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Jia C, Chai R, Zhang M, Guo X, Zhou X, Ding N, Lei C, Dong Z, Zhao J, Ren H, Lu D. Improvement of Saccharomyces cerevisiae strain tolerance to vanillin through heavy ion radiation combined with adaptive laboratory evolution. J Biotechnol 2024; 394:112-124. [PMID: 39197754 DOI: 10.1016/j.jbiotec.2024.08.014] [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: 06/05/2024] [Revised: 08/12/2024] [Accepted: 08/23/2024] [Indexed: 09/01/2024]
Abstract
Vanillin is an inhibitor of lignocellulose hydrolysate, which can reduce the ability of Saccharomyces cerevisiae to utilize lignocellulose, which is an important factor limiting the development of the ethanol fermentation industry. In this study, mutants of vanillin-tolerant yeast named H6, H7, X3, and X8 were bred by heavy ion irradiation (HIR) combined with adaptive laboratory evolution (ALE). Phenotypic tests revealed that the mutants outperformed the original strain WT in tolerance, growth rate, genetic stability and fermentation ability. At 1.6 g/L vanillin concentration, the average OD600 value obtained for mutant strains was 0.95 and thus about 3.4-fold higher than for the wild-type. When the concentration of vanillin was 2.0 g/L, the glucose utilization rate of the mutant was 86.3 % within 96 h, while that of the original strain was only 70.0 %. At this concentration of vanillin, the mitochondrial membrane potential of the mutant strain recovered faster than that of the original strain, and the ROS scavenging ability was stronger. We analyzed the whole transcriptome sequencing map and the whole genome resequencing of the mutant, and found that DEGs such as FLO9, GRC3, PSP2 and SWF1, which have large differential expression multiples and obvious mutation characteristics, play an important role in cell flocculation, rDNA transcription, inhibition of DNA polymerase mutation and protein palmitoylation. These functions can help cells resist vanillin stress. The results show that combining HIR with ALE is an effective mutagenesis strategy. This approach can efficiently obtain Saccharomyces cerevisiae mutants with improved vanillin tolerance, and provide reference for obtaining robust yeast strains with lignocellulose inhibitor tolerance.
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Affiliation(s)
- Chenglin Jia
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ran Chai
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Miaomiao Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaopeng Guo
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China.
| | - Xiang Zhou
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Ding
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cairong Lei
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziyi Dong
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingru Zhao
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiwei Ren
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Dong Lu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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De Guidi I, Galeote V, Blondin B, Legras JL. Copper-based grape pest management has impacted wine aroma. Sci Rep 2024; 14:10124. [PMID: 38698114 PMCID: PMC11066116 DOI: 10.1038/s41598-024-60335-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 04/22/2024] [Indexed: 05/05/2024] Open
Abstract
Despite the high energetic cost of the reduction of sulfate to H2S, required for the synthesis of sulfur-containing amino acids, some wine Saccharomyces cerevisiae strains have been reported to produce excessive amounts of H2S during alcoholic fermentation, which is detrimental to wine quality. Surprisingly, in the presence of sulfite, used as a preservative, wine strains produce more H2S than wild (oak) or wine velum (flor) isolates during fermentation. Since copper resistance caused by the amplification of the sulfur rich protein Cup1p is a specific adaptation trait of wine strains, we analyzed the link between copper resistance mechanism, sulfur metabolism and H2S production. We show that a higher content of copper in the must increases the production of H2S, and that SO2 increases the resistance to copper. Using a set of 51 strains we observed a positive and then negative relation between the number of copies of CUP1 and H2S production during fermentation. This complex pattern could be mimicked using a multicopy plasmid carrying CUP1, confirming the relation between copper resistance and H2S production. The massive use of copper for vine sanitary management has led to the selection of resistant strains at the cost of a metabolic tradeoff: the overproduction of H2S, resulting in a decrease in wine quality.
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Affiliation(s)
- Irene De Guidi
- SPO, INRAE, Institut Agro, Université de Montpellier, 34060, Montpellier, France
| | - Virginie Galeote
- SPO, INRAE, Institut Agro, Université de Montpellier, 34060, Montpellier, France
| | - Bruno Blondin
- SPO, INRAE, Institut Agro, Université de Montpellier, 34060, Montpellier, France
| | - Jean-Luc Legras
- SPO, INRAE, Institut Agro, Université de Montpellier, 34060, Montpellier, France.
