A naturally occurring feline APOBEC3 variant that loses anti-lentiviral activity by lacking two amino acid residues

Abstract Rhizopus oryzae (heterotypic synonym: R. arrhizus) intrinsic voriconazole and fluconazole resistance has been linked to its CYP51A gene. However, the amino acid residues involved in this phenotype have not yet been established. A comparison between R. oryzae and Aspergillus fumigatus Cyp51Ap sequences showed differences in several amino acid residues. Some of them were already linked with voriconazole resistance in A. fumigatus. The objective of this work was to analyze the role of two natural polymorphisms in the intrinsic voriconazole resistance phenotype of R. oryzae (Y129F and T290A, equivalent to Y121F and T289A seen in triazole-resistant A. fumigatus). We have generated A. fumigatus chimeric strains harboring different R. oryzae CYP51A genes (wild-type and mutants). These mutant R. oryzae CYP51A genes were designed to carry nucleotide changes that produce mutations at Cyp51Ap residues 129 and 290 (emulating the Cyp51Ap protein of azole susceptible A. fumigatus). Antifungal susceptibilities were evaluated for all the obtained mutants. The polymorphism T290A (alone or in combination with Y129F) had no impact on triazole MIC. On the other hand, a > 8-fold decrease in voriconazole MICs was observed in A. fumigatus chimeric strains harboring the RoCYP51Ap-F129Y. This phenotype supports the assumption that the naturally occurring polymorphism Y129F at R. oryzae Cyp51Ap is responsible for its voriconazole resistance phenotype. In addition, these chimeric mutants were posaconazole hypersusceptible. Thus, our experimental data demonstrate that the RoCYP51Ap-F129 residue strongly impacts VRC susceptibility and that it would be related with posaconazole-RoCYP51Ap interaction. Lay summary Rhizopus oryzae is intrinsically resistant to voriconazole, a commonly used antifungal agent. In this work, we analyze the role of two natural polymorphisms present in the target of azole drugs. We established that F129 residue is responsible of the intrinsic voriconazole resistance in this species.

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Computed conformational states of the 20 naturally occurring amino acid residues and of the prototype residue α-aminobutyric acid

Macromolecules ◽

10.1021/ma00241a004 ◽

1983 ◽

Vol 16 (7) ◽

pp. 1043-1049 ◽

Cited By ~ 183

Author(s):

Max Vasquez ◽

George Nemethy ◽

Harold A. Scheraga

Keyword(s):

Amino Acid ◽

Aminobutyric Acid ◽

Amino Acid Residues ◽

Conformational States ◽

Naturally Occurring

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Results supporting the concept of the oxidant-mediated protein amino acid conversion, a naturally occurring protein engineering process, in human cells

F1000Research ◽

10.12688/f1000research.11376.2 ◽

2018 ◽

Vol 6 ◽

pp. 594

Author(s):

Yuichiro J. Suzuki ◽

Jian-Jiang Hao

Keyword(s):

Amino Acid ◽

Protein Engineering ◽

Glutamic Acid ◽

Human Cells ◽

Amino Acid Residues ◽

Engineering Process ◽

Protein Amino Acid ◽

Peroxiredoxin 6 ◽

Naturally Occurring ◽

Cultured Human Cells

Reactive oxygen species (ROS) play an important role in the development of various pathological conditions as well as aging. ROS oxidize DNA, proteins, lipids, and small molecules. Carbonylation is one mode of protein oxidation that occurs in response to the iron-catalyzed, hydrogen peroxide-dependent oxidation of amino acid side chains. Although carbonylated proteins are generally believed to be eliminated through degradation, we previously discovered the protein de-carbonylation mechanism, in which the formed carbonyl groups are chemically eliminated without proteins being degraded. Major amino acid residues that are susceptible to carbonylation include proline and arginine, both of which are oxidized to become glutamyl semialdehyde, which contains a carbonyl group. The further oxidation of glutamyl semialdehyde produces glutamic acid. Thus, we hypothesize that through the ROS-mediated formation of glutamyl semialdehyde, the proline, arginine, and glutamic acid residues within the protein structure can be converted to each other. Mass spectrometry provided results supporting that proline 45 (a well-conserved residue within the catalytic sequence) of the peroxiredoxin 6 molecule may be converted into glutamic acid in cultured human cells, opening up a revolutionizing concept that biological oxidation elicits the naturally occurring protein engineering process.

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Differential Recognition of Influenza A Viruses by M158–66Epitope-Specific CD8+T Cells Is Determined by Extraepitopic Amino Acid Residues

Journal of Virology ◽

10.1128/jvi.02439-15 ◽

2015 ◽

Vol 90 (2) ◽

pp. 1009-1022 ◽

Cited By ~ 15

Author(s):

Carolien E. van de Sandt ◽

Joost H. C. M. Kreijtz ◽

Martina M. Geelhoed-Mieras ◽

Nella J. Nieuwkoop ◽

Monique I. Spronken ◽

...

