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

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.

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Single Amino Acid Variant Discovery in Small Numbers of Cells

Journal of Proteome Research ◽

10.1021/acs.jproteome.8b00694 ◽

2018 ◽

Cited By ~ 7

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

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

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkaa155 ◽

2020 ◽

Cited By ~ 1

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.

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Plant expression of NifD protein variants resistant to mitochondrial degradation

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2002365117 ◽

2020 ◽

Vol 117 (37) ◽

pp. 23165-23173 ◽

Cited By ~ 2

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.

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RETRIEVING MUTATION-SPECIFIC INFORMATION FOR HUMAN PROTEINS IN UNIPROT/SWISS-PROT KNOWLEDGEBASE

Journal of Bioinformatics and Computational Biology ◽

10.1142/s021972000700320x ◽

2007 ◽

Vol 05 (06) ◽

pp. 1215-1231 ◽

Cited By ~ 16

Author(s):

YUM LINA YIP ◽

NATHALIE LACHENAL ◽

VIOLAINE PILLET ◽

ANNE-LISE VEUTHEY

Keyword(s):

Information Retrieval ◽

Amino Acid ◽

Single Amino Acid ◽

Specific Information ◽

Regular Expressions ◽

Retrieval Method ◽

The Public ◽

Automatic Information ◽

Human Proteins ◽

Single Amino Acid Polymorphisms

The UniProt/Swiss-Prot Knowledgebase records about 30,500 variants in 5,664 proteins (Release 52.2). Most of these variants are manually curated single amino acid polymorphisms (SAPs) with references to the literature. In order to keep the list of published documents related to SAPs up to date, an automatic information retrieval method is developed to recover texts mentioning SAPs. The method is based on the use of regular expressions (patterns) and rules for the detection and validation of mutations. When evaluated using a corpus of 9,820 PubMed references, the precision of the retrieval was determined to be 89.5% over all variants. It was also found that the use of nonstandard mutation nomenclature and sequence positional correction is necessary to retrieve a significant number of relevant articles. The method was applied to the 5,664 proteins with variants. This was performed by first submitting a PubMed query to retrieve articles using gene or protein names and a list of mutation-related keywords; the SAP detection procedure was then used to recover relevant documents. The method was found to be efficient in retrieving new references on known polymorphisms. New references on known SAPs will be rendered accessible to the public via the Swiss-Prot variant pages.

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