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Zhong B, Xu W, Gong M, Xian W, Xie H, Wu Z. Molecular mechanisms of selenite reduction by Lactiplantibacillus plantarum BSe: An integrated genomic and transcriptomic analysis. JOURNAL OF HAZARDOUS MATERIALS 2024; 468:133850. [PMID: 38401219 DOI: 10.1016/j.jhazmat.2024.133850] [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: 12/11/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024]
Abstract
The reduction of selenite [Se(Ⅳ)] by microorganisms is a green and efficient detoxification strategy. We found that Se(Ⅳ) inhibited exopolysaccharide and protein secretion by Lactiplantibacillus plantarum BSe and compromised cell integrity. In this study, L. plantarum BSe reduced Se(Ⅳ) by increasing related enzyme activity and electron transfer. Genomic analysis demonstrated that L. plantarum BSe should be able to reduce Se(Ⅳ). Further transcriptome analysis showed that L. plantarum BSe enhanced its tolerance to Se(Ⅳ) by upregulating the expression of surface proteins and transporters, thus reducing the extracellular Se(Ⅳ) concentration through related enzymatic reactions and siderophore-mediated pathways. Lactiplantibacillus plantarum BSe was able to regulate the expression of related genes involved in quorum sensing and a two-component system and then select appropriate strategies for Se(Ⅳ) transformation in response to varying environmental Se(Ⅳ) concentrations. In addition, azo reductase was linked to the reduction of Se(Ⅳ) for the first time. The present study established a multipath model for the reduction of Se(Ⅳ) by L. plantarum, providing new insights into the biological reduction of Se(Ⅳ) and the biogeochemical cycle of selenium.
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Affiliation(s)
- Bin Zhong
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Weijun Xu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; Pan Asia (Jiangmen) Institute of Biological Engineering and Health, Jiangmen 529080, China
| | - Ming Gong
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; Yiweyi Biological Manufacturing (Jiangmen) Co., LTD, Jiangmen 529080, China
| | - Wei Xian
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Hanyi Xie
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Zhenqiang Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China.
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Giolito ML, Bigliani G, Meinero R, Taubas JV. Palmitoylation of CYSTM (CYSPD) proteins in yeast. J Biol Chem 2024; 300:105609. [PMID: 38159851 PMCID: PMC10840359 DOI: 10.1016/j.jbc.2023.105609] [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: 06/22/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
A superfamily of proteins called cysteine transmembrane is widely distributed across eukaryotes. These small proteins are characterized by the presence of a conserved motif at the C-terminal region, rich in cysteines, that has been annotated as a transmembrane domain. Orthologs of these proteins have been involved in resistance to pathogens and metal detoxification. The yeast members of the family are YBR016W, YDL012C, YDR034W-B, and YDR210W. Here, we begin the characterization of these proteins at the molecular level and show that Ybr016w, Ydr034w-b, and Ydr210w are palmitoylated proteins. Protein S-acylation or palmitoylation, is a posttranslational modification that consists of the addition of long-chain fatty acids to cysteine residues. We provide evidence that Ybr016w, Ydr210w, and Ydr034w-b are localized to the plasma membrane and exhibit varying degrees of polarity toward the daughter cell, which is dependent on endocytosis and recycling. We suggest the names CPP1, CPP2, and CPP3 (C terminally palmitoylated protein) for YBR016W, YDR210W, and YDR034W-B, respectively. We show that palmitoylation is responsible for the binding of these proteins to the membrane indicating that the cysteine transmembrane on these proteins is not a transmembrane domain. We propose renaming the C-terminal cysteine-rich domain as cysteine-rich palmitoylated domain. Loss of the palmitoyltransferase Erf2 leads to partial degradation of Ybr016w (Cpp1), whereas in the absence of the palmitoyltransferase Akr1, members of this family are completely degraded. For Cpp1, we show that this degradation occurs via the proteasome in an Rsp5-dependent manner, but is not exclusively due to a lack of Cpp1 palmitoylation.
