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Kuwayama N, Powers EN, Siketanc M, Sousa CI, Reynaud K, Jovanovic M, Hondele M, Ingolia NT, Brar GA. Analyses of translation factors Dbp1 and Ded1 reveal the cellular response to heat stress to be separable from stress granule formation. Cell Rep 2024; 43:115059. [PMID: 39675003 DOI: 10.1016/j.celrep.2024.115059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 11/05/2024] [Accepted: 11/21/2024] [Indexed: 12/17/2024] Open
Abstract
Ded1 and Dbp1 are paralogous conserved DEAD-box ATPases involved in translation initiation in yeast. In long-term starvation states, Dbp1 expression increases and Ded1 decreases, whereas in cycling mitotic cells, Dbp1 is absent. Inserting DBP1 in place of DED1 cannot replace Ded1 function in supporting mitotic translation, partly due to inefficient translation of the DBP1 coding region. Global translation measurements, activity of mRNA-tethered proteins, and growth assays show that-even at matched protein levels-Ded1 is better than Dbp1 at activating translation, especially for mRNAs with structured 5' leaders. Heat-stressed cells normally downregulate translation of structured housekeeping transcripts and halt growth, but neither occurs in Dbp1-expressing cells. This failure to halt growth in response to heat is not based on deficient stress granule formation or failure to reduce bulk translation. Rather, it depends on heat-triggered loss of Ded1 function mediated by an 11-amino-acid interval within its intrinsically disordered C terminus.
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Affiliation(s)
- Naohiro Kuwayama
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Emily Nicole Powers
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Matej Siketanc
- Biozentrum, Center for Molecular Life Sciences, University of Basel, 4056 Basel, Switzerland
| | - Camila Ines Sousa
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kendra Reynaud
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Maria Hondele
- Biozentrum, Center for Molecular Life Sciences, University of Basel, 4056 Basel, Switzerland
| | - Nicholas Thomas Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gloria Ann Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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2
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Kang Y, Xiao K, Wang D, Peng Z, Luo R, Liu X, Hu L, Hu G. Metabolic Engineering of Saccharomyces cerevisiae for High-Level Production of l-Pipecolic Acid from Glucose. ACS Synth Biol 2024; 13:3378-3388. [PMID: 39267441 DOI: 10.1021/acssynbio.4c00464] [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] [Indexed: 09/17/2024]
Abstract
l-Pipecolic acid (L-PA), an essential chiral cyclic nonprotein amino acid, is gaining prominence in the food and pharmaceutical sectors due to its wide-ranging biological and pharmacological properties. Historically, L-PA has been synthesized chemically for commercial purposes. This study introduces a novel and efficient microbial production method for L-PA using engineered strain Saccharomyces cerevisiae BY4743. Initially, an optimized biosynthetic pathway was constructed within S. cerevisiae, converting glucose to L-PA with a yield of 0.60 g/L in a 250 mL shake flask in vivo. Subsequently, a multifaceted engineering strategy was implemented to enhance L-PA production: substrate-enzyme affinity modification, global transcription machinery engineering modification, and Kozak sequence optimization for enhanced L-PA production. Approaches above led to an impressive 8.6-fold increase in L-PA yield, reaching 5.47 g/L in shake flask cultures. Further scaling up in a 5 L fed-batch fermenter achieved a remarkable L-PA concentration of 74.54 g/L. This research offers innovative insights into the industrial-scale production of L-PA.
