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1.
Nature ; 626(8001): 1125-1132, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38355796

RESUMO

To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage1,2. In bacteria, two families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats and environmental stressors have confounded their discovery3-6. Here, by combining cryogenic electron microscopy, genetics and biochemistry, we identify Balon, a new hibernation factor in the cold-adapted bacterium Psychrobacter urativorans. We show that Balon is a distant homologue of the archaeo-eukaryotic translation factor aeRF1 and is found in 20% of representative bacteria. During cold shock or stationary phase, Balon occupies the ribosomal A site in both vacant and actively translating ribosomes in complex with EF-Tu, highlighting an unexpected role for EF-Tu in the cellular stress response. Unlike typical A-site substrates, Balon binds to ribosomes in an mRNA-independent manner, initiating a new mode of ribosome hibernation that can commence while ribosomes are still engaged in protein synthesis. Our work suggests that Balon-EF-Tu-regulated ribosome hibernation is a ubiquitous bacterial stress-response mechanism, and we demonstrate that putative Balon homologues in Mycobacteria bind to ribosomes in a similar fashion. This finding calls for a revision of the current model of ribosome hibernation inferred from common model organisms and holds numerous implications for how we understand and study ribosome hibernation.


Assuntos
Proteínas de Bactérias , Resposta ao Choque Frio , Fatores de Terminação de Peptídeos , Biossíntese de Proteínas , Psychrobacter , Proteínas Ribossômicas , Ribossomos , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/ultraestrutura , Fator Tu de Elongação de Peptídeos/química , Fator Tu de Elongação de Peptídeos/metabolismo , Fator Tu de Elongação de Peptídeos/ultraestrutura , Proteínas Ribossômicas/química , Proteínas Ribossômicas/genética , Proteínas Ribossômicas/metabolismo , Proteínas Ribossômicas/ultraestrutura , Ribossomos/química , Ribossomos/metabolismo , Ribossomos/ultraestrutura , Psychrobacter/química , Psychrobacter/genética , Psychrobacter/metabolismo , Psychrobacter/ultraestrutura , Microscopia Crioeletrônica , Fatores de Terminação de Peptídeos/química , Fatores de Terminação de Peptídeos/genética , Fatores de Terminação de Peptídeos/metabolismo , Fatores de Terminação de Peptídeos/ultraestrutura
2.
Nature ; 626(8001): 1025-1033, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38418912

RESUMO

Reaction conditions that are generally applicable to a wide variety of substrates are highly desired, especially in the pharmaceutical and chemical industries1-6. Although many approaches are available to evaluate the general applicability of developed conditions, a universal approach to efficiently discover these conditions during optimizations is rare. Here we report the design, implementation and application of reinforcement learning bandit optimization models7-10 to identify generally applicable conditions by efficient condition sampling and evaluation of experimental feedback. Performance benchmarking on existing datasets statistically showed high accuracies for identifying general conditions, with up to 31% improvement over baselines that mimic state-of-the-art optimization approaches. A palladium-catalysed imidazole C-H arylation reaction, an aniline amide coupling reaction and a phenol alkylation reaction were investigated experimentally to evaluate use cases and functionalities of the bandit optimization model in practice. In all three cases, the reaction conditions that were most generally applicable yet not well studied for the respective reaction were identified after surveying less than 15% of the expert-designed reaction space.

3.
Proc Natl Acad Sci U S A ; 121(11): e2321700121, 2024 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-38442159

RESUMO

Ribosomes are often used in synthetic biology as a tool to produce desired proteins with enhanced properties or entirely new functions. However, repurposing ribosomes for producing designer proteins is challenging due to the limited number of engineering solutions available to alter the natural activity of these enzymes. In this study, we advance ribosome engineering by describing a novel strategy based on functional fusions of ribosomal RNA (rRNA) with messenger RNA (mRNA). Specifically, we create an mRNA-ribosome fusion called RiboU, where the 16S rRNA is covalently attached to selenocysteine insertion sequence (SECIS), a regulatory RNA element found in mRNAs encoding selenoproteins. When SECIS sequences are present in natural mRNAs, they instruct ribosomes to decode UGA codons as selenocysteine (Sec, U) codons instead of interpreting them as stop codons. This enables ribosomes to insert Sec into the growing polypeptide chain at the appropriate site. Our work demonstrates that the SECIS sequence maintains its functionality even when inserted into the ribosome structure. As a result, the engineered ribosomes RiboU interpret UAG codons as Sec codons, allowing easy and site-specific insertion of Sec in a protein of interest with no further modification to the natural machinery of protein synthesis. To validate this approach, we use RiboU ribosomes to produce three functional target selenoproteins in Escherichia coli by site-specifically inserting Sec into the proteins' active sites. Overall, our work demonstrates the feasibility of creating functional mRNA-rRNA fusions as a strategy for ribosome engineering, providing a novel tool for producing Sec-containing proteins in live bacterial cells.