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Affiliation(s)
- María Luz Giolito
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Gonzalo Bigliani
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Rocío Meinero
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Javier Valdez Taubas
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
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Liu L, Liu F, Yan Z, Zhou H, Song W. Transcriptome analysis of damage mechanism of Candida utilis under U(VI) stress. MARINE POLLUTION BULLETIN 2023; 196:115650. [PMID: 37839133 DOI: 10.1016/j.marpolbul.2023.115650] [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: 08/20/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 10/17/2023]
Abstract
Marine radioactive pollution has a great impact on Marine microorganisms, but the damage mechanism by hexavalent uranium (U(VI)) exposure has been rarely known. In this study, Candida utilis (C. utilis) were exposed to U(VI) for 50, 100 and 150 mg/L, and then morphologic change and RNA-Seq in C. utilis were determined. U(VI) exposure significantly induced the changes of morphological characteristics of C. utilis. There were 39 DEGs in the 50 mg/L treated group, including 30 up-regulated genes and 9 down-regulated genes. There were 196 DEGs, 31 up-regulated and 165 down-regulated in the 100 mg/L treated group. The 150 mg/L treated group had 272 DEGs, 74 up-regulated and 198 down-regulated, compared with the control group. The results showed that the number of DEGs increased dose-dependently with U(VI) treatment. The results of this study provide a theoretical basis for the mechanism of radioactive wastewater damage to Marine microorganisms.
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Affiliation(s)
- Lei Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health & Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China; School of Environment and Chemical Engineering, Anhui Vocational and Technical College, Hefei 230011, PR China
| | - Fang Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health & Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China
| | - Zhuna Yan
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health & Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China
| | - Han Zhou
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health & Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China
| | - Wencheng Song
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health & Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, PR China; Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions and School for Radiological and Interdisciplinary Sciences, Soochow University, 215123 Suzhou, PR China.
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Ray S, Gaudet R. Structures and coordination chemistry of transporters involved in manganese and iron homeostasis. Biochem Soc Trans 2023; 51:897-923. [PMID: 37283482 PMCID: PMC10330786 DOI: 10.1042/bst20210699] [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: 03/31/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/08/2023]
Abstract
A repertoire of transporters plays a crucial role in maintaining homeostasis of biologically essential transition metals, manganese, and iron, thus ensuring cell viability. Elucidating the structure and function of many of these transporters has provided substantial understanding into how these proteins help maintain the optimal cellular concentrations of these metals. In particular, recent high-resolution structures of several transporters bound to different metals enable an examination of how the coordination chemistry of metal ion-protein complexes can help us understand metal selectivity and specificity. In this review, we first provide a comprehensive list of both specific and broad-based transporters that contribute to cellular homeostasis of manganese (Mn2+) and iron (Fe2+ and Fe3+) in bacteria, plants, fungi, and animals. Furthermore, we explore the metal-binding sites of the available high-resolution metal-bound transporter structures (Nramps, ABC transporters, P-type ATPase) and provide a detailed analysis of their coordination spheres (ligands, bond lengths, bond angles, and overall geometry and coordination number). Combining this information with the measured binding affinity of the transporters towards different metals sheds light into the molecular basis of substrate selectivity and transport. Moreover, comparison of the transporters with some metal scavenging and storage proteins, which bind metal with high affinity, reveal how the coordination geometry and affinity trends reflect the biological role of individual proteins involved in the homeostasis of these essential transition metals.
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Affiliation(s)
- Shamayeeta Ray
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, U.S.A
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, U.S.A
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Ding Q, Liu H, Lin R, Wang Z, Jian S, Zhang M. Genome-wide functional characterization of Canavalia rosea cysteine-rich trans-membrane module (CrCYSTM) genes to reveal their potential protective roles under extreme abiotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 200:107786. [PMID: 37257408 DOI: 10.1016/j.plaphy.2023.107786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 06/02/2023]
Abstract
Cysteine-rich transmembrane module (CYSTM) proteins constitute small molecular protein families and have been identified across eukaryotes, including yeast, humans, and several plant species. Plant CYSTMs play vital roles in growth regulation, development, phytohormone signal transduction, pathogen defense, environmental stress response, and even heavy metal binding and detoxification. Canavalia rosea (Sw.) DC is a perennial halophyte with great semi-arid and saline-alkali tolerance. In this study, the CrCYSTM family including 10 members were identified in the C. rosea genome, with the purpose of clarifying the possible roles of CrCYSTMs in C. rosea plants development and stress resistance. The phylogenetic relationships, exon-intron structure, domain structure, chromosomal localization, and putative cis-acting elements in promoter regions were predicted and analyzed. Transcriptome analysis combined with quantitative reverse transcription PCR showed that different CrCYSTM members exhibited varied expression patterns in different tissues and under different abiotic stress challenges. In addition, several CrCYSTMs were cloned and functionally characterized for their roles in abiotic stress tolerance with yeast expression system. Overall, these findings provide a foundation for functionally characterizing plant CYSTMs to unravel their possible roles in the adaptation of C. rosea to tropical coral reefs. Our results also lay the foundation for further research on the roles of plant CYSTM genes in abiotic stress signaling, especially for heavy metal detoxification.
