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Yang J, Sun N, Wang W, Zhang R, Sun S, Li B, Shi Y, Zeng J, Jia S. Genomic analysis and mechanisms exploration of a stress tolerance and high-yield pullulan producing strain. Front Genet 2024; 15:1469600. [PMID: 39371418 PMCID: PMC11449735 DOI: 10.3389/fgene.2024.1469600] [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: 07/24/2024] [Accepted: 09/10/2024] [Indexed: 10/08/2024] Open
Abstract
Pullulan is a kind of natural polymer, which is widely used in medicine and food because of its solubility, plasticity, edible, non-toxicity and good biocompatibility. It is of great significance to improve the yield of pullulan by genetic modification of microorganisms. It was previously reported that Aureobasidium melanogenum TN3-1 isolated from honey-comb could produce high-yield of pullulan, but the molecular mechanisms of its production of pullulan had not been completely solved. In this study, the reported strains of Aureobasidium spp. were further compared and analyzed at genome level. It was found that genome duplication and genome genetic variations might be the crucial factors for the high yield of pullulan and stress resistance. This particular phenotype may be the result of adaptive evolution, which can adapt to its environment through genetic variation and adaptive selection. In addition, the TN3-1 strain has a large genome, and the special regulatory sequences of its specific genes and promoters may ensure a unique characteristics. This study is a supplement of the previous studies, and provides basic data for the research of microbial genome modification in food and healthcare applications.
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Affiliation(s)
- Jing Yang
- School of Basic Medicine, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ning Sun
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- First clinical medical college, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Wenru Wang
- School of Basic Medicine, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ruihua Zhang
- School of Basic Medicine, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Siqi Sun
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Biqi Li
- School of Basic Medicine, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yue Shi
- School of Basic Medicine, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Junfeng Zeng
- School of Basic Medicine, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Shulei Jia
- School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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2
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Leonov A, Feldman R, Piano A, Arlia-Ciommo A, Junio JAB, Orfanos E, Tafakori T, Lutchman V, Mohammad K, Elsaser S, Orfali S, Rajen H, Titorenko VI. Diverse geroprotectors differently affect a mechanism linking cellular aging to cellular quiescence in budding yeast. Oncotarget 2022; 13:918-943. [PMID: 35937500 PMCID: PMC9348708 DOI: 10.18632/oncotarget.28256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/01/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Anna Leonov
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Rachel Feldman
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Amanda Piano
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | | | | | - Emmanuel Orfanos
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Tala Tafakori
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Vicky Lutchman
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Karamat Mohammad
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Sarah Elsaser
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Sandra Orfali
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Harshvardhan Rajen
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
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Yeom J, Groisman EA. Reduced ATP-dependent proteolysis of functional proteins during nutrient limitation speeds the return of microbes to a growth state. Sci Signal 2021; 14:14/667/eabc4235. [PMID: 33500334 DOI: 10.1126/scisignal.abc4235] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
When cells run out of nutrients, the growth rate greatly decreases. Here, we report that microorganisms, such as the bacterium Salmonella enterica serovar Typhimurium, speed up the return to a rapid growth state by preventing the proteolysis of functional proteins by ATP-dependent proteases while in the slow-growth state or stationary phase. This reduction in functional protein degradation resulted from a decrease in the intracellular concentration of ATP that was nonetheless sufficient to allow the continued degradation of nonfunctional proteins by the same proteases. Protein preservation occurred under limiting magnesium, carbon, or nitrogen conditions, indicating that this response was not specific to low availability of a particular nutrient. Nevertheless, the return to rapid growth required proteins that mediate responses to the specific nutrient limitation conditions, because the transcriptional regulator PhoP was necessary for rapid recovery only after magnesium starvation. Reductions in intracellular ATP and in ATP-dependent proteolysis also enabled the yeast Saccharomyces cerevisiae to recover faster from stationary phase. Our findings suggest that protein preservation during a slow-growth state is a conserved microbial strategy that facilitates the return to a growth state once nutrients become available.
