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Paira S, Chakraborty A, Das B. The Sequential Recruitments of Rab-GTPase Ypt1p and the NNS Complex onto pre- HAC1 mRNA Promote Its Nuclear Degradation in Baker's Yeast. Mol Cell Biol 2023; 43:371-400. [PMID: 37533322 PMCID: PMC10448977 DOI: 10.1080/10985549.2023.2227016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 08/04/2023] Open
Abstract
Induction of unfolded protein response involves activation of transcription factor Hac1p that is encoded by HAC1 pre-mRNA harboring an intron and a bipartite element (BE), which is subjected to nuclear mRNA decay by the nuclear exosome/Cbc1p-Tif4631p-dependent Exosome Targeting (CTEXT) complex. Using a combination of genetic and biochemical approaches, we demonstrate that a Rab-GTPase Ypt1p controls unfolded protein response signaling dynamics. This regulation relies on the nuclear localization of a small fraction of the cellular Ypt1p pool in the absence of endoplasmic reticulum (ER)-stress causing a strong association of the nuclear Ypt1p with pre-HAC1 mRNA that eventually promotes sequential recruitments of NNS, CTEXT, and the nuclear exosome onto this pre-mRNA. Recruitment of these decay factors onto pre-HAC1 mRNA is accompanied by its rapid nuclear decay that produces a precursor RNA pool lacking functional BE thereby causing its inefficient targeting to Ire1p foci leading to their diminished splicing and translation. ER stress triggers rapid relocalization of the nuclear pool of Ypt1p to the cytoplasm leading to its dissociation from pre-HAC1 mRNA thereby causing decreased recruitment of these decay factors to precursor HAC1 RNA leading to its diminished degradation. Reduced decay results in an increased abundance of pre-HAC1 mRNA with intact functional BE leading to its enhanced recruitment to Ire1p foci.
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Affiliation(s)
- Sunirmal Paira
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Anish Chakraborty
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Biswadip Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
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De Groeve M, Laukens B, Schotte P. Optimizing expression of Nanobody® molecules in Pichia pastoris through co-expression of auxiliary proteins under methanol and methanol-free conditions. Microb Cell Fact 2023; 22:135. [PMID: 37481525 PMCID: PMC10362571 DOI: 10.1186/s12934-023-02132-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/24/2023] [Indexed: 07/24/2023] Open
Abstract
BACKGROUND Ablynx NV, a subsidiary of Sanofi, has a long-standing focus on the development of Nanobody® molecules as biopharmaceuticals (Nanobody® is a registered trademark of Ablynx NV). Nanobody molecules are single variable domains, and they have been met with great success part due to their favorable expression properties in several microbial systems. Nevertheless, the search for the host of the future is an ongoing and challenging process. Komagataella phaffi (Pichia pastoris) is one of the most suitable organisms to produce Nanobody molecules. In addition, genetic engineering of Pichia is easy and an effective approach to improve titers. RESULTS Here we report that P. pastoris engineered to co-express genes encoding four auxiliary proteins (HAC1, KAR2, PDI and RPP0), leads to a marked improvement in the expression of Nanobody molecules using the AOX1 methanol induction system. Titer improvement is mainly attributed to HAC1, and its beneficial effect was also observed in a methanol-free expression system. CONCLUSION Our findings are based on over a thousand fed-batch fermentations and offer a valuable guide to produce Nanobody molecules in P. pastoris. The presented differences in expressability between types of Nanobody molecules will be helpful for researchers to select both the type of Nanobody molecule and Pichia strain and may stimulate further the development of a more ecological methanol-free expression platform.
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Affiliation(s)
- Manu De Groeve
- Centre of Excellence in Host creation and Upstream processing at Sanofi R&D, Ghent, Belgium
| | - Bram Laukens
- Centre of Excellence in Host creation and Upstream processing at Sanofi R&D, Ghent, Belgium
| | - Peter Schotte
- Centre of Excellence in Host creation and Upstream processing at Sanofi R&D, Ghent, Belgium.
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Faye A, Barnaud A, Kane NA, Cubry P, Mariac C, Burgarella C, Rhoné B, Faye A, Olodo KF, Cisse A, Couderc M, Dequincey A, Zekraouï L, Moussa D, Tidjani M, Vigouroux Y, Berthouly-Salazar C. Genomic footprints of selection in early-and late-flowering pearl millet landraces. Front Plant Sci 2022; 13:880631. [PMID: 36311100 PMCID: PMC9597309 DOI: 10.3389/fpls.2022.880631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 08/11/2022] [Indexed: 06/16/2023]
Abstract
Pearl millet is among the top three-cereal production in one of the most climate vulnerable regions, sub-Saharan Africa. Its Sahelian origin makes it adapted to grow in poor sandy soils under low soil water regimes. Pearl millet is thus considered today as one of the most interesting crops to face the global warming. Flowering time, a trait highly correlated with latitude, is one of the key traits that could be modulated to face future global changes. West African pearl millet landraces, can be grouped into early- (EF) and late-flowering (LF) varieties, each flowering group playing a specific role in the functioning and resilience of Sahelian smallholders. The aim of this study was thus to detect genes linked to flowering but also linked to relevant traits within each flowering group. We thus investigated genomic and phenotypic diversity in 109 pearl millet landrace accessions, i.e., 66 early-flowering and 43 late-flowering, grown in the groundnut basin, the first area of rainfed agriculture in Senegal dominated by dry cereals (millet, maize, and sorghum) and legumes (groundnuts, cowpeas). We were able to confirm the role of PhyC gene in pearl millet flowering and identify several other genes that appear to be as much as important, such as FSR12 and HAC1. HAC1 and two other genes appear to be part of QTLs previously identified and deserve further investigation. At the same time, we were able to highlight a several genes and variants that could contribute to the improvement of pearl millet yield, especially since their impact was demonstrated across flowering cycles.
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Affiliation(s)
- Adama Faye
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
| | - Adeline Barnaud
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
| | - Ndjido Ardo Kane
- LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
- CERAAS, Institut Sénégalais de Recherches Agricoles, Thiès, Senegal
| | - Philippe Cubry
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Cédric Mariac
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Concetta Burgarella
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Bénédicte Rhoné
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Aliou Faye
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
| | - Katina Floride Olodo
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
- CERAAS, Institut Sénégalais de Recherches Agricoles, Thiès, Senegal
| | - Aby Cisse
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
- CERAAS, Institut Sénégalais de Recherches Agricoles, Thiès, Senegal
| | - Marie Couderc
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Anaïs Dequincey
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Leïla Zekraouï
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Djibo Moussa
- DIADE, Institut de Recherche pour le Développement (IRD), Niamey, Niger
| | - Moussa Tidjani
- DIADE, Institut de Recherche pour le Développement (IRD), Niamey, Niger
| | - Yves Vigouroux
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Cécile Berthouly-Salazar
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LNRPV, Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
- Laboratoire Mixte International LAPSE, Campus de Bel Air, route des Hydrocarbures, Dakar, Senegal
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Abstract
Protein-folding homeostasis in the endoplasmic reticulum (ER) is maintained by the unfolded protein response (UPR). UPR in Saccharomyces cerevisiae is regulated by a bZIP transcription factor, Hac1p. Under non-stress condition, HAC1 mRNA is translationally repressed. When un- or mis-folded proteins accumulate in the ER, HAC1 mRNA undergoes non-conventional mRNA splicing. The spliced HAC1 mRNA is translationally active and produces functional Hac1p, which initiates a transcriptional response that restores ER protein-folding homeostasis. Thus, the activation of yeast UPR is tightly regulated by HAC1 mRNA splicing. Here, we describe two methods that are used to monitor the splicing and translational status of HAC1 mRNA in budding yeast.
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Affiliation(s)
- Weihan Li
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
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5
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Abstract
HAC1 mRNA remains translationally repressed in the cytoplasm of the budding yeast Saccharomyces cerevisiae. Under conditions of cellular stress, a dual kinase RNase IRE1 (Inositol Requiring Enzyme-1) cleaves out an intervening sequence from the HAC1 mRNA. Cleaved mRNAs are then ligated by tRNA ligase, thus generating a spliced mRNA that translates an active transcription factor. This unconventional splicing of HAC1 mRNA in the cytoplasm is a molecular marker for various cellular stresses including oxidative stress and endoplasmic reticulum (ER) stress. This article describes a PCR-based protocol to detect the HAC1 mRNA splicing.
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Affiliation(s)
- Jagadeesh Kumar Uppala
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Madhusudan Dey
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
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Paira S, Das B. Determination of the Stability and Intracellular (Intra-Nuclear) Targeting and Recruitment of Pre- HAC1 mRNA in the Saccharomyces cerevisiae During the Activation of UPR. Methods Mol Biol 2022; 2378:121-140. [PMID: 34985698 DOI: 10.1007/978-1-0716-1732-8_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nuclear degradation of pre-HAC1 mRNA and its subsequent targeting plays a vital role in the activation as well as attenuation of Unfolded Protein Response (UPR) in Saccharomyces cerevisiae. Accurate measurement of the degradation of precursor HAC1 mRNA therefore appears vital to determine the phase of activation or attenuation of this important intracellular signaling pathway. Typically, pre-HAC1 mRNA degradation is measured by the transcription shut-off experiment in which RNA Polymerase II transcription is inhibited by a potent transcription inhibitor to prevent the de novo synthesis of all Polymerase II transcripts followed by the measurement of the steady-state levels of a specific (e.g., pre-HAC1) mRNA at different times after the inhibition of the transcription. The rate of the decay is subsequently determined from the slope of the decay curve and is expressed as half-life (T1/2). Estimation of the half-life values and comparison of this parameter determined under different physiological cues (such as in absence or presence of redox/ER/heat stress) gives a good estimate of the stability of the mRNA under these conditions and helps gaining an insight into the mechanism of the biological process such as activation or attenuation of UPR.Intra-nuclear targeting of the pre-HAC1 mRNA from the site of its transcription to the site of non-canonical splicing, where the kinase-endonuclease Ire1p clusters into the oligomeric structures constitutes an important aspect of the activation of Unfolded Protein Response pathway. These oligomeric structures are detectable as the Ire1p foci/spot in distinct locations across the nuclear-ER membrane under confocal micrograph using immunofluorescence procedure. Extent of the targeting of the pre-HAC1 mRNA is measurable in a quantified manner by co-expressing fluorescent-labeled pre-HAC1 mRNA and Ire1p protein followed by estimating their co-localization using FACS (Fluorescence-Activated Cell Sorter) analysis. Here, we describe detailed protocol of both determination of intra-nuclear decay rate and targeting-frequency of pre-HAC1 mRNA that were optimized in our laboratory.
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Affiliation(s)
- Sunirmal Paira
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Biswadip Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India.