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Affiliation(s)
- Qianqian Ding
- Guangdong Provincial Key Laboratory of Applied Botany&South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Hao Liu
- Guangdong Provincial Key Laboratory of Applied Botany&South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Ruoyi Lin
- Guangdong Provincial Key Laboratory of Applied Botany&South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of the Chinese Academy of Sciences, Beijing, 100039, China; Dongguan Research Institute of Forestry/Forest Ecosystem Research Station in City Cluster of the Pearl River Estuary, Dongguan, 523106, China
| | - Zhengfeng Wang
- Guangdong Provincial Key Laboratory of Applied Botany&South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems&Carbon Sequestration in Terrestrial Ecosystem, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Shuguang Jian
- Guangdong Provincial Key Laboratory of Applied Botany&South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems&Carbon Sequestration in Terrestrial Ecosystem, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Mei Zhang
- Guangdong Provincial Key Laboratory of Applied Botany&South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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Zvonarev A, Ledova L, Ryazanova L, Valiakhmetov A, Farofonova V, Kulakovskaya T. The YBR056W-A and Its Ortholog YDR034W-B of S. cerevisiae Belonging to CYSTM Family Participate in Manganese Stress Overcoming. Genes (Basel) 2023; 14:genes14050987. [PMID: 37239347 DOI: 10.3390/genes14050987] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
The CYSTM (cysteine-rich transmembrane module) protein family comprises small molecular cysteine-rich tail-anchored membrane proteins found in many eukaryotes. The Saccharomyces cerevisiae strains carrying the CYSTM genes YDRO34W-B and YBR056W-A (MNC1) fused with GFP were used to test the expression of these genes under different stresses. The YBR056W-A (MNC1) and YDR034W-B genes are expressed under stress conditions caused by the toxic concentrations of heavy metal ions, such as manganese, cobalt, nickel, zinc, cuprum, and 2.4-dinitrophenol uncoupler. The expression level of YDR034W-B was higher than that of YBR056W-A under alkali and cadmium stresses. The Ydr034w-b-GFP and Ybr056w-a-GFP proteins differ in the cellular localization: Ydr034w-b-GFP was mainly observed in the plasma membrane and vacuolar membrane, while Ybr056w-a-GFP was observed in the cytoplasm, probably in intracellular membranes. The null-mutants in both genes demonstrated decreased cell concentration and lytic phenotype when cultivated in the presence of excess manganese. This allows for speculations about the involvement of Mnc1 and Ydr034w-b proteins in manganese stress overcoming.
