scholarly journals Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection

2021 ◽  
Author(s):  
Renee Salz ◽  
Robbin Bouwmeester ◽  
Ralf Gabriels ◽  
Sven Degroeve ◽  
Lennart Martens ◽  
...  
Keyword(s):  
Amino Acid ◽  
Single Amino Acid ◽  
Amino Acid Variant ◽  
Variant Detection

Functional and Structural Characterization of Acquired Pan-Aminoglycoside Resistance 16S rRNA Methyltransferase NpmB1

2021 ◽  
Author(s):  
Akito Kawai ◽  
Masahiro Suzuki ◽  
Kentaro Tsukamoto ◽  
Yusuke Minato ◽  
Yohei Doi
Keyword(s):  
Amino Acid ◽  
16S Rrna ◽  
Amino Acid Identity ◽  
Single Amino Acid ◽  
Aminoglycoside Resistance ◽  
E Coli ◽  
The United Kingdom ◽  
Amino Acid Variant ◽  
A Site

Post-translational methylation of the A site of 16S rRNA at position A1408 leads to pan-aminoglycoside resistance encompassing both 4,5- and 4,6-disubstituted 2-deoxystreptamine (DOS) aminoglycosides. To date, NpmA is the only acquired enzyme with such function. Here, we present function and structure of NpmB1 whose sequence was identified in Escherichia coli genomes registered from the United Kingdom. NpmB1 possesses 40% amino acid identity with NpmA1 and confers resistance to all clinically relevant aminoglycosides including 4,5-DOS agents. Phylogenetic analysis of NpmB1 and NpmB2, its single amino acid variant, revealed that the encoding gene was likely acquired by E. coli from a soil bacterium. The structure of NpmB1 suggests that it requires a structural change of the β6/7 linker in order to bind to 16S rRNA. These findings establish NpmB1 and NpmB2 as the second group of acquired pan-aminoglycoside resistance 16S rRNA methyltransferases.

scholarly journals Single Amino Acid Variant Discovery in Small Numbers of Cells

2018 ◽  
Author(s):  
Zhijing Tan ◽  
Xinpei Yi ◽  
Nicholas J. Carruthers ◽  
Paul M. Stemmer ◽  
David M. Lubman
Keyword(s):  
Amino Acid ◽  
Single Amino Acid ◽  
Variant Discovery ◽  
Amino Acid Variant

Screening of OXA-244 producers, a difficult-to-detect and emerging OXA-48 variant?

2020 ◽  
Author(s):  
Cecile Emeraud ◽  
Laura Biez ◽  
Delphine Girlich ◽  
Agnès B Jousset ◽  
Thierry Naas ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Hydrolytic Activity ◽  
Single Amino Acid ◽  
Broth Microdilution ◽  
Mlst Analysis ◽  
E Coli ◽  
Amino Acid Variant ◽  
High Prevalence ◽  
High Concentrations

Abstract Background OXA-244, a single amino acid variant of OXA-48, demonstrates weaker hydrolytic activity towards carbapenems and temocillin compared with OXA-48. Of note, these antimicrobials are present in high concentrations in several carbapenemase-producing Enterobacterales (CPE) screening media. As a result, some screening media fail to grow OXA-244-producing isolates, while the prevalence of OXA-244 producers is constantly increasing in France. Methods Here, we evaluate the performance of three commercially available CPE screening media [ChromID® CARBA SMART (bioMérieux), Brilliance™ CRE (Thermo Fisher) and mSuperCARBA™ (MAST Diagnostic)] for their ability to detect OXA-244 producers (n = 101). As OXA-244 producers may also express an ESBL, two additional ESBL screening media were tested (Brilliance™ ESBL and ChromID® BLSE). MICs of temocillin and imipenem were determined by broth microdilution. The clonality of OXA-244-producing Escherichia coli isolates (n = 97) was assessed by MLST. Results Overall, the sensitivity of the ChromID® CARBA SMART, Brilliance™ CRE and mSuperCARBA™ media were 14% (95% CI = 8.1%–22.5%), 54% (95% CI = 43.3%–63.4%) and 99% (95% CI = 93.8%–100%), respectively, for the detection of OXA-244 producers. Among the 101 OXA-244-producing isolates, 96% were E. coli and 77%–78% grew on ESBL screening media. MLST analysis identified five main STs among OXA-244-producing E. coli isolates: ST38 (n = 37), ST361 (n = 17), ST69 (n = 12), ST167 (n = 11) and ST10 (n = 8). Conclusions Our results demonstrated that the mSuperCARBA™ medium is very efficient in the detection of OXA-244 producers, unlike the ChromID® CARBA SMART medium. The high prevalence of ESBLs among OXA-244 producers allowed detection of 77%–78% of them using ESBL-specific screening media.

scholarly journals Plant expression of NifD protein variants resistant to mitochondrial degradation

2020 ◽  
Vol 117 (37) ◽  
pp. 23165-23173 ◽  
Author(s):  
Robert S. Allen ◽  
Christina M. Gregg ◽  
Shoko Okada ◽  
Amratha Menon ◽  
Dawar Hussain ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Design ◽  
Nitrogenase Activity ◽  
Plant Mitochondria ◽  
Single Amino Acid ◽  
Synthetic Proteins ◽  
Amino Acid Variant ◽  
Absolute Requirement ◽  
Oxygen Sensitive ◽  
Protein Variants