Keyword(s):

Amino Acid ◽

Influenza A Virus ◽

Influenza A ◽

Rational Design ◽

Amino Acid Residues ◽

Virus Infections ◽

Human Influenza ◽

Influenza A Viruses ◽

Specific Ctls ◽

Naturally Occurring

ABSTRACTNatural influenza A virus infections elicit both virus-specific antibody and CD4+and CD8+T cell responses. Influenza A virus-specific CD8+cytotoxic T lymphocytes (CTLs) contribute to clearance of influenza virus infections. Viral CTL epitopes can display variation, allowing influenza A viruses to evade recognition by epitope-specific CTLs. Due to functional constraints, some epitopes, like the immunodominant HLA-A*0201-restricted matrix protein 1 (M158–66) epitope, are highly conserved between influenza A viruses regardless of their subtype or host species of origin. We hypothesized that human influenza A viruses evade recognition of this epitope by impairing antigen processing and presentation by extraepitopic amino acid substitutions. Activation of specific T cells was used as an indication of antigen presentation. Here, we show that the M158–66epitope in the M1 protein derived from human influenza A virus was poorly recognized compared to the M1 protein derived from avian influenza A virus. Furthermore, we demonstrate that naturally occurring variations at extraepitopic amino acid residues affect CD8+T cell recognition of the M158–66epitope. These data indicate that human influenza A viruses can impair recognition by M158–66-specific CTLs while retaining the conserved amino acid sequence of the epitope, which may represent a yet-unknown immune evasion strategy for influenza A viruses. This difference in recognition may have implications for the viral replication kinetics in HLA-A*0201 individuals and spread of influenza A viruses in the human population. The findings may aid the rational design of universal influenza vaccines that aim at the induction of cross-reactive virus-specific CTL responses.IMPORTANCEInfluenza viruses are an important cause of acute respiratory tract infections. Natural influenza A virus infections elicit both humoral and cellular immunity. CD8+cytotoxic T lymphocytes (CTLs) are directed predominantly against conserved internal proteins and confer cross-protection, even against influenza A viruses of various subtypes. In some CTL epitopes, mutations occur that allow influenza A viruses to evade recognition by CTLs. However, the immunodominant HLA-A*0201-restricted M158–66epitope does not tolerate mutations without loss of viral fitness. Here, we describe naturally occurring variations in amino acid residues outside the M158–66epitope that influence the recognition of the epitope. These results provide novel insights into the epidemiology of influenza A viruses and their pathogenicity and may aid rational design of vaccines that aim at the induction of CTL responses.

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Evolution of a Pathway to Novel Long-Chain Carotenoids

Journal of Bacteriology ◽

10.1128/jb.186.5.1531-1536.2004 ◽

2004 ◽

Vol 186 (5) ◽

pp. 1531-1536 ◽

Cited By ~ 49

Author(s):

Daisuke Umeno ◽

Frances H. Arnold

Keyword(s):

Escherichia Coli ◽

Amino Acid ◽

Amino Acid Residues ◽

Laboratory Evolution ◽

Important Amino Acid ◽

Naturally Occurring ◽

Long Chain

ABSTRACT Using methods of laboratory evolution to force the C30 carotenoid synthase CrtM to function as a C40 synthase, followed by further mutagenesis at functionally important amino acid residues, we have discovered that synthase specificity is controlled at the second (rearrangement) step of the two-step reaction. We used this information to engineer CrtM variants that can synthesize previously unknown C45 and C50 carotenoid backbones (mono- and diisopentenylphytoenes) from the appropriate isoprenyldiphosphate precursors. With this ability to produce new backbones in Escherichia coli comes the potential to generate whole series of novel carotenoids by using carotenoid-modifying enzymes, including desaturases, cyclases, hydroxylases, and dioxygenases, from naturally occurring pathways.

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Evidence for the oxidant-mediated amino acid conversion, a naturally occurring protein engineering process, in human cells

F1000Research ◽

10.12688/f1000research.11376.1 ◽

2017 ◽

Vol 6 ◽

pp. 594 ◽

Cited By ~ 1

Author(s):

Yuichiro J. Suzuki ◽

Jian-Jiang Hao

Keyword(s):

Amino Acid ◽

Protein Engineering ◽

Glutamic Acid ◽

Human Cells ◽

Amino Acid Residues ◽

Engineering Process ◽

Peroxiredoxin 6 ◽

Naturally Occurring ◽

Cultured Human Cells ◽

Major Amino Acid

Reactive oxygen species (ROS) play an important role in the development of various pathological conditions as well as aging. ROS oxidize DNA, proteins, lipids, and small molecules. Carbonylation is one mode of protein oxidation that occurs in response to the iron-catalyzed, hydrogen peroxide-dependent oxidation of amino acid side chains. Although carbonylated proteins are generally believed to be eliminated through proteasome-dependent degradation, we previously discovered the protein de-carbonylation mechanism, in which the formed carbonyl groups are chemically eliminated without proteins being degraded. Major amino acid residues that are susceptible to carbonylation include proline and arginine, both of which are oxidized to become glutamyl semialdehyde, which contains a carbonyl group. The further oxidation of glutamyl semialdehyde produces glutamic acid. Thus, we hypothesize that through the ROS-mediated formation of glutamyl semialdehyde, the proline, arginine, and glutamic acid residues within the protein structure are interchangeable. In support of this hypothesis, mass spectrometry demonstrated that proline 45 (a well-conserved residue within the catalytic sequence) of the peroxiredoxin 6 molecule can be converted into glutamic acid in cultured human cells, establishing a revolutionizing concept that biological oxidation elicits the naturally occurring protein engineering process.

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