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Affiliation(s)
- Anton Zvonarev
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, 142290 Pushchino, Russia
| | - Larisa Ledova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, 142290 Pushchino, Russia
| | - Lubov Ryazanova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, 142290 Pushchino, Russia
| | - Airat Valiakhmetov
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, 142290 Pushchino, Russia
| | - Vasilina Farofonova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institute for Biological Instrumentation of the Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Tatiana Kulakovskaya
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, 142290 Pushchino, Russia
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Ran X, Zhu Z, Long H, Tian Q, You L, Wu X, Liu Q, Huang S, Li S, Niu X, Wang J. Manganese Stress Adaptation Mechanisms of Bacillus safensis Strain ST7 From Mine Soil. Front Microbiol 2021; 12:758889. [PMID: 34899642 PMCID: PMC8656422 DOI: 10.3389/fmicb.2021.758889] [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: 08/15/2021] [Accepted: 10/21/2021] [Indexed: 11/23/2022] Open
Abstract
The mechanism of bacterial adaption to manganese-polluted environments was explored using 50 manganese-tolerant strains of bacteria isolated from soil of the largest manganese mine in China. Efficiency of manganese removal by the isolated strains was investigated using atomic absorption spectrophotometry. Bacillus safensis strain ST7 was the most effective manganese-oxidizing bacteria among the tested isolates, achieving up to 82% removal at a Mn(II) concentration of 2,200 mg/L. Bacteria-mediated manganese oxide precipitates and high motility were observed, and the growth of strain ST7 was inhibited while its biofilm formation was promoted by the presence of Mn(II). In addition, strain ST7 could grow in the presence of high concentrations of Al(III), Cr(VI), and Fe(III). Genome-wide analysis of the gene expression profile of strain ST7 using the RNA-seq method revealed that 2,580 genes were differently expressed under Mn(II) exposure, and there were more downregulated genes (n = 2,021) than upregulated genes (n = 559) induced by Mn stress. KAAS analysis indicated that these differently expressed genes were mainly enriched in material metabolisms, cellular processes, organism systems, and genetic and environmental information processing pathways. A total of twenty-six genes from the transcriptome of strain ST7 were involved in lignocellulosic degradation. Furthermore, after 15 genes were knocked out by homologous recombination technology, it was observed that the transporters, multicopper oxidase, and proteins involved in sporulation and flagellogenesis contributed to the removal of Mn(II) in strain ST7. In summary, B. safensis ST7 adapted to Mn exposure by changing its metabolism, upregulating cation transporters, inhibiting sporulation and flagellogenesis, and activating an alternative stress-related sigB pathway. This bacterial strain could potentially be used to restore soil polluted by multiple heavy metals and is a candidate to support the consolidated bioprocessing community.
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Affiliation(s)
- Xueqin Ran
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Animal Science/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Zhongmei Zhu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Animal Science/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Hong Long
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Animal Science/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Qun Tian
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Animal Science/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Longjiang You
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Animal Science/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Xingdiao Wu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Animal Science/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Qin Liu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Animal Science/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Shihui Huang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Animal Science/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Sheng Li
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Animal Science/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Xi Niu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Animal Science/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Jiafu Wang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Animal Science/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
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Tomashevsky A, Kulakovskaya E, Trilisenko L, Kulakovskiy IV, Kulakovskaya T, Fedorov A, Eldarov M. VTC4 Polyphosphate Polymerase Knockout Increases Stress Resistance of Saccharomyces cerevisiae Cells. BIOLOGY 2021; 10:487. [PMID: 34070801 PMCID: PMC8227513 DOI: 10.3390/biology10060487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 11/17/2022]
Abstract
Inorganic polyphosphate (polyP) is an important factor of alkaline, heavy metal, and oxidative stress resistance in microbial cells. In yeast, polyP is synthesized by Vtc4, a subunit of the vacuole transporter chaperone complex. Here, we report reduced but reliably detectable amounts of acid-soluble and acid-insoluble polyPs in the Δvtc4 strain of Saccharomyces cerevisiae, reaching 10% and 20% of the respective levels of the wild-type strain. The Δvtc4 strain has decreased resistance to alkaline stress but, unexpectedly, increased resistance to oxidation and heavy metal excess. We suggest that increased resistance is achieved through elevated expression of DDR2, which is implicated in stress response, and reduced expression of PHO84 encoding a phosphate and divalent metal transporter. The decreased Mg2+-dependent phosphate accumulation in Δvtc4 cells is consistent with reduced expression of PHO84. We discuss a possible role that polyP level plays in cellular signaling of stress response mobilization in yeast.
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Affiliation(s)
- Alexander Tomashevsky
- Federal Scientific Center, Pushchino Research Center for Biology of the Russian Academy of Sciences, Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, pr. Nauki 5, 142290 Pushchino, Russia; (A.T.); (E.K.); (L.T.)
| | - Ekaterina Kulakovskaya
- Federal Scientific Center, Pushchino Research Center for Biology of the Russian Academy of Sciences, Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, pr. Nauki 5, 142290 Pushchino, Russia; (A.T.); (E.K.); (L.T.)
| | - Ludmila Trilisenko
- Federal Scientific Center, Pushchino Research Center for Biology of the Russian Academy of Sciences, Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, pr. Nauki 5, 142290 Pushchino, Russia; (A.T.); (E.K.); (L.T.)
| | - Ivan V. Kulakovskiy
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Tatiana Kulakovskaya
- Federal Scientific Center, Pushchino Research Center for Biology of the Russian Academy of Sciences, Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, pr. Nauki 5, 142290 Pushchino, Russia; (A.T.); (E.K.); (L.T.)
| | - Alexey Fedorov
- Federal Scientific Center for Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Russian Academy of Sciences, Leninsky prosp. 33-2, 119071 Moscow, Russia; (A.F.); (M.E.)
| | - Mikhail Eldarov
- Federal Scientific Center for Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Russian Academy of Sciences, Leninsky prosp. 33-2, 119071 Moscow, Russia; (A.F.); (M.E.)