Assuntos
Magnoliopsida , Selenocisteína , RNA Mensageiro/genética , RNA Ribossômico 16S , Selenoproteínas/genética , Ribossomos/genética , Códon de Terminação/genética , Escherichia coli/genética
4.
Nucleic Acids Res ; 52(2): 513-524, 2024 Jan 25.
Artigo em Inglês | MEDLINE | ID: mdl-38100361

RESUMO

Protein translation is orchestrated through tRNA aminoacylation and ribosomal elongation. Among the highly conserved structure of tRNAs, they have distinguishing features which promote interaction with their cognate aminoacyl tRNA synthetase (aaRS). These key features are referred to as identity elements. In our study, we investigated the tRNA:aaRS pair that installs the 22nd amino acid, pyrrolysine (tRNAPyl:PylRS). Pyrrolysyl-tRNA synthetases (PylRSs) are naturally encoded in some archaeal and bacterial genomes to acylate tRNAPyl with pyrrolysine. Their large amino acid binding pocket and poor recognition of the tRNA anticodon have been instrumental in incorporating >200 noncanonical amino acids. PylRS enzymes can be divided into three classes based on their genomic structure. Two classes contain both an N-terminal and C-terminal domain, however the third class (ΔpylSn) lacks the N-terminal domain. In this study we explored the tRNA identity elements for a ΔpylSn tRNAPyl from Candidatus Methanomethylophilus alvus which drives the orthogonality seen with its cognate PylRS (MaPylRS). From aminoacylation and translation assays we identified five key elements in ΔpylSn tRNAPyl necessary for MaPylRS activity. The absence of a base (position 8) and a G-U wobble pair (G28:U42) were found to affect the high-resolution structure of the tRNA, while molecular dynamic simulations led us to acknowledge the rigidity imparted from the G-C base pairs (G3:C70 and G5:C68).


Enzymes known as PylRS offer the remarkable ability to expand the natural genetic code of a living cell with unnatural amino acids. Currently, over 200 unnatural amino acids can be genetically encoded with the help of PylRS and its partner tRNAPyl, enabling us to endow proteins with novel properties, or regulate protein activity using light or inducible cross-linking. One intriguing feature of PylRS enzymes is their ability to avoid cross-reactivity when two PylRS homologs from different organisms-such as those from the archaea Methanosarcina mazei and Methanomethylophilus alvus-are co-expressed in a single cell. This makes it possible to simultaneously encode two unnatural amino acids in a single protein. This study illuminates the elusive mechanism of PylRS specificity by using cryo-electron microscopy, biochemistry and molecular simulations. The interaction of PylRS from M. alvus with its tRNAPyl is best described as two pieces of a jigsaw puzzle; in which PylRS recognizes the unique shape of its cognate tRNA instead of specific nucleotides in the tRNA sequence like other tRNA-binding enzymes. This finding may streamline the rational design of tools for simultaneous genetic incorporation of multiple unnatural amino acids, thereby facilitating the development of valuable proteins for research, medicine, and biotechnology.


