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Soluble protein expression is an important first step during various types of protein studies. Here, we present the screening strategy of secretable mutant. The strategy aimed to identify those cysteine residues that provoke protein misfolding in the heterologous expression system. Intentional mutagenesis studies should consider the size of the library and the time required for expression screening. Here, we proposed a cysteine-to-serine shuffling mutation strategy (CS shuffling) using a Saccharomyces cerevisiae expression system. This strategy of site-directed shuffling mutagenesis of cysteine-to-serine residues aims to identify the cysteine residues that cause protein misfolding in heterologous expression. In the case of a nonglycosylated mutant of the taste-modifying protein miraculin (MCL), which was used here as a model protein, 25% of all constructs obtained from CS shuffling expressed MCL mutant, and serine mutations were found at Cys47 or Cys92, which are involved in the formation of the disulfide bond. This indicates that these residues had the potential to provoke protein misfolding via incorrect disulfide bonding. The CS shuffling can be performed using a small library and within one week, and is an effective screening strategy of soluble protein expression.
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http://dx.doi.org/10.1007/s10529-010-0399-1 | DOI Listing |
Genome Biol
September 2025
Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Biology, Plön, Germany.
Background: Most RNA-seq datasets harbor genes with extreme expression levels in some samples. Such extreme outliers are usually treated as technical errors and are removed from the data before further statistical analysis. Here we focus on the patterns of such outlier gene expression to investigate whether they provide insights into the underlying biology.
View Article and Find Full Text PDFTheor Appl Genet
September 2025
State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
Hybrid breeding based on male sterility requires the removal of male parents, which is time- and labor-intensive; however, the use of female sterile male parent can solve this problem. In the offspring of distant hybridization between Brassica oleracea and Brassica napus, we obtained a mutant, 5GH12-279, which not only fails to generate gynoecium (thereby causing female sterility) but also has serrated leaves that could be used as a phenotypic marker in seedling screening. Genetic analysis revealed that this trait was controlled by a single dominant gene.
View Article and Find Full Text PDFEMBO J
September 2025
School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia.
Insulin resistance is a heritable risk factor for many chronic diseases; however, the genetic drivers remain elusive. In seeking these, we performed genetic mapping of insulin sensitivity in 670 chow-fed Diversity Outbred in Australia (DOz) mice and identified a genome-wide significant locus (QTL) on chromosome 8 encompassing 17 defensin genes. By taking a systems genetics approach, we identified alpha-defensin 26 (Defa26) as the causal gene in this region.
View Article and Find Full Text PDFNat Protoc
September 2025
Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
Structural biology is fundamental to understanding the molecular basis of biological processes. While machine learning-based protein structure prediction has advanced considerably, experimentally determined structures remain indispensable for guiding structure-function analyses and for improving predictive modeling. However, experimental studies of protein complexes continue to pose challenges, particularly due to the necessity of high protein concentrations and purity for downstream analyses such as cryogenic electron microscopy.
View Article and Find Full Text PDFNat Biotechnol
September 2025
Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA.
RNA-protein interactions critically regulate gene expression and cellular processes, yet their comprehensive mapping remains challenging due to their structural diversity. We introduce PRIM-seq (protein-RNA interaction mapping by sequencing), a method for concurrent de novo identification of RNA-binding proteins and their associated RNAs. PRIM-seq generates unique chimeric DNA sequences by proximity ligation of RNAs with protein-linked DNA barcodes, which are subsequently decoded through sequencing.
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