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Biology subjects

Orsburn, B. C.

Publications and source records attributed to Orsburn, B. C..

5 recordsLinked to original sources

EstG is a novel esterase required for cell envelope integrity

Proper regulation of the bacterial cell envelope is critical for cell survival. Identification and characterization of enzymes that maintain cell envelope homeostasis is crucial, as they can be targets for effective antibiotics. In this study, we have identified a novel enzyme, called EstG, whose activity protects cells from a variety of lethal assaults in the -proteobacterium Caulobacter crescentus. Despite homology to transpeptidase family cell wall enzymes and an ability to protect against cell wall-targeting antibiotics, EstG does not demonstrate biochemical activity towards cell wall substrates. Instead, EstG is genetically connected to the periplasmic enzymes OpgH and BglX, responsible for synthesis and hydrolysis of osmoregulated periplasmic glucans (OPGs), respectively. The crystal structure of EstG revealed similarities to esterases and transesterases, and we demonstrated esterase activity of EstG in vitro. Using biochemical fractionation, we identified a cyclic hexamer of glucose as a likely substrate of EstG. This molecule is the first OPG described in Caulobacter and establishes a novel class of OPGs, the regulation and modification of which is important for stress survival and adaptation to fluctuating environments. Our data indicate that EstG, BglX, and OpgH comprise a previously unknown OPG pathway in Caulobacter. Ultimately, we propose that EstG is a novel enzyme that, instead of acting on the cell wall, acts on cyclic OPGs to provide resistance to a variety of cellular stresses.

microbiology↗

Diagnostic Ion Data Analysis Reduction (DIDAR) allows rapid quality control analysis and filtering of multiplexed single cell proteomics data

Recent advances in the sensitivity and speed of mass spectrometers utilized for proteomics and metabolomics workflows has led to a dramatic increase in data file size and density. For a field already challenged by data complexity due to a dependence on desktop PC architecture and the Windows operating systems, further compromises appear inevitable as data density scales. As one method to reduce data complexity, we present herein a light-weight python script that can rapidly filter and provide analysis metrics from tandem mass spectra based on the presence and number of diagnostic fragment ions determined by the end user. Diagnostic Ion Data Analysis Reduction (DIDAR) can be applied to any mass spectrometry dataset to create smaller output files containing only spectra likely to contain post-translational modifications or chemical labels of interest. In this study we describe the application DIDAR within the context of multiplexed single cell proteomics workflows. When applied in this manner using reporter fragment ions as diagnostic signatures, DIDAR can provide quality control metrics based on the presence of reporter ions derived from single human cells and simplified output files for search engine analysis. The simple output metric text files can be used to rapidly flag entire LCMS runs with technical issues and remove them from downstream analysis based on end user minimum requirements. Acquisition files that pass these criteria are further improved through the automatic removal of spectra where insufficient signal from single cells is observed. We describe the application of DIDAR to two recently described multiplexed single cell proteomics datasets. Abstract Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/481489v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@1380a32org.highwire.dtl.DTLVardef@258660org.highwire.dtl.DTLVardef@199411eorg.highwire.dtl.DTLVardef@824aa1_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

Single Cell Proteomics Using a Trapped Ion Mobility Time-of-Flight Mass Spectrometer Provides Insight into the Post-translational Modification Landscape of Individual Human Cells

Single cell proteomics is a powerful tool with potential for markedly enhancing understanding of cellular processes. Previously reported single cell proteomics innovations employ Orbitrap mass spectrometers. In this study we describe the development, optimization, and application of multiplexed single cell proteomics to the analysis of human-derived cells using trapped ion mobility time-of-flight mass spectrometry. This method, denoted as pasefRiQ is an advance as it allows accurate peptide quantification at picogram peptide concentrations. When employing a peptide carrier channel to boost protein sequence coverage, we obtain over 40,000 tandem mass spectra in 30 minutes, while achieving higher sequence coverage of each identified protein than described for SCOPE2. Using NCI-H-358 cells, which are a human bronchioalveolar carcinoma and KRASG12C model cell line, we demonstrate that the level of coverage achieved using this method enables the quantification of up to 1,255 proteins per cell and the detection of multiple classes of post-translational modifications in single cells. Further, when cells were treated with sotorasib, a KRASG12C covalent inhibitor, pasefRiQ revealed cell-to-cell variability in the impact of the drug on the NCI-H-358 cells, providing insight missed by traditional analyses. We provide multiple resources necessary for the application of single cell proteomics to drug treatment studies including tools to reduce cell cycle linked proteomic effects from masking pharmacological phenotypes. Significance StatementThis work describes the establishment of a single cell proteomics method using a time-of-flight mass spectrometer. Through this approach, we demonstrate the confident identification of post- translational modifications in single human-derived cells. Additionally, using a KRASG12C covalent inhibitor as a model compound we show that this method can be used to understand pharmacological responses of single human-derived cultured cells.

biochemistry↗

A simple tool extends TIMSTOF compatibility with historic data processing tools and enables ion mobility-enhanced spectral libraries

Trapped ion mobility mass spectrometry is proving to be a disruptive technology in LCMS based proteomics. One primary drawback of this hardware is the lack of compatibility with the hundreds of data processing pipelines historically in use. This study describes a simple data conversion tool that "folds" the TIMSTOF ion mobility data into the MS2 fragmentation spectra allowing simple downstream processing. Little to no detriment in the assignment of peptide spectral matches is observed when "folding" the 1/k0 value into the low mass region. To demonstrate one utility of TIMS Folding, spectral libraries are provided in multiple common formats that were constructed from the same files both with and without folded ion mobility data. When new data is acquired and folded using the same parameters prior to data processing the folded ion mobility data can be used as an additional metric for peptide match confidence against folded spectral libraries.

biochemistry↗

Aliquoting of isobaric labeling reagents for low concentration and single cell proteomics samples

The introduction of isobaric tagging reagents enabled more accurate, high-throughput quantitative proteomics by enabling multiple samples to be multiplexed. One drawback of these workflows is the relative expense of the proprietary isobaric reagents, which is often only second to the expense of the instruments themselves. These highly reactive chemical tags are only commercially available in relatively large aliquots compared to the typical amounts of peptides analyzed in proteomic workflows today. Excess reagents are typically disposed of following a single labeling experiment or those performed within a few days of opening a new kit. We present a simple procedure to aliquot commercial isobaric tagging reagents and demonstrate the successful and high efficiency labeling of multiple samples over a period of six months. The samples presented herein were selected as the most diverse ones labeled by prepared aliquots from a single labeling reagent kit over this period. We observe comparable labeling efficiency from 100 microgram to 100 picograms of peptide when labeling samples from both human digest standards, cancer cell lines prepared in-house and from cells directly obtained from human organ donors, despite differences in cell type, lysis, and digestion procedures. No labeling experiment of whole human proteomics samples achieved less than 92% labeling efficiency over this period. When preparing phosphoproteomic samples 6 months after the date of the aliquoting procedure, we observed a decrease in labeling efficiency to approximately 86%, indicating the end of the useful lifetime of aliquots prepared in this manner. Over this period, we have effectively reduced the reagent costs of each experiment to less than 10% of the predicted costs when following the manufacturer instructions for use and disposal. While aliquoting of reagents can be performed by hand, we provide a complete template for automatic aliquoting using an affordable liquid handling robot, including plans for 3D printing of two parts we have found useful for streamlining this procedure. Abstract Graphic O_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC="FIGDIR/small/449560v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@18cd7eeorg.highwire.dtl.DTLVardef@1b48065org.highwire.dtl.DTLVardef@159761forg.highwire.dtl.DTLVardef@5a0896_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