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  1. Free, publicly-accessible full text available September 20, 2024
  2. Abstract

    The absence of orthogonal aminoacyl-transfer RNA (tRNA) synthetases that accept non-l-α-amino acids is a primary bottleneck hindering the in vivo translation of sequence-defined hetero-oligomers and biomaterials. Here we report that pyrrolysyl-tRNA synthetase (PylRS) and certain PylRS variants accept α-hydroxy, α-thio andN-formyl-l-α-amino acids, as well as α-carboxy acid monomers that are precursors to polyketide natural products. These monomers are accommodated and accepted by the translation apparatus in vitro; those with reactive nucleophiles are incorporated into proteins in vivo. High-resolution structural analysis of the complex formed between one PylRS enzyme and am-substituted 2-benzylmalonic acid derivative revealed an active site that discriminates prochiral carboxylates and accommodates the large size and distinct electrostatics of an α-carboxy substituent. This work emphasizes the potential of PylRS-derived enzymes for acylating tRNA with monomers whose α-substituent diverges substantially from the α-amine of proteinogenic amino acids. These enzymes or derivatives thereof could synergize with natural or evolved ribosomes and/or translation factors to generate diverse sequence-defined non-protein heteropolymers.

     
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  3. Abstract

    A frequently expressed viewpoint across the Earth science community is that global soil moisture estimates from satellite L‐band (1.4 GHz) measurements represent moisture only in a shallow surface layer (0–5 cm) and consequently are of limited value for studying global terrestrial ecosystems because plants use water from deeper rootzones. Using this argumentation, many observation‐based land surface studies avoid satellite‐observed soil moisture. Here, based on peer‐reviewed literature across several fields, we argue that such a viewpoint is overly limiting for two reasons. First, microwave soil emission depth considerations and statistical considerations of vertically correlated soil moisture information together indicate that L‐band measurements carry information about soil moisture extending below the commonly referenced 5 cm in many conditions. However, spatial variations of effective depths of representation remain uncertain. Second, in reviewing isotopic tracer field studies of plant water uptake, we find a prevalence of vegetation that primarily draws moisture from these upper soil layers. This is especially true for grasslands and croplands covering more than a third of global vegetated surfaces. Even some deeper‐rooted species (i.e., shrubs and trees) preferentially or seasonally draw water from the upper soil layers. Therefore, L‐band satellite soil moisture estimates are more relevant to global vegetation water uptake than commonly appreciated (i.e., relevant beyond only shallow soil processes like soil evaporation). Our commentary encourages the application of satellite soil moisture across a broader range of terrestrial hydrosphere and biosphere studies while urging more rigorous estimates of its effective depth of representation.

     
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  4. Abstract

    Heterologous tRNAs used for noncanonical amino acid (ncAA) mutagenesis in mammalian cells typically show poor activity. We recently introduced a virus‐assisted directed evolution strategy (VADER) that can enrich improved tRNA mutants from naïve libraries in mammalian cells. However, VADER was limited to processing only a few thousand mutants; the inability to screen a larger sequence space precluded the identification of highly active variants with distal synergistic mutations. Here, we report VADER2.0, which can process significantly larger mutant libraries. It also employs a novel library design, which maintains base‐pairing between distant residues in the stem regions, allowing us to pack a higher density of functional mutants within a fixed sequence space. VADER2.0 enabled simultaneous engineering of the entire acceptor stem ofM. mazeipyrrolysyl tRNA (tRNAPyl), leading to a remarkably improved variant, which facilitates more efficient incorporation of a wider range of ncAAs, and enables facile development of viral vectors and stable cell‐lines for ncAA mutagenesis.

     
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  5. Abstract

    Heterologous tRNAs used for noncanonical amino acid (ncAA) mutagenesis in mammalian cells typically show poor activity. We recently introduced a virus‐assisted directed evolution strategy (VADER) that can enrich improved tRNA mutants from naïve libraries in mammalian cells. However, VADER was limited to processing only a few thousand mutants; the inability to screen a larger sequence space precluded the identification of highly active variants with distal synergistic mutations. Here, we report VADER2.0, which can process significantly larger mutant libraries. It also employs a novel library design, which maintains base‐pairing between distant residues in the stem regions, allowing us to pack a higher density of functional mutants within a fixed sequence space. VADER2.0 enabled simultaneous engineering of the entire acceptor stem ofM. mazeipyrrolysyl tRNA (tRNAPyl), leading to a remarkably improved variant, which facilitates more efficient incorporation of a wider range of ncAAs, and enables facile development of viral vectors and stable cell‐lines for ncAA mutagenesis.

     
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  6. Abstract

    We have developed a novel visible‐light‐catalyzed bioconjugation reaction, PhotoCLIC, that enables chemoselective attachment of diverse aromatic amine reagents onto a site‐specifically installed 5‐hydroxytryptophan residue (5HTP) on full‐length proteins of varied complexity. The reaction uses catalytic amounts of methylene blue and blue/red light‐emitting diodes (455/650 nm) for rapid site‐specific protein bioconjugation. Characterization of the PhotoCLIC product reveals a unique structure formed likely through a singlet oxygen‐dependent modification of 5HTP. PhotoCLIC has a wide substrate scope and its compatibility with strain‐promoted azide‐alkyne click reaction, enables site‐specific dual‐labeling of a target protein.

     
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  7. Abstract

    We have developed a novel visible‐light‐catalyzed bioconjugation reaction, PhotoCLIC, that enables chemoselective attachment of diverse aromatic amine reagents onto a site‐specifically installed 5‐hydroxytryptophan residue (5HTP) on full‐length proteins of varied complexity. The reaction uses catalytic amounts of methylene blue and blue/red light‐emitting diodes (455/650 nm) for rapid site‐specific protein bioconjugation. Characterization of the PhotoCLIC product reveals a unique structure formed likely through a singlet oxygen‐dependent modification of 5HTP. PhotoCLIC has a wide substrate scope and its compatibility with strain‐promoted azide‐alkyne click reaction, enables site‐specific dual‐labeling of a target protein.

     
    more » « less