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11
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Guo SH, Yu L, Liu YM, Wang FF, Chen YC, Wang Y, Qiu BL, Sang W. Digital gene expression profiling in larvae of Tribolium castaneum at different periods post UV-B exposure. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 174:514-523. [PMID: 30861439 DOI: 10.1016/j.ecoenv.2019.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/18/2019] [Accepted: 03/03/2019] [Indexed: 06/09/2023]
Abstract
UV-B radiation is an important environmental factor. Exposure to excess UV-B radiation can cause serious effects on the development, survival, and reproduction of different organisms. Plants and animals have developed many different strategies to cope with UV-B-induced damage, but the physiological response of insects to UV-B remains unclear. In the present study, the red flour beetle Tribolium castaneum (Herbst) was used to assess the stress response of UV-B. The underlying molecular mechanisms were explored using RNA sequencing. We investigated the transcriptomic profile of T. castaneum larvae at 4 and 24 h after treatment with UV-B radiation via digital gene expression analysis. The 310 and 996 differentially expressed genes were detected at 4 and 24 h, respectively. Then the biological functions and associated metabolic processes of these genes were determined by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis. The reliability of the data was verified using qRT-PCR. The results indicated that several differentially expressed genes are involved in antioxidation, DNA repair, protein folding, carbon flux diversion, and the extracellular matrix to protect against UV-B-induced damage. This study will increase our understanding of the molecular mechanism underlying insect response to UV-B radiation.
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Affiliation(s)
- Shu-Hao Guo
- Key Laboratory of Bio-Pesticide Creation and Application, South China Agricultural University, Guangzhou 510640, China
| | - Lin Yu
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
| | - Yan-Mei Liu
- Key Laboratory of Bio-Pesticide Creation and Application, South China Agricultural University, Guangzhou 510640, China
| | - Fei-Feng Wang
- Key Laboratory of Bio-Pesticide Creation and Application, South China Agricultural University, Guangzhou 510640, China
| | - Yu-Chen Chen
- Key Laboratory of Bio-Pesticide Creation and Application, South China Agricultural University, Guangzhou 510640, China
| | - Ye Wang
- Key Laboratory of Bio-Pesticide Creation and Application, South China Agricultural University, Guangzhou 510640, China
| | - Bao-Li Qiu
- Key Laboratory of Bio-Pesticide Creation and Application, South China Agricultural University, Guangzhou 510640, China
| | - Wen Sang
- Key Laboratory of Bio-Pesticide Creation and Application, South China Agricultural University, Guangzhou 510640, China.
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12
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Trilisenko L, Zvonarev A, Valiakhmetov A, Penin AA, Eliseeva IA, Ostroumov V, Kulakovskiy IV, Kulakovskaya T. The Reduced Level of Inorganic Polyphosphate Mobilizes Antioxidant and Manganese-Resistance Systems in Saccharomyces cerevisiae. Cells 2019; 8:cells8050461. [PMID: 31096715 PMCID: PMC6562782 DOI: 10.3390/cells8050461] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/13/2019] [Accepted: 05/15/2019] [Indexed: 12/23/2022] Open
Abstract
Inorganic polyphosphate (polyP) is crucial for adaptive reactions and stress response in microorganisms. A convenient model to study the role of polyP in yeast is the Saccharomyces cerevisiae strain CRN/PPN1 that overexpresses polyphosphatase Ppn1 with stably decreased polyphosphate level. In this study, we combined the whole-transcriptome sequencing, fluorescence microscopy, and polyP quantification to characterize the CRN/PPN1 response to manganese and oxidative stresses. CRN/PPN1 exhibits enhanced resistance to manganese and peroxide due to its pre-adaptive state observed in normal conditions. The pre-adaptive state is characterized by up-regulated genes involved in response to an external stimulus, plasma membrane organization, and oxidation/reduction. The transcriptome-wide data allowed the identification of particular genes crucial for overcoming the manganese excess. The key gene responsible for manganese resistance is PHO84 encoding a low-affinity manganese transporter: Strong PHO84 down-regulation in CRN/PPN1 increases manganese resistance by reduced manganese uptake. On the contrary, PHM7, the top up-regulated gene in CRN/PPN1, is also strongly up-regulated in the manganese-adapted parent strain. Phm7 is an unannotated protein, but manganese adaptation is significantly impaired in Δphm7, thus suggesting its essential function in manganese or phosphate transport.