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Affiliation(s)
- Yaqi Kang
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, PR China
| | - Kaixing Xiao
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, PR China
| | - Dan Wang
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, PR China
| | - Zhiyao Peng
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, PR China
| | - Ruoshi Luo
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, PR China
| | - Xuemei Liu
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, PR China
| | - Lin Hu
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, PR China
| | - Ge Hu
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, PR China
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3
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Mavridou D, Psatha K, Aivaliotis M. Integrative Analysis of Multi-Omics Data to Identify Deregulated Molecular Pathways and Druggable Targets in Chronic Lymphocytic Leukemia. J Pers Med 2024; 14:831. [PMID: 39202022 PMCID: PMC11355716 DOI: 10.3390/jpm14080831] [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: 06/25/2024] [Revised: 07/25/2024] [Accepted: 07/27/2024] [Indexed: 09/03/2024] Open
Abstract
Chronic Lymphocytic Leukemia (CLL) is the most common B-cell malignancy in the Western world, characterized by frequent relapses despite temporary remissions. Our study integrated publicly available proteomic, transcriptomic, and patient survival datasets to identify key differences between healthy and CLL samples. We exposed approximately 1000 proteins that differentiate healthy from cancerous cells, with 608 upregulated and 415 downregulated in CLL cases. Notable upregulated proteins include YEATS2 (an epigenetic regulator), PIGR (Polymeric immunoglobulin receptor), and SNRPA (a splicing factor), which may serve as prognostic biomarkers for this disease. Key pathways implicated in CLL progression involve RNA processing, stress resistance, and immune response deficits. Furthermore, we identified three existing drugs-Bosutinib, Vorinostat, and Panobinostat-for potential further investigation in drug repurposing in CLL. We also found limited correlation between transcriptomic and proteomic data, emphasizing the importance of proteomics in understanding gene expression regulation mechanisms. This generally known disparity highlights once again that mRNA levels do not accurately predict protein abundance due to many regulatory factors, such as protein degradation, post-transcriptional modifications, and differing rates of translation. These results demonstrate the value of integrating omics data to uncover deregulated proteins and pathways in cancer and suggest new therapeutic avenues for CLL.
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Affiliation(s)
- Dimitra Mavridou
- Laboratory of Biological Chemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
- Functional Proteomics and Systems Biology (FunPATh), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), GR-57001 Thessaloniki, Greece;
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - Konstantina Psatha
- Functional Proteomics and Systems Biology (FunPATh), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), GR-57001 Thessaloniki, Greece;
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
- Laboratory of Medical Biology—Genetics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - Michalis Aivaliotis
- Laboratory of Biological Chemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
- Functional Proteomics and Systems Biology (FunPATh), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), GR-57001 Thessaloniki, Greece;
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
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Thurm AR, Finkel Y, Andrews C, Cai XS, Benko C, Bintu L. High-throughput discovery of regulatory effector domains in human RNA-binding proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.19.604317. [PMID: 39071298 PMCID: PMC11275849 DOI: 10.1101/2024.07.19.604317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
RNA regulation plays an integral role in tuning gene expression and is controlled by thousands of RNA-binding proteins (RBPs). We develop and use a high-throughput recruitment assay (HT-RNA-Recruit) to identify regulatory domains within human RBPs by recruiting over 30,000 protein tiles from 367 RBPs to a reporter mRNA. We discover over 100 unique RNA-regulatory effectors in 86 distinct RBPs, presenting evidence that RBPs contain functionally separable domains that dictate their post-transcriptional control of gene expression, and identify some with unique activity at 5' or 3'UTRs. We identify some domains that downregulate gene expression both when recruited to DNA and RNA, and dissect their mechanisms of regulation. Finally, we build a synthetic RNA regulator that can stably maintain gene expression at desired levels that are predictable by a mathematical model. This work serves as a resource for human RNA-regulatory effectors and expands the synthetic repertoire of RNA-based genetic control tools. Highlights HT-RNA-Recruit identifies hundreds of RNA-regulatory effectors in human proteins.Recruitment to 5' and 3' UTRs identifies regulatory domains unique to each position.Some protein domains have both transcriptional and post-transcriptional regulatory activity.We develop a synthetic RNA regulator and a mathematical model to describe its behavior.
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Teyssonniere EM, Shichino Y, Mito M, Friedrich A, Iwasaki S, Schacherer J. Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast. Nucleic Acids Res 2024; 52:2434-2445. [PMID: 38261993 PMCID: PMC10954453 DOI: 10.1093/nar/gkae030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 12/21/2023] [Accepted: 01/11/2024] [Indexed: 01/25/2024] Open
Abstract
Gene expression is known to vary among individuals, and this variability can impact the phenotypic diversity observed in natural populations. While the transcriptome and proteome have been extensively studied, little is known about the translation process itself. Here, we therefore performed ribosome and transcriptomic profiling on a genetically and ecologically diverse set of natural isolates of the Saccharomyces cerevisiae yeast. Interestingly, we found that the Euclidean distances between each profile and the expression fold changes in each pairwise isolate comparison were higher at the transcriptomic level. This observation clearly indicates that the transcriptional variation observed in the different isolates is buffered through a phenomenon known as post-transcriptional buffering at the translation level. Furthermore, this phenomenon seemed to have a specific signature by preferentially affecting essential genes as well as genes involved in complex-forming proteins, and low transcribed genes. We also explored the translation of the S. cerevisiae pangenome and found that the accessory genes related to introgression events displayed similar transcription and translation levels as the core genome. By contrast, genes acquired through horizontal gene transfer events tended to be less efficiently translated. Together, our results highlight both the extent and signature of the post-transcriptional buffering.