Assuntos
Aminoacil-tRNA Sintetases , Archaea , Microbioma Gastrointestinal , Humanos , Aminoácidos/metabolismo , Aminoacil-tRNA Sintetases/isolamento & purificação , Aminoacil-tRNA Sintetases/metabolismo , Archaea/enzimologia , RNA de Transferência/química , RNA de Transferência/metabolismo , Aminoacilação de RNA de Transferência
5.
Mol Biol Evol ; 41(1)2024 Jan 03.
Artigo em Inglês | MEDLINE | ID: mdl-37987564

RESUMO

Ribosomes from different species can markedly differ in their composition by including dozens of ribosomal proteins that are unique to specific lineages but absent in others. However, it remains unknown how ribosomes acquire new proteins throughout evolution. Here, to help answer this question, we describe the evolution of the ribosomal protein msL1/msL2 that was recently found in ribosomes from the parasitic microorganism clade, microsporidia. We show that this protein has a conserved location in the ribosome but entirely dissimilar structures in different organisms: in each of the analyzed species, msL1/msL2 exhibits an altered secondary structure, an inverted orientation of the N-termini and C-termini on the ribosomal binding surface, and a completely transformed 3D fold. We then show that this fold switching is likely caused by changes in the ribosomal msL1/msL2-binding site, specifically, by variations in rRNA. These observations allow us to infer an evolutionary scenario in which a small, positively charged, de novo-born unfolded protein was first captured by rRNA to become part of the ribosome and subsequently underwent complete fold switching to optimize its binding to its evolving ribosomal binding site. Overall, our work provides a striking example of how a protein can switch its fold in the context of a complex biological assembly, while retaining its specificity for its molecular partner. This finding will help us better understand the origin and evolution of new protein components of complex molecular assemblies-thereby enhancing our ability to engineer biological molecules, identify protein homologs, and peer into the history of life on Earth.


Assuntos
Parasitos , Proteínas Ribossômicas , Animais , Proteínas Ribossômicas/genética , Ribossomos/genética , Ribossomos/metabolismo , RNA Ribossômico/genética , Sítios de Ligação , Parasitos/genética
6.
Nucleic Acids Res ; 51(15): 8048-8059, 2023 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-37395434

RESUMO

Ribosomal genes are widely used as 'molecular clocks' to infer evolutionary relationships between species. However, their utility as 'molecular thermometers' for estimating optimal growth temperature of microorganisms remains uncertain. Previously, some estimations were made using the nucleotide composition of ribosomal RNA (rRNA), but the universal application of this approach was hindered by numerous outliers. In this study, we aimed to address this problem by identifying additional indicators of thermal adaptation within the sequences of ribosomal proteins. By comparing sequences from 2021 bacteria with known optimal growth temperature, we identified novel indicators among the metal-binding residues of ribosomal proteins. We found that these residues serve as conserved adaptive features for bacteria thriving above 40°C, but not at lower temperatures. Furthermore, the presence of these metal-binding residues exhibited a stronger correlation with the optimal growth temperature of bacteria compared to the commonly used correlation with the 16S rRNA GC content. And an even more accurate correlation was observed between the optimal growth temperature and the YVIWREL amino acid content within ribosomal proteins. Overall, our work suggests that ribosomal proteins contain a more accurate record of bacterial thermal adaptation compared to rRNA. This finding may simplify the analysis of unculturable and extinct species.


Assuntos
RNA Ribossômico , Proteínas Ribossômicas , Bactérias/genética , Filogenia , Proteínas Ribossômicas/genética , RNA Ribossômico/genética , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/química , Temperatura , Thermus thermophilus/genética
7.
Support Care Cancer ; 32(7): 427, 2024 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-38869647

RESUMO

PURPOSE: Sensory chemotherapy-induced peripheral neuropathy (CIPN) is well-recognized, but motor CIPN remains understudied. This secondary analysis focused on the long-term severity and impact of motor disorders, their relation to sensory CIPN, neuropathic pain, psychological distress, and health-related quality of life (HRQoL) after oxaliplatin-based chemotherapy in colorectal cancer (CRC) survivors. METHODS: Data from a multicenter, cross-sectional study were re-analyzed to explore motor CIPN among CRC survivors up to 5 years post-chemotherapy, with no longitudinal follow-up. Questionnaires assessed sensory and motor CIPN (QLQ-CIPN20), neuropathic pain (DN4), anxiety and depression (HADS), and HRQoL (QLQ-C30). RESULTS: Among 405 CRC survivors, 31.1% had sensory CIPN as previously described. When categorizing the 405 CRC survivors based on the years since their last oxaliplatin-based chemotherapy, the motor scores derived from the QLQ-CIPN20 showed no significant difference between years (p = 0.08). Motor CIPN scores correlated with female gender, higher oxaliplatin dose intensity, sensory CIPN, and neuropathic pain. Motor CIPN also linked to decreased HRQoL and increased psychological distress. CONCLUSION: The study underscores the detrimental impact of motor disorders on CRC survivors post-oxaliplatin-based chemotherapy. Oncologists should prioritize assessing and managing motor manifestations alongside sensory symptoms to enhance post-cancer quality of life. TRIAL REGISTRATION: NCT02970526 (2016-11-22). https://classic. CLINICALTRIALS: gov/ct2/show/NCT02970526?term=NCT02970526&draw=2&rank=1 .