To engineer Mo-dependent nitrogenase function in plants, expression of the structural proteins NifD and NifK will be an absolute requirement. Although mitochondria have been established as a suitable eukaryotic environment for biosynthesis of oxygen-sensitive enzymes such as NifH, expression of NifD in this organelle has proven difficult due to cryptic NifD degradation. Here, we describe a solution to this problem. Using molecular and proteomic methods, we found NifD degradation to be a consequence of mitochondrial endoprotease activity at a specific motif within NifD. Focusing on this functionally sensitive region, we designed NifD variants comprising between one and three amino acid substitutions and distinguished several that were resistant to degradation when expressed in both plant and yeast mitochondria. Nitrogenase activity assays of these resistant variants in Escherichia coli identified a subset that retained function, including a single amino acid variant (Y100Q). We found that other naturally occurring NifD proteins containing alternate amino acids at the Y100 position were also less susceptible to degradation. The Y100Q variant also enabled expression of a NifD(Y100Q)–linker–NifK translational polyprotein in plant mitochondria, confirmed by identification of the polyprotein in the soluble fraction of plant extracts. The NifD(Y100Q)–linker–NifK retained function in bacterial nitrogenase assays, demonstrating that this polyprotein permits expression of NifD and NifK in a defined stoichiometry supportive of activity. Our results exemplify how protein design can overcome impediments encountered when expressing synthetic proteins in novel environments. Specifically, these findings outline our progress toward the assembly of the catalytic unit of nitrogenase within mitochondria.

scholarly journals Quantitative Analysis of Single Amino Acid Variant Peptides Associated with Pancreatic Cancer in Serum by an Isobaric Labeling Quantitative Method

2014 ◽  
Vol 13 (12) ◽  
pp. 6058-6066 ◽  
Author(s):  
Song Nie ◽  
Haidi Yin ◽  
Zhijing Tan ◽  
Michelle A. Anderson ◽  
Mack T. Ruffin ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Quantitative Analysis ◽  
Amino Acid ◽  
Quantitative Method ◽  
Single Amino Acid ◽  
Amino Acid Variant

scholarly journals SuSPect: Enhanced Prediction of Single Amino Acid Variant (SAV) Phenotype Using Network Features

2014 ◽  
Vol 426 (14) ◽  
pp. 2692-2701 ◽  
Author(s):  
Christopher M. Yates ◽  
Ioannis Filippis ◽  
Lawrence A. Kelley ◽  
Michael J.E. Sternberg
Keyword(s):  
Amino Acid ◽  
Single Amino Acid ◽  
Amino Acid Variant

scholarly journals DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins

2017 ◽  
Vol 45 (W1) ◽  
pp. W201-W206 ◽  
Author(s):  
Daniele Raimondi ◽  
Ibrahim Tanyalcin ◽  
Julien Ferté ◽  
Andrea Gazzo ◽  
Gabriele Orlando ◽  
...  
Keyword(s):  
Amino Acid ◽  
Interactive Visualization ◽  
Single Amino Acid ◽  
Amino Acid Variant ◽  
Human Proteins

scholarly journals A single-amino-acid variant of the H60 CD8 epitope generates specific immunity with diverse TCR recruitment

2012 ◽  
Vol 33 (4) ◽  
pp. 393-399 ◽  
Author(s):  
Su Jeong Ryu ◽  
Ji Yeong Jeon ◽  
Jun Chang ◽  
Thomas J. Sproule ◽  
Derry C. Roopenian ◽  
...  
Keyword(s):  
Amino Acid ◽  
Single Amino Acid ◽  
Specific Immunity ◽  
Amino Acid Variant

scholarly journals Single Amino Acid Variant Profiles of Subpopulations in the MCF-7 Breast Cancer Cell Line

2017 ◽  
Vol 16 (2) ◽  
pp. 842-851 ◽  
Author(s):  
Zhijing Tan ◽  
Song Nie ◽  
Sean P. McDermott ◽  
Max S. Wicha ◽  
David M. Lubman
Keyword(s):  
Breast Cancer ◽  
Amino Acid ◽  
Cell Line ◽  
Cancer Cell ◽  
Breast Cancer Cell ◽  
Breast Cancer Cell Line ◽  
Cancer Cell Line ◽  
Single Amino Acid ◽  
Amino Acid Variant ◽  
Mcf 7

scholarly journals The Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection

2020 ◽  
Author(s):  
Renee Salz ◽  
Robbin Bouwmeester ◽  
Ralf Gabriels ◽  
Sven Degroeve ◽  
Lennart Martens ◽  
...  
Keyword(s):  
Amino Acid ◽  
Cell Line ◽  
Peptide Identification ◽  
Shotgun Proteomics ◽  
True Positive Rate ◽  
Single Amino Acid ◽  
Proteomics Data ◽  
Rna Sequences ◽  
Amino Acid Variant ◽  
Long Read

AbstractDiscovery of variant peptides such as single amino acid variant (SAAV) in shotgun proteomics data is essential for personalized proteomics. Both the resolution of shotgun proteomics methods and the search engines have improved dramatically, allowing for confident identification of SAAV peptides. However, it is not yet known if these methods are truly successful in accurately identifying SAAV peptides without prior genomic information in the search database. We studied this in unprecedented detail by exploiting publicly available long-read RNA seq and shotgun proteomics data from the gold standard reference cell line NA12878. Searching spectra from this cell line with the state-of-the-art open modification search engine ionbot against carefully curated search databases resulted in 96.7% false positive SAAVs and an 85% lower true positive rate than searching with peptide search databases that incorporate prior genetic information. While adding genetic variants to the search database remains indispensable for correct peptide identification, inclusion of long-read RNA sequences in the search database contributes only 0.3% new peptide identifications. These findings reveal the differences in SAAV detection that result from various approaches, providing guidance to researchers studying SAAV peptides and developers of peptide spectrum identification tools.

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