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Affiliation(s)
- Jinki Yeom
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore.,Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 03080, Korea.,Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA. .,Yale Microbial Sciences Institute, P.O. Box 27389, West Haven, CT 06516, USA
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4
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Li J, Hochstrasser M. Microautophagy regulates proteasome homeostasis. Curr Genet 2020; 66:683-687. [PMID: 32077993 DOI: 10.1007/s00294-020-01059-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 01/28/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023]
Abstract
Proteasomes are highly abundant protein complexes that are responsible for most regulated protein degradation in cells under favorable growth conditions. When yeast cells are under nutritional stress, most proteasomes exit the nucleus and either accumulate in cytoplasmic condensates called proteasome storage granules (PSGs) or are directed to the vacuole by autophagy. Nitrogen starvation does not cause PSG formation but leads to degradation of proteasomes through the classical macroautophagy pathway. By contrast, carbon starvation or extended incubation in stationary phase results in both PSG formation and macroautophagy of proteasomes. Unexpectedly, we found that glucose limitation also causes proteasomes to be taken up directly into vacuoles by a microautophagy mechanism. Macro- and micro-autophagy occur in parallel in glucose-starved cells, and microautophagy appears biased toward aberrant or inactive proteasomes, leaving functional proteasomes to accumulate in PSGs. PSGs dissolve and proteasomes remobilize to the nucleus within minutes after glucose refeeding. We showed that AMP-activated protein kinase (AMPK) and endosomal-sorting-complex-required-for-transport (ESCRT) factors are required for proteasome microautophagy and also impact PSG dissipation and nuclear reimport of proteasomes after glucose refeeding. The insoluble protein deposit (IPOD) compartment provides an alternative means of proteasome homeostasis, including when microautophagy is impaired. Our findings reveal a surprising diversity of mechanisms for proteasome quality and quantity control during starvation. A mechanistic understanding of the AMPK-regulated ESCRT-mediated microautophagy pathway could provide new avenues for manipulating proteasome homeostasis and treating human disease.
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Affiliation(s)
- Jianhui Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA. .,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA.
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5
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Ramos-Moreno L, Ramos J, Michán C. Overlapping responses between salt and oxidative stress in Debaryomyces hansenii. World J Microbiol Biotechnol 2019; 35:170. [PMID: 31673816 DOI: 10.1007/s11274-019-2753-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/22/2019] [Indexed: 11/26/2022]
Abstract
Debaryomyces hansenii is a halotolerant yeast of importance in basic and applied research. Previous reports hinted about possible links between saline and oxidative stress responses in this yeast. The aim of this work was to study that hypothesis at different molecular levels, investigating after oxidative and saline stress: (i) transcription of seven genes related to oxidative and/or saline responses, (ii) activity of two main anti-oxidative enzymes, (iii) existence of common metabolic intermediates, and (iv) generation of damages to biomolecules as lipids and proteins. Our results showed how expression of genes related to oxidative stress was induced by exposure to NaCl and KCl, and, vice versa, transcription of some genes related to osmotic/salt stress responses was regulated by H2O2. Moreover, and contrary to S. cerevisiae, in D. hansenii HOG1 and MSN2 genes were modulated by stress at their transcriptional level. At the enzymatic level, saline stress also induced antioxidative enzymatic defenses as catalase and glutathione reductase. Furthermore, we demonstrated that both stresses are connected by the generation of intracellular ROS, and that hydrogen peroxide can affect the accumulation of in-cell sodium. On the other hand, no significant alterations in lipid oxidation or total glutathione content were observed upon exposure to both stresses tested. The results described in this work could help to understand the responses to both stressors, and to improve the biotechnological potential of D. hansenni.