Assuntos
Antineoplásicos , Neoplasias Colorretais , Oxaliplatina , Doenças do Sistema Nervoso Periférico , Qualidade de Vida , Humanos , Oxaliplatina/efeitos adversos , Masculino , Feminino , Doenças do Sistema Nervoso Periférico/induzido quimicamente , Pessoa de Meia-Idade , Estudos Transversais , Idoso , Neoplasias Colorretais/tratamento farmacológico , Antineoplásicos/efeitos adversos , Inquéritos e Questionários , Índice de Gravidade de Doença , Transtornos Motores/induzido quimicamente , Neuralgia/induzido quimicamente , Adulto , Sobreviventes de Câncer/psicologia
8.
Proc Natl Acad Sci U S A ; 118(35)2021 08 31.
Artigo em Inglês | MEDLINE | ID: mdl-34413202

RESUMO

Inaccurate expression of the genetic code, also known as mistranslation, is an emerging paradigm in microbial studies. Growing evidence suggests that many microbial pathogens can deliberately mistranslate their genetic code to help invade a host or evade host immune responses. However, discovering different capacities for deliberate mistranslation remains a challenge because each group of pathogens typically employs a unique mistranslation mechanism. In this study, we address this problem by studying duplicated genes of aminoacyl-transfer RNA (tRNA) synthetases. Using bacterial prolyl-tRNA synthetase (ProRS) genes as an example, we identify an anomalous ProRS isoform, ProRSx, and a corresponding tRNA, tRNAProA, that are predominately found in plant pathogens from Streptomyces species. We then show that tRNAProA has an unusual hybrid structure that allows this tRNA to mistranslate alanine codons as proline. Finally, we provide biochemical, genetic, and mass spectrometric evidence that cells which express ProRSx and tRNAProA can translate GCU alanine codons as both alanine and proline. This dual use of alanine codons creates a hidden proteome diversity due to stochastic Ala→Pro mutations in protein sequences. Thus, we show that important plant pathogens are equipped with a tool to alter the identity of their sense codons. This finding reveals the initial example of a natural tRNA synthetase/tRNA pair for dedicated mistranslation of sense codons.


Assuntos
Aminoacil-tRNA Sintetases/metabolismo , Códon , Escherichia coli/metabolismo , Código Genético , Biossíntese de Proteínas , Aminoacil-RNA de Transferência/metabolismo , Streptomyces/metabolismo , Alanina/genética , Alanina/metabolismo , Sequência de Aminoácidos , Aminoacil-tRNA Sintetases/genética , Escherichia coli/genética , Escherichia coli/crescimento & desenvolvimento , Prolina/genética , Prolina/metabolismo , Aminoacil-RNA de Transferência/genética , Homologia de Sequência , Streptomyces/genética , Streptomyces/crescimento & desenvolvimento , Especificidade por Substrato
9.
Proc Natl Acad Sci U S A ; 117(30): 17924-17931, 2020 07 28.
Artigo em Inglês | MEDLINE | ID: mdl-32661175

RESUMO

Antibiotic resistance frequently evolves through fitness trade-offs in which the genetic alterations that confer resistance to a drug can also cause growth defects in resistant cells. Here, through experimental evolution in a microfluidics-based turbidostat, we demonstrate that antibiotic-resistant cells can be efficiently inhibited by amplifying the fitness costs associated with drug-resistance evolution. Using tavaborole-resistant Escherichia coli as a model, we show that genetic mutations in leucyl-tRNA synthetase (that underlie tavaborