In the rapidly evolving landscape of synthetic biology and glycobiology, the selection of an optimal microbial host, or "chassis," is the foundational step that determines the success of industrial bioproduction. CD BioGlyco offers a premier proteomics-based chassis screening service, a specialized subset of our chassis development platform. While traditional screening methods often rely on phenotypic observation or genomic potential, our proteomics-driven approach dives deeper into the functional reality of the cell.
By analyzing the complete set of proteins expressed by a strain, we provide a high-resolution map of metabolic flux, protein folding capacity, and post-translational modification (PTM) efficiency. This service is specifically engineered to bridge the gap between genetic design and actual cellular performance, ensuring that the selected chassis is not just "viable," but is the most robust and efficient factory for your specific glycan or protein product.
Key Technologies
Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS)
By coupling high-resolution chromatography with advanced Orbitrap mass spectrometers, we identify and quantify thousands of proteins in a single run, allowing us to detect subtle expression differences between candidate strains that genomic sequencing alone would miss.
Targeted Proteomics (MRM/PRM)
For clients focused on specific metabolic bottlenecks or glycosylation enzymes, we employ multiple reaction monitoring (MRM) or parallel reaction monitoring (PRM). These targeted approaches provide absolute quantification of key proteins with high sensitivity and reproducibility, ideal for validating the stability of engineered pathways.
Data-Independent Acquisition (DIA)
This technology allows for a "digital record" of the proteome. DIA provides a more comprehensive and reproducible dataset compared to traditional methods, ensuring that no low-abundance regulatory proteins are overlooked during the chassis screening process.
Proteomics: Decoding the Cellular Machinery to Empower Your Bioproduction
At CD BioGlyco, our proteomics-based chassis screening service is designed to handle the most complex challenges in microbial host selection. The transition from a genetic blueprint to a high-yielding industrial strain is often hindered by "host-context dependency," where a perfectly designed pathway fails due to the host's internal proteomic environment. Our service scope addresses this by providing an exhaustive functional profile of candidate strains.
We begin with chassis strain screening, where we evaluate a diverse library of microbial candidates, ranging from traditional E. coli and S. cerevisiae to unconventional "non-model" organisms. Unlike standard high-throughput screening (HTS) that only measures final titers, our proteomics-based chassis strain screening identifies why a strain performs well or poorly. We analyze protein turnover rates, subcellular localization, and the abundance of chaperone proteins that assist in the folding of complex glycoproteins.
By comparing the proteomic profiles of high-performing versus low-performing variants, we pinpoint specific enzymes that are underexpressed or misfolded. This data allows our clients to move beyond trial-and-error, providing a rational basis for the next round of genetic engineering. Furthermore, for glycobiology applications, we specifically monitor the expression levels of native glycosyltransferases and sugar-nucleotide transporters to ensure the chassis can support high-fidelity glycan synthesis. Our proteomic analysis measures how candidate strains react to pH shifts, osmotic stress, and metabolite toxicity at the protein level. This ensures the selected chassis is robust enough for large-scale industrialization.
Workflow
Strain Library Preparation and Cultivation
We begin by prepping the candidate chassis strains, which may include wild-type isolates, mutant libraries, or engineered variants. Strains are cultivated under standardized conditions or tailored environments that mimic the client's final production scale to ensure relevant proteomic responses.
Sample Preparation and Protein Extraction
Using optimized lysis buffers and mechanical disruption, we extract the total protein content. We employ specialized protocols to ensure the recovery of membrane-bound proteins and low-abundance signaling factors, which are often crucial for chassis performance.
Proteomic Profiling via LC-MS/MS
The extracted proteins are digested into peptides and analyzed using our high-resolution LC-MS/MS platforms. We utilize both label-free quantification (LFQ) and tandem mass tags (TMT)-labeling, depending on the required throughput and quantitative precision.
Bioinformatic Data Analysis
Our computational team processes the raw MS data using advanced software to identify proteins and quantify their abundance. We perform differential expression analysis to identify the "proteomic signatures" associated with high productivity and strain stability.
Functional Correlation and Path-Mapping
We map the identified proteins to metabolic pathways and cellular processes. This step allows us to correlate protein levels with phenotypic traits like growth rate, glycan yield, and metabolic efficiency, providing a clear picture of the host's suitability.