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Affiliation(s)
- Laura Ramos-Moreno
- Departamento de Microbiología, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, 14071, Córdoba, España, Spain
| | - José Ramos
- Departamento de Microbiología, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, 14071, Córdoba, España, Spain
| | - Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, 14071, Córdoba, España, Spain.
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A role for the yeast PCNA unloader Elg1 in eliciting the DNA damage checkpoint. Curr Genet 2019; 66:79-84. [PMID: 31332476 DOI: 10.1007/s00294-019-01020-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 12/28/2022]
Abstract
During cell proliferation, the genome is constantly threatened by cellular and external factors. When the DNA is damaged, or when its faithful duplication is delayed by DNA polymerase stalling, the cells induce a coordinated response termed the DNA damage response (DDR) or checkpoint. Elg1 forms an RFC-like complex in charge of unloading the DNA polymerase processively factor PCNA during DNA replication and DNA repair. Using checkpoint-inducible strains, a recently published paper (Sau et al. in mBio 10(3):e01159-19. https://doi.org/10.1128/mbio.01159-19, 2019) uncovered a role for Elg1 in eliciting the DNA damage checkpoint (DC), one of the branches of the DDR. The apical kinase Mec1/ATR phosphorylates Elg1, as well as the adaptor proteins Rad9/53BP1 and Dpb11/TopBP1, which are recruited to the site of DNA damage to amplify the checkpoint signal. In the absence of Elg1, Rad9 and Dpb11 are recruited but fail to be phosphorylated and the signal is therefore not amplified. Thus, Elg1 appears to coordinate DNA repair and the induction of the DNA damage checkpoint.
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7
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Unraveling quiescence-specific repressive chromatin domains. Curr Genet 2019; 65:1145-1151. [PMID: 31055637 DOI: 10.1007/s00294-019-00985-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 01/30/2023]
Abstract
Quiescence is a highly conserved inactive life stage in which the cell reversibly exits the cell cycle in response to external cues. Quiescence is essential for diverse processes such as the maintenance of adult stem cell stores, stress resistance, and longevity, and its misregulation has been implicated in cancer. Although the non-cycling nature of quiescent cells has made obtaining sufficient quantities of quiescent cells for study difficult, the development of a Saccharomyces cerevisiae model of quiescence has recently enabled detailed investigation into mechanisms underlying the quiescent state. Like their metazoan counterparts, quiescent budding yeast exhibit widespread transcriptional silencing and dramatic chromatin condensation. We have recently found that the structural maintenance of chromosomes (SMC) complex condensin binds throughout the quiescent budding yeast genome and induces the formation of large chromatin loop domains. In the absence of condensin, quiescent cell chromatin is decondensed and transcription is de-repressed. Here, we briefly discuss our findings in the larger context of the genome organization field.
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Sagot I, Laporte D. Quiescence, an individual journey. Curr Genet 2019; 65:695-699. [PMID: 30649583 DOI: 10.1007/s00294-018-00928-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 12/21/2018] [Accepted: 12/24/2018] [Indexed: 12/14/2022]
Abstract
Quiescence is operationally characterized as a temporary and reversible proliferation arrest. There are many preconceived ideas about quiescence, quiescent cells being generally viewed as insignificant sleeping G1 cells. In fact, quiescence is central for organism physiology and its dysregulation involved in many pathologies. The quiescent state encompasses very diverse cellular situations depending on the cell type and its environment. This diversity challenges not only quiescence uniformity but also the universality of the molecular mechanisms beyond quiescence regulation. In this mini-perspective, we discuss recent advances in the concept of quiescence, and illustrate that this multifaceted cellular state is gaining increasing attention in many fields of biology.
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Affiliation(s)
- Isabelle Sagot
- Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires, Unité Mixte de Recherche 5095, Université de Bordeaux, CS61390, Bordeaux Cedex, 33077, France.
| | - Damien Laporte
- Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires, Unité Mixte de Recherche 5095, Université de Bordeaux, CS61390, Bordeaux Cedex, 33077, France
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