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Affiliation(s)
- Ludmila Trilisenko
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Center for Biological Research of the Russian Academy of Sciences, pr. Nauki 5, Pushchino 142290, Russia.
| | - Anton Zvonarev
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Center for Biological Research of the Russian Academy of Sciences, pr. Nauki 5, Pushchino 142290, Russia.
| | - Airat Valiakhmetov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Center for Biological Research of the Russian Academy of Sciences, pr. Nauki 5, Pushchino 142290, Russia.
| | - Alexey A Penin
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny per. 19 bld .1, Moscow 127051, Russia.
| | - Irina A Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Pushchino 142290, Russia.
| | - Vladimir Ostroumov
- Institute of Physicochemical and Biological Problems of Soil Science, FRC Pushchino Center for Biological Research of the Russian Academy of Sciences, pr. Nauki 2, Pushchino 142290, Russia.
| | - Ivan V Kulakovskiy
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow GSP-1 119991, Russia.
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow GSP-1 119991, Russia.
- Institute of Mathematical Problems of Biology RAS-the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Vitkevicha 1, Pushchino 142290, Russia.
| | - Tatiana Kulakovskaya
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Center for Biological Research of the Russian Academy of Sciences, pr. Nauki 5, Pushchino 142290, Russia.
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13
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Ruas FAD, Barboza NR, Castro-Borges W, Guerra-Sá R. Manganese alters expression of proteins involved in the oxidative stress of Meyerozyma guilliermondii. J Proteomics 2019; 196:173-188. [DOI: 10.1016/j.jprot.2018.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 10/25/2018] [Accepted: 11/01/2018] [Indexed: 01/12/2023]
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14
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Kulakovskaya T. Inorganic polyphosphates and heavy metal resistance in microorganisms. World J Microbiol Biotechnol 2018; 34:139. [DOI: 10.1007/s11274-018-2523-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/23/2018] [Indexed: 12/11/2022]
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15
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Xu Y, Yu Z, Zhang D, Huang J, Wu C, Yang G, Yan K, Zhang S, Zheng C. CYSTM, a Novel Non-Secreted Cysteine-Rich Peptide Family, Involved in Environmental Stresses in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2018; 59:423-438. [PMID: 29272523 DOI: 10.1093/pcp/pcx202] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/12/2017] [Indexed: 05/24/2023]
Abstract
The cysteine-rich transmembrane module (CYSTM) is comprised of a small molecular protein family that is found in a diversity of tail-anchored membrane proteins across eukaryotes. This protein family belongs to novel uncharacteristic non-secreted cysteine-rich peptides (NCRPs) according to their conserved domain and small molecular weight, and genome-wide analysis of this family has not yet been undertaken in plants. In this study, 13 CYSTM genes were identified and located on five chromosomes with diverse densities in Arabidopsis thaliana. The CYSTM proteins could be classified into four subgroups based on domain similarity and phylogenetic topology. Encouragingly, the CYSTM members were expressed in at least one of the tested tissues and dramatically responded to various abiotic stresses, indicating that they played vital roles in diverse developmental processes, especially in stress responses. CYSTM peptides displayed a complex subcellular localization, and most were detected at the plasma membrane and cytoplasm. Of particular interest, CYSTM members could dimerize with themselves or others through the C-terminal domain, and we built a protein-protein interaction map between CYSTM members in Arabidopsis for the first time. In addition, an analysis of CYSTM3 overexpression lines revealed negative regulation for this gene in salt stress responses. We demonstrate that the CYSTM family, as a novel and ubiquitous non-secreted cysteine-rich peptide family, plays a vital role in resistance to abiotic stress. Collectively, our comprehensive analysis of CYSTM members will facilitate future functional studies of the small peptides.
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Affiliation(s)
- Yang Xu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Zipeng Yu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Di Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Jinguang Huang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Changai Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Guodong Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Kang Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Shizhong Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Chengchao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
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