| | - Francis-André Wollman
- Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, UMR CNRS/UPMC 7141, Paris, France
- * E-mail: (JB); (FAW)
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Morrow CA, Fraser JA. Ploidy variation as an adaptive mechanism in human pathogenic fungi. Semin Cell Dev Biol 2013; 24:339-46. [PMID: 23380396 DOI: 10.1016/j.semcdb.2013.01.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 01/25/2013] [Accepted: 01/25/2013] [Indexed: 12/24/2022]
Abstract
Changes in ploidy have a profound and usually negative influence on cellular viability and proliferation, yet the vast majority of cancers and tumours exhibit an aneuploid karyotype. Whether this genomic plasticity is a cause or consequence of malignant transformation remains uncertain. Systemic fungal pathogens regularly develop aneuploidies in a similar manner during human infection, often far in excess of the natural rate of chromosome nondisjunction. As both processes fundamentally represent cells evolving under selective pressures, this suggests that changes in chromosome number may be a concerted mechanism to adapt to the hostile host environment. Here, we examine the mechanisms by which aneuploidy and polyploidy are generated in the fungal pathogens Candida albicans and Cryptococcus neoformans and investigate whether these represent an adaptive strategy under severe stress through the rapid generation of large-scale mutations. Insights into fungal ploidy changes, strategies for tolerating aneuploidies and proliferation during infection may yield novel targets for both antifungal and anticancer therapies.
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Affiliation(s)
- Carl A Morrow
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane QLD 4072, Australia
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