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Affiliation(s)
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
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Patnaik PK, Barlit H, Labunskyy VM. Manipulating mRNA-binding protein Cth2 function in budding yeast Saccharomyces cerevisiae. STAR Protoc 2024; 5:102807. [PMID: 38165801 PMCID: PMC10797207 DOI: 10.1016/j.xpro.2023.102807] [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: 10/02/2023] [Revised: 11/14/2023] [Accepted: 12/14/2023] [Indexed: 01/04/2024] Open
Abstract
Here, we present a protocol for modulating the function of the Cth2 mRNA-binding protein (RBP) in Saccharomyces cerevisiae. We describe steps to amplify and integrate mutations in Cth2 that affect its stability and function. Next, we detail the functional assay to verify the activity of the wild-type and mutant versions of Cth2 in yeast cells. This protocol can be adopted to modify the function of other RBPs with their respective functional mutations. For complete details on the use and execution of this protocol, please refer to Patnaik et al. (2022).1.
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Affiliation(s)
- Praveen K Patnaik
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA.
| | - Hanna Barlit
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Vyacheslav M Labunskyy
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA.
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Lobel JH, Ingolia NT. Defining the mechanisms and properties of post-transcriptional regulatory disordered regions by high-throughput functional profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578453. [PMID: 38370681 PMCID: PMC10871298 DOI: 10.1101/2024.02.01.578453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Disordered regions within RNA binding proteins are required to control mRNA decay and protein synthesis. To understand how these disordered regions modulate gene expression, we surveyed regulatory activity across the entire disordered proteome using a high-throughput functional assay. We identified hundreds of regulatory sequences within intrinsically disordered regions and demonstrate how these elements cooperate with core mRNA decay machinery to promote transcript turnover. Coupling high-throughput functional profiling with mutational scanning revealed diverse molecular features, ranging from defined motifs to overall sequence composition, underlying the regulatory effects of disordered peptides. Machine learning analysis implicated aromatic residues in particular contexts as critical determinants of repressor activity, consistent with their roles in forming protein-protein interactions with downstream effectors. Our results define the molecular principles and biochemical mechanisms that govern post-transcriptional gene regulation by disordered regions and exemplify the encoding of diverse yet specific functions in the absence of well-defined structure.
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Affiliation(s)
- Joseph H Lobel
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Lead contact
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Powers EN, Kuwayama N, Sousa C, Reynaud K, Jovanovic M, Ingolia NT, Brar GA. Dbp1 is a low performance paralog of RNA helicase Ded1 that drives impaired translation and heat stress response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.575095. [PMID: 38260653 PMCID: PMC10802583 DOI: 10.1101/2024.01.12.575095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Ded1 and Dbp1 are paralogous conserved RNA helicases that enable translation initiation in yeast. Ded1 has been heavily studied but the role of Dbp1 is poorly understood. We find that the expression of these two helicases is controlled in an inverse and condition-specific manner. In meiosis and other long-term starvation states, Dbp1 expression is upregulated and Ded1 is downregulated, whereas in mitotic cells, Dbp1 expression is extremely low. Inserting the DBP1 ORF in place of the DED1 ORF cannot replace the function of Ded1 in supporting translation, partly due to inefficient mitotic translation of the DBP1 mRNA, dependent on features of its ORF sequence but independent of codon optimality. Global measurements of translation rates and 5' leader translation, activity of mRNA-tethered helicases, ribosome association, and low temperature growth assays show that-even at matched protein levels-Ded1 is more effective than Dbp1 at activating translation, especially for mRNAs with structured 5' leaders. Ded1 supports halting of translation and cell growth in response to heat stress, but Dbp1 lacks this function, as well. These functional differences in the ability to efficiently mediate translation activation and braking can be ascribed to the divergent, disordered N- and C-terminal regions of these two helicases. Altogether, our data show that Dbp1 is a "low performance" version of Ded1 that cells employ in place of Ded1 under long-term conditions of nutrient deficiency.
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