4.7 Article

Impact of protein uptake and degradation on recombinant protein secretion in yeast

期刊

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
卷 98, 期 16, 页码 7149-7159

出版社

SPRINGER
DOI: 10.1007/s00253-014-5783-7

关键词

Endocytosis; Saccharomyces cerevisiae; Protein degradation; Protein production; Secretion

资金

  1. NIH Kirschstein NRSA fellowship
  2. The Knut and Alice Wallenberg Foundation
  3. EU Framework VII project SYSINBIO [212766]
  4. European Research Council project INSYSBIO [247013]
  5. Novo Nordisk Foundation
  6. Chalmers Foundation
  7. Novo Nordisk Fonden [NNF10CC1016517] Funding Source: researchfish
  8. European Research Council (ERC) [247013] Funding Source: European Research Council (ERC)

向作者/读者索取更多资源

Protein titers, a key bioprocessing metric, depend both on the synthesis of protein and the degradation of protein. Secreted recombinant protein production in Saccharomyces cerevisiae is an attractive platform as minimal media can be used for cultivation, thus reducing fermentation costs and simplifying downstream purification, compared to other systems that require complex media. As such, engineering S. cerevisiae to improve titers has been then the subject of significant attention, but the majority of previous efforts have been focused on improving protein synthesis. Here, we characterize the protein uptake and degradation pathways of S. cerevisiae to better understand its impact on protein secretion titers. We do find that S. cerevisiae can consume significant (in the range of 1 g/L/day) quantities of whole proteins. Characterizing the physiological state and combining metabolomics and transcriptomics, we identify metabolic and regulatory markers that are consistent with uptake of whole proteins by endocytosis, followed by intracellular degradation and catabolism of substituent amino acids. Uptake and degradation of recombinant protein products may be common in S. cerevisiae protein secretion systems, and the current data should help formulate strategies to mitigate product loss.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.7
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

Review Dentistry, Oral Surgery & Medicine

Portable and wearable electromyographic devices for the assessment of sleep bruxism and awake bruxism: A literature review

Taihiko Yamaguchi, Saki Mikami, Masana Maeda, Taishi Saito, Toshinori Nakajima, Wataru Yachida, Akihito Gotouda

Summary: This article reviews the current state of portable/wearable EMG devices for assessment of bruxism. The results show that ultra-miniaturized wearable EMG devices with performance equivalent to conventional devices have been developed and used during sleep and in the daytime, with a high level of diagnostic accuracy for sleep bruxism. However, a definite cut-off value for awake bruxism has not been established.

CRANIO-THE JOURNAL OF CRANIOMANDIBULAR & SLEEP PRACTICE (2023)

Article Microbiology

Identification of a novel gene required for competitive growth at high temperature in the thermotolerant yeast Kluyveromyces marxianus

Noemi Montini, Tyler W. Doughty, Ivan Domenzain, Darren A. Fenton, Pavel V. Baranov, Ronan Harrington, Jens Nielsen, Verena Siewers, John P. Morrissey

Summary: Research indicates that under high-temperature growth conditions, the expression of specific genes in Kluyveromyces marxianus increases, suggesting a role in adaptation to harsh environments. One identified gene, KLMX_70384, has been confirmed to be essential for competitive growth at high temperatures.

MICROBIOLOGY-SGM (2022)

Article Biochemistry & Molecular Biology

GotEnzymes: an extensive database of enzyme parameter predictions

Feiran Li, Yu Chen, Mihail Anton, Jens Nielsen

Summary: Enzyme parameters are crucial for understanding, modeling, and engineering cells. Experimental measurements only cover a small portion of enzyme-compound pairs, and even less in non-model organisms. Artificial intelligence techniques have accelerated the exploration of enzyme properties by predicting them in a high-throughput manner. GotEnzymes is a comprehensive database that provides predicted enzyme parameters using AI approaches, allowing for interactive web exploration and programmatic access.

NUCLEIC ACIDS RESEARCH (2023)

Editorial Material Biotechnology & Applied Microbiology

Harnessing synthetic biology for mushroom farming

Gen Zou, Jens B. Nielsen, Yongjun Wei

Summary: Recent advances in synthetic biology have revolutionized mushroom farming by shifting the focus from traditional cultivation to comprehensive applications using cutting-edge biotechnologies. Promising applications in this field include precision breeding, exploration of biosynthetic gene clusters, development of mushroom chassis cells, and construction of cell factories for high-value products.

TRENDS IN BIOTECHNOLOGY (2023)

Article Multidisciplinary Sciences

Generation and analysis of context-specific genome-scale metabolic models derived from-cell data

Johan Gustafsson, Mihail Anton, Fariba Roshanzamir, Rebecka Jornsten, Eduard J. Kerkhoven, Jonathan L. Robinson, Jens Nielsen

Summary: Single-cell RNA sequencing combined with genome-scale metabolic models has the potential to unravel metabolism differences across cell types and cell states. This study develops a method for generating cell-type-specific models and evaluates the impact of RNA-Seq normalization methods on model topology. The approach successfully detects unique metabolic profiles and cancer-associated differences.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2023)

Article Biochemical Research Methods

HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer

Le Yuan, Hongzhong Lu, Feiran Li, Jens Nielsen, Eduard J. Kerkhoven

Summary: In this study, a computational toolbox called HGTphyloDetect was developed, which combines high-throughput analysis with phylogenetic inference to accurately identify horizontal gene transfer (HGT) events and illustrate the transmission pathway among evolutionarily distant or closely related species. The HGTphyloDetect toolbox is user-friendly, capable of detecting HGT events with high efficiency and low false discovery rate.

BRIEFINGS IN BIOINFORMATICS (2023)

Article Multidisciplinary Sciences

Yeast increases glycolytic flux to support higher growth rates accompanied by decreased metabolite regulation and lower protein phosphorylation

Min Chen, Tingting Xie, Huan Li, Yingping Zhuang, Jianye Xia, Jens Nielsen

Summary: Supply and regulation of Gibbs free energy and precursors in cellular metabolism are essential for cellular function. In this study, we used multi-omics data under different conditions to investigate the regulation of central carbon metabolism (CCM) in yeast. We identified a metabolism-specific CCM flux regulation mechanism, which is affected by posttranslational modification and allosteric regulation.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2023)

Article Green & Sustainable Science & Technology

A one-carbon chemicals conversion strategy to produce precursor of biofuels with Saccharomyces cerevisiae

Kai Wang, Yangyang Da, Haoran Bi, Yanhui Liu, Biqiang Chen, Meng Wang, Zihe Liu, Jens Nielsen, Tianwei Tan

Summary: By improving the formate utilization capability and NAD(P)H production of a yeast strain, a platform strain for the synthesis of free fatty acids (FFAs) from CO2 and formate was successfully constructed. Continuous optimization resulted in a 21.8-fold increase in formate utilization rate and a 33.7-fold increase in FFA production. The FFAs produced can be easily converted into biodiesel through downstream technologies.

RENEWABLE ENERGY (2023)

Article Chemistry, Analytical

Multiplexed CRISPR-Based Nucleic Acid Detection Using a Single Cas Protein

Jinyu Fu, Linghao Zhang, Yanlin Long, Zihe Liu, Geng Meng, Huimin Zhao, Xin Su, Shuobo Shi

Summary: In this study, a multiplexed CRISPR-based nucleic acid detection system with single-nucleotide resolution using a single Cas protein was developed. This system, called CRISPR-TMSD, integrated the toehold-mediated strand displacement reaction and the cis-cleavage activity of the Cas protein. By utilizing target-specific reporters, multiplexed detection was achieved using just one Cas protein. The combination with recombinase polymerase amplification allowed for extremely sensitive detection, with a detection limit as low as 1 copy/μL. This work presents a new strategy for designing CRISPR-based diagnostic systems and has the potential to expand the applications of CRISPR-based diagnostics.

ANALYTICAL CHEMISTRY (2023)

Article Multidisciplinary Sciences

A polycistronic system for multiplexed and precalibrated expression of multigene pathways in fungi

Qun Yue, Jie Meng, Yue Qiu, Miaomiao Yin, Liwen Zhang, Weiping Zhou, Zhiqiang An, Zihe Liu, Qipeng Yuan, Wentao Sun, Chun Li, Huimin Zhao, Istvan Molnar, Yuquan Xu, Shuobo Shi

Summary: Unlike prokaryotic hosts, most genes in eukaryotes are transcribed to monocistronic mRNA for single protein translation. Here, the authors develop a polycistronic system for multiplexed and precalibrated expression of multiple genes, and show its application in constructing yeast cell factories for terpenoids production.

NATURE COMMUNICATIONS (2023)

Article Chemistry, Analytical

Accurate Monitoring of 24-h Real-World Movement Behavior in People with Cerebral Palsy Is Possible Using Multiple Wearable Sensors and Deep Learning

Ivana Bardino Novosel, Anina Ritterband-Rosenbaum, Georgios Zampoukis, Jens Bo Nielsen, Jakob Lorentzen

Summary: This study developed and trained an image-based Convolutional Neural Network (CNN) to recognize specific movement classifiers relevant to individuals with cerebral palsy (CP). Monitoring and quantifying movement behavior in CP patients using multiple wearable sensors and CNN is of great value for improving their health outcomes.

SENSORS (2023)

Article Materials Science, Multidisciplinary

InAs-Al hybrid devices passing the topological gap protocol

Morteza Aghaee, Arun Akkala, Zulfi Alam, Rizwan Ali, Alejandro Alcaraz Ramirez, Mariusz Andrzejczuk, Andrey E. Antipov, Pavel Aseev, Mikhail Astafev, Bela Bauer, Jonathan Becker, Srini Boddapati, Frenk Boekhout, Jouri Bommer, Tom Bosma, Leo Bourdet, Samuel Boutin, Philippe Caroff, Lucas Casparis, Maja Cassidy, Sohail Chatoor, Anna Wulf Christensen, Noah Clay, William S. Cole, Fabiano Corsetti, Ajuan Cui, Paschalis Dalampiras, Anand Dokania, Gijs de Lange, Michiel de Moor, Juan Carlos Estrada Saldana, Saeed Fallahi, Zahra Heidarnia Fathabad, John Gamble, Geoff Gardner, Deshan Govender, Flavio Griggio, Ruben Grigoryan, Sergei Gronin, Jan Gukelberger, Esben Bork Hansen, Sebastian Heedt, Jesus Herranz Zamorano, Samantha Ho, Ulrik Laurens Holgaard, Henrik Ingerslev, Linda Johansson, Jeffrey Jones, Ray Kallaher, Farhad Karimi, Torsten Karzig, Cameron King, Maren Elisabeth Kloster, Christina Knapp, Dariusz Kocon, Jonne Koski, Pasi Kostamo, Peter Krogstrup, Mahesh Kumar, Tom Laeven, Thorvald Larsen, Kongyi Li, Tyler Lindemann, Julie Love, Roman Lutchyn, Morten Hannibal Madsen, Michael Manfra, Signe Markussen, Esteban Martinez, Robert McNeil, Elvedin Memisevic, Trevor Morgan, Andrew Mullally, Chetan Nayak, Jens Nielsen, William Hvidtfelt Padkaer Nielsen, Bas Nijholt, Anne Nurmohamed, Eoin OFarrell, Keita Otani, Sebastian Pauka, Karl Petersson, Luca Petit, Dmitry I. Pikulin, Frank Preiss, Marina Quintero-Perez, Mohana Rajpalke, Katrine Rasmussen, Davydas Razmadze, Outi Reentila, David Reilly, Richard Rouse, Ivan Sadovskyy, Lauri Sainiemi, Sydney Schreppler, Vadim Sidorkin, Amrita Singh, Shilpi Singh, Sarat Sinha, Patrick Sohr, Tomas Stankevic, Lieuwe Stek, Henri Suominen, Judith Suter, Vicky Svidenko, Sam Teicher, Mine Temuerhan, Nivetha Thiyagarajah, Raj Tholapi, Mason Thomas, Emily Toomey, Shivendra Upadhyay, Ivan Urban, Saulius Vaitiekenas, Kevin Van Hoogdalem, David Van Woerkom, Dmitrii V. Viazmitinov, Dominik Vogel, Steven Waddy, John Watson, Joseph Weston, Georg W. Winkler, Chung Kai Yang, Sean Yau, Daniel Yi, Emrah Yucelen, Alex Webster, Ruichen Zhao

Summary: In this study, measurements and simulations of semiconductor-superconductor heterostructure devices were conducted to observe topological superconductivity and Majorana zero modes. The devices were optimized to ensure robustness against nonuniformity and disorder. Experimental results indicate the presence of a topological superconducting phase, which is a prerequisite for experiments involving Majorana zero modes fusion and braiding.

PHYSICAL REVIEW B (2023)

Article Endocrinology & Metabolism

Metabolic reconfiguration enables synthetic reductive metabolism in yeast

Tao Yu, Quanli Liu, Xiang Wang, Xiangjian Liu, Yun Chen, Jens Nielsen

Summary: This study demonstrates the establishment of a synthetic decarboxylation cycle in the yeast cytosol, which enhances the production of reduced chemicals. By implementing rational design, metabolic rewiring, and recombinant expression, the researchers achieved a significant increase in free fatty acid yield.

NATURE METABOLISM (2022)

暂无数据