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7
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Tehfe A, Roseshter T, Wei Y, Xia X. Does Saccharomyces cerevisiae Require Specific Post-Translational Silencing against Leaky Translation of Hac1up? Microorganisms 2021; 9:620. [PMID: 33802931 DOI: 10.3390/microorganisms9030620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/13/2021] [Accepted: 03/16/2021] [Indexed: 11/24/2022] Open
Abstract
HAC1 encodes a key transcription factor that transmits the unfolded protein response (UPR) from the endoplasmic reticulum (ER) to the nucleus and regulates downstream UPR genes in Saccharomyces cerevisiae. In response to the accumulation of unfolded proteins in the ER, Ire1p oligomers splice HAC1 pre-mRNA (HAC1u) via a non-conventional process and allow the spliced HAC1 (HAC1i) to be translated efficiently. However, leaky splicing and translation of HAC1u may occur in non-UPR cells to induce undesirable UPR. To control accidental UPR activation, multiple fail-safe mechanisms have been proposed to prevent leaky HAC1 splicing and translation and to facilitate rapid degradation of translated Hac1up and Hac1ip. Among proposed regulatory mechanisms is a degron sequence encoded at the 5′ end of the HAC1 intron that silences Hac1up expression. To investigate the necessity of an intron-encoded degron sequence that specifically targets Hac1up for degradation, we employed publicly available transcriptomic data to quantify leaky HAC1 splicing and translation in UPR-induced and non-UPR cells. As expected, we found that HAC1u is only efficiently spliced into HAC1i and efficiently translated into Hac1ip in UPR-induced cells. However, our analysis of ribosome profiling data confirmed frequent occurrence of leaky translation of HAC1u regardless of UPR induction, demonstrating the inability of translation fail-safe to completely inhibit Hac1up production. Additionally, among 32 yeast HAC1 surveyed, the degron sequence is highly conserved by Saccharomyces yeast but is poorly conserved by all other yeast species. Nevertheless, the degron sequence is the most conserved HAC1 intron segment in yeasts. These results suggest that the degron sequence may indeed play an important role in mitigating the accumulation of Hac1up to prevent accidental UPR activation in the Saccharomyces yeast.
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8
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Tsvetkov P, Eisen TJ, Heinrich SU, Brune Z, Hallacli E, Newby GA, Kayatekin C, Pincus D, Lindquist S. Persistent Activation of mRNA Translation by Transient Hsp90 Inhibition. Cell Rep 2020; 32:108001. [PMID: 32783929 PMCID: PMC10088179 DOI: 10.1016/j.celrep.2020.108001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 10/23/2022] Open
Abstract
The heat shock protein 90 (Hsp90) chaperone functions as a protein-folding buffer and plays a role promoting the evolution of new heritable traits. To better understand how Hsp90 can affect mRNA translation, we screen more than 1,600 factors involved in mRNA regulation for physical interactions with Hsp90 in human cells. The mRNA binding protein CPEB2 strongly binds Hsp90 via its prion domain. In a yeast model, transient inhibition of Hsp90 results in persistent activation of a CPEB translation reporter even in the absence of exogenous CPEB that persists for 30 generations after the inhibitor is removed. Ribosomal profiling reveals that some endogenous yeast mRNAs, including HAC1, show a persistent change in translation efficiency following transient Hsp90 inhibition. Thus, transient loss of Hsp90 function can promote a nongenetic inheritance of a translational state affecting specific mRNAs, introducing a mechanism by which Hsp90 can promote phenotypic variation.
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Affiliation(s)
- Peter Tsvetkov
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Timothy J Eisen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Sven U Heinrich
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Zarina Brune
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Erinc Hallacli
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Greg A Newby
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Can Kayatekin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - David Pincus
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
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9
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Qu Z, Zhang L, Zhu S, Yuan W, Hang J, Yin D, Tang X, Zheng J, Wang Z, Sun J. Overexpression of the transcription factor HAC1 improves nerolidol production in engineered yeast. Enzyme Microb Technol 2020; 134:109485. [PMID: 32044032 DOI: 10.1016/j.enzmictec.2019.109485] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/28/2019] [Accepted: 11/30/2019] [Indexed: 11/24/2022]
Abstract
Increasing the metabolic flux of the mevalonate pathway, reducing the metabolic flux of competing pathway and utilizing the diauxie-inducible system constructed by GAL promoters are strategies commonly used in yeast metabolic engineering for the production of terpenoids. Using these strategies, we constructed a series of yeast strains with a strengthened mevalonate pathway and finally produced 336.5 mg/L nerolidol in a shake flask. The spliced HAC1 mRNA assay indicated that the unfolded protein response (UPR) occurred in the strains that we constructed. UPR strains exhibited the low transcriptional activities of GAL1 promoter. HAC1-overexpressing strain exhibited dramatically enhanced transcriptional activity of GAL1 promoter at 72 h of fermentation in flasks. HAC1 overexpression also increased the nerolidol titer by 47.7 %, reaching 497.0 mg/L and increased cell vitality. RNA-seq showed that the genes whose transcription responded to HAC1-overexpression were involved in the regulation of monocarboxylic acid metabolic processes and cellular amino acid biosynthetic process, indicating that the metabolic regulation may be part of the reason of the improved nerolidol synthesis. Our findings enrich the knowledge of the relationship between the construction of sesquiterpene-producing cell factories and UPR regulation. This study provides an effective strategy for sesquiterpene production in yeast.
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Hinckley WE, Keymanesh K, Cordova JA, Brusslan JA. The HAC1 histone acetyltransferase promotes leaf senescence and regulates the expression of ERF022. Plant Direct 2019; 3:e00159. [PMID: 31468026 PMCID: PMC6710649 DOI: 10.1002/pld3.159] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/12/2019] [Accepted: 07/23/2019] [Indexed: 05/08/2023]
Abstract
Nutrient remobilization during leaf senescence nourishes the growing plant. Understanding the regulation of this process is essential for reducing our dependence on nitrogen fertilizers and increasing agricultural sustainability. Our laboratory is interested in chromatin changes that accompany the transition to leaf senescence. Previously, darker green leaves were reported for Arabidopsis thaliana hac1 mutants, defective in a gene encoding a histone acetyltransferase in the CREB-binding protein family. Here, we show that two Arabidopsis hac1 alleles display delayed age-related developmental senescence, but have normal dark-induced senescence. Using a combination of ChIP-seq for H3K9ac and RNA-seq for gene expression, we identified 43 potential HAC1 targets during age-related developmental senescence. Genetic analysis demonstrated that one of these potential targets, ERF022, is a positive regulator of leaf senescence. ERF022 is regulated additively by HAC1 and MED25, suggesting MED25 may recruit HAC1 to the ERF022 promoter to increase its expression in older leaves.
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Affiliation(s)
- Will E. Hinckley
- Department of Biological SciencesCalifornia State UniversityLong BeachCAUSA
| | | | | | - Judy A. Brusslan
- Department of Biological SciencesCalifornia State UniversityLong BeachCAUSA
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11
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Xia X. Translation Control of HAC1 by Regulation of Splicing in Saccharomyces cerevisiae. Int J Mol Sci 2019; 20:ijms20122860. [PMID: 31212749 PMCID: PMC6627864 DOI: 10.3390/ijms20122860] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/30/2019] [Accepted: 06/10/2019] [Indexed: 12/19/2022] Open
Abstract
Hac1p is a key transcription factor regulating the unfolded protein response (UPR) induced by abnormal accumulation of unfolded/misfolded proteins in the endoplasmic reticulum (ER) in Saccharomyces cerevisiae. The accumulation of unfolded/misfolded proteins is sensed by protein Ire1p, which then undergoes trans-autophosphorylation and oligomerization into discrete foci on the ER membrane. HAC1 pre-mRNA, which is exported to the cytoplasm but is blocked from translation by its intron sequence looping back to its 5’UTR to form base-pair interaction, is transported to the Ire1p foci to be spliced, guided by a cis-acting bipartite element at its 3’UTR (3’BE). Spliced HAC1 mRNA can be efficiently translated. The resulting Hac1p enters the nucleus and activates, together with coactivators, a large number of genes encoding proteins such as protein chaperones to restore and maintain ER homeostasis and secretary protein quality control. This review details the translation regulation of Hac1p production, mediated by the nonconventional splicing, in the broad context of translation control and summarizes the evolution and diversification of the UPR signaling pathway among fungal, metazoan and plant lineages.
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Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, Marie-Curie Private, Ottawa, ON K1N 9A7, Canada.