Reporting and Recommendation
Clients receive a detailed report including protein expression heatmaps, pathway enrichment analysis, and a prioritized list of recommended chassis strains. We provide clear, data-driven justifications for each selection.
Publication Data
DoI: 10.1093/plphys/kiaf186
Journal: Plant Physiology
IF: 6.9
Published: 2025
Results: This study employs APEX2-based proximity proteomics to map the compartmentalome of the cyanobacterium Synechococcus sp. PCC 7002, defining proteomes of the cytoplasm, thylakoid lumen, and periplasm/outer membrane (P-OM). By expressing APEX2 fusions in target compartments, the authors identified 1,687 proteins (53% of the genome), with 105 localized to the thylakoid lumen (enriched in photosynthesis/protein assembly) and 163 to the P-OM (dominated by transport/binding proteins). Forty dually localized proteins support a thylakoid membrane (TM) biogenesis model linking the inner membrane and periplasm. Signal sequence analysis revealed conserved traits: Sec-translocated proteins targeting the thylakoid lumen have more hydrophobic, alpha-helical H-regions, while P-OM proteins have hydrophilic H-regions, conserved across cyanobacterial species with TMs.
Fig.1 Thylakoid lumen proteome analysis. (Dahlgren, et al., 2025)
Applications
Biopharmaceutical Production
Identifying the best microbial hosts for producing recombinant glycoproteins, monoclonal antibodies (mAbs), and vaccines, ensuring high-fidelity post-translational modifications and minimal host cell protein (HCP) contamination.
Industrial Enzyme Engineering
Screening for chassis strains capable of high-level secretion and folding of industrial enzymes, such as cellulases or amylases, used in sustainable bio-manufacturing processes.
Synthetic Glycan Synthesis
Selecting hosts optimized for the production of human-milk oligosaccharides (HMOs), glycosaminoglycans, and other high-value carbohydrates used in the food and nutraceutical industries.
Metabolic Engineering Research
Providing a systems-biology view for researchers looking to understand host-pathway interactions and optimize carbon flux toward specific secondary metabolites or biofuels.
Advantages
Unmatched Analytical Depth
We go beyond the genome. Our proteomics service reveals the actual functional state of the cell, identifying regulatory hurdles that genomic and transcriptomic assays often miss.
Glyco-Centric Expertise
As a leader in glycobiology, CD BioGlyco understands the specific proteomic requirements for glycan synthesis, including the monitoring of sugar-nucleotide metabolism and glycosylation machinery.
High-Throughput Capability
Our automated sample preparation and rapid MS acquisition allow us to screen hundreds of strains simultaneously, shortening the development timeline for our clients.
Customized Screening Matrices
We don't believe in a one-size-fits-all approach. We tailor our proteomic assays to focus on the specific proteins and pathways most relevant to your target product.
Frequently Asked Questions
Customer Review
"The proteomic profiling provided by CD BioGlyco was a game-changer for our HMO production project. We had three candidate strains with identical growth profiles, but only the MS data revealed that one strain had a significantly higher expression of the necessary sugar-nucleotide transporters. It saved us months of wasted fermentation trials."
– L.Z., Senior Scientist
"We were struggling with protein aggregation in our yeast chassis. CD BioGlyco's proteomics service identified a lack of specific chaperones under stress conditions. Following their recommendation, we engineered the host, and our yields increased fourfold."
– W.S., Lead Researcher
"Professional, data-heavy, and highly insightful. The depth of the proteomic report was beyond what we expected, providing us with several new targets for our metabolic engineering pipeline."
CD BioGlyco provides a world-class proteomics-based chassis screening service that empowers researchers and industrial manufacturers to select the most efficient microbial hosts with scientific certainty. By leveraging advanced LC-MS/MS technologies and deep bioinformatic expertise, we transform complex biological data into a roadmap for successful bioproduction. Whether you are developing life-saving biologics or sustainable industrial chemicals, our platform ensures your chassis is optimized for peak performance. Please feel free to contact us to help you design the optimal screening strategy for your unique goals.
Reference
Dahlgren, K.; et al. Spatial proteomics reveals signal sequence characteristics correlated with localization in cyanobacteria. Plant Physiology. 2025, 198(4): kiaf186. (Open Access)
For research use only. Not intended for any clinical use.
Fig.1 Thylakoid lumen proteome analysis. (Dahlgren, et al., 2025)