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12
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Li L, Huang C, Zhao F, Deng T, Lin Y, Zheng S, Liang S, Han S. Improved production and characterization of Volvariella volvacea Endoglucanase 1 expressed in Pichia pastoris. Protein Expr Purif 2018; 152:107-113. [PMID: 29551715 DOI: 10.1016/j.pep.2018.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/11/2018] [Accepted: 03/11/2018] [Indexed: 01/17/2023]
Abstract
Endoglucanase 1 (EG1) isolated from the straw mushroom has great potential in the textile and paper industries. Improving EG1 expression level will add to its value for industrial applications. In this study, we employed two combined strategies to enhance the expression quantity of EG1, which are increase the copy number of EG1 and enhance the folding and secretion efficiency of EG1 in the endoplasmic reticulum by overexpress HAC1. Multiple plasmids, which contains four copies of EG1, were constructed by isocaudamers, resulted a recombinant strain with EG1 activity up to 39.6 U/mL, 262% higher than that measured in the strain containing only a single copy. A significant increase in activity (151%) was found when eight copies of EG1 was introduced into a different host, compared with a host harboring four copies. Further overexpression of the HAC1 transcription factor in the host harboring eight EG1 copies led to activity of 91.9 U/mL, which is 619% higher than that measured in the original strain. Finally, EG1 activity of 650.1 U/mL was achieved in a 3-L scaled-up fed-batch fermenter and the protein yield was 4.05 g/L. The characteristics of recombinant EG1 were also investigated, the optimal values for enzyme activity were 60 °C and pH 5.0, which yielded a catalytic efficiency of 312.9 mL mg-1min-1 using carboxymethyl cellulose(CMC) as the substrate.
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Affiliation(s)
- Ling Li
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Cong Huang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Fengguang Zhao
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Tao Deng
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Ying Lin
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Suiping Zheng
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuli Liang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuangyan Han
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China.
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Poothong J, Sopha P, Kaufman RJ, Tirasophon W. IRE1α nucleotide sequence cleavage specificity in the unfolded protein response. FEBS Lett 2017; 591:406-414. [PMID: 28027394 DOI: 10.1002/1873-3468.12546] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/21/2016] [Accepted: 12/21/2016] [Indexed: 11/05/2022]
Abstract
Inositol-requiring enzyme 1 (IRE1) is a conserved sensor of the unfolded protein response that has protein kinase and endoribonuclease (RNase) enzymatic activities and thereby initiates HAC1/XBP1 splicing. Previous studies demonstrated that human IRE1α (hIRE1α) does not cleave Saccharomyces cerevisiae HAC1 mRNA. Using an in vitro cleavage assay, we show that adenine to cytosine nucleotide substitution at the +1 position in the 3' splice site of HAC1 RNA is required for specific cleavage by hIRE1α. A similar restricted nucleotide specificity in the RNA substrate was observed for XBP1 splicing in vivo. Together these findings underscore the essential role of cytosine nucleotide at +1 in the 3' splice site for determining cleavage specificity of hIRE1α.
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Affiliation(s)
- Juthakorn Poothong
- The Institute of Molecular Biosciences, Mahidol University, Salaya, Thailand.,Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Pattarawut Sopha
- The Institute of Molecular Biosciences, Mahidol University, Salaya, Thailand
| | - Randal J Kaufman
- Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Witoon Tirasophon
- The Institute of Molecular Biosciences, Mahidol University, Salaya, Thailand
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14
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Sathe L, Bolinger C, Mannan MAU, Dever TE, Dey M. Evidence That Base-pairing Interaction between Intron and mRNA Leader Sequences Inhibits Initiation of HAC1 mRNA Translation in Yeast. J Biol Chem 2015; 290:21821-32. [PMID: 26175153 DOI: 10.1074/jbc.m115.649335] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Indexed: 01/01/2023] Open
Abstract
The Hac1 transcription factor in yeast up-regulates a collection of genes that control protein homeostasis. Base-pairing interactions between sequences in the intron and the 5'-untranslated region (5' UTR) of the HAC1 mRNA represses Hac1 protein production under basal conditions, whereas cytoplasmic splicing of the intron by the Ire1 kinase-endonuclease, activated under endoplasmic reticulum stress conditions, relieves the inhibition and enables Hac1 synthesis. Using a random mutational screen as well as site-directed mutagenesis, we identify point mutations within the 5' UTR-intron interaction site that derepress translation of the unspliced HAC1 mRNA. We also show that insertion of an in-frame AUG start codon upstream of the interaction site releases the translational block, demonstrating that an elongating ribosome can disrupt the interaction. Moreover, overexpression of translation initiation factor eIF4A, a helicase, enhances production of Hac1 from an mRNA containing an upstream AUG start codon at the beginning of the base-paired region. These results suggest that the major block of translation occurs at the initiation stage. Supporting this interpretation, the point mutations that enhanced Hac1 production resulted in an increased percentage of the HAC1 mRNA associating with polysomes versus free ribosomal subunits. Thus, our results provide evidence that the 5' UTR-intron interaction represses translation initiation on the unspliced HAC1 mRNA.
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Affiliation(s)
- Leena Sathe
- From the Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211 and
| | - Cheryl Bolinger
- Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892
| | - M Amin-ul Mannan
- From the Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211 and
| | - Thomas E Dever
- Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, Maryland 20892
| | - Madhusudan Dey
- From the Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211 and
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15
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Lin XQ, Liang SL, Han SY, Zheng SP, Ye YR, Lin Y. Quantitative iTRAQ LC-MS/MS proteomics reveals the cellular response to heterologous protein overexpression and the regulation of HAC1 in Pichia pastoris. J Proteomics 2013; 91:58-72. [PMID: 23851310 DOI: 10.1016/j.jprot.2013.06.031] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 06/06/2013] [Accepted: 06/28/2013] [Indexed: 12/23/2022]
Abstract
UNLABELLED The methylotrophic yeast Pichia pastoris is an attractive platform for a plethora of recombinant proteins. There is growing evidence that host cells producing recombinant proteins are exposed to a variety of cellular stresses resulting in the induction of the unfolded protein response (UPR) pathway. At present, there is only limited information about the cellular reactions of the host cells at the level of the proteome, especially with regard to recombinant protein secretion. Here we monitored xylanase A secretion from Bacillus halodurans C-125 (xynA) in P. pastoris, using strains containing different copy numbers of the gene encoding xylanase A and co-overexpressing the gene encoding the UPR-regulating transcription factor HAC1 by applying a quantitative proteomics approach (iTRAQ-LC-MS/MS). Many important cellular processes, including carbon metabolism, stress response and protein folding are affected in the investigated conditions. Notably, the analysis revealed that strong over-expression of xynA can efficiently improve protein production but simultaneously cause an unfolded protein burden with a subsequent induction of the UPR. This limits the further improvement of protein production levels. Remarkably, constitutive expression of the gene encoding HAC1 lessens the unfolded protein burden by attenuating protein synthesis and increasing ER protein folding efficiency which is beneficial for protein secretion. BIOLOGICAL SIGNIFICANCE Pichia pastoris expression systems have been successfully used for over 20years in basic research and in the biotechnology industry for the production and secretion of a wide range of recombinant proteins. In particular, secretion of recombinant proteins is still one of the main reasons for using P. pastoris. It has become obvious that many protein products can lead to severe stress on the host cell when being over-expressed, thus limiting the potential yield. Detailed understanding of the physiological responses to such stresses gives rise to engineering of host cells that can better cope with the stress factors. Therefore, the regulatory mechanism of heterologous protein secretion by quantitative mass-spectrometry (MS) proteomics is a growing field and an important endeavor in improving protein annotation. Many important cellular processes, including carbon and amino acid metabolism, stress response and protein folding are affected in the over-expression strains. This data represent a first step towards a systems wide approach to assess the response with recombinant protein induced stress in P. pastoris.
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Affiliation(s)
- Xiao-qiong Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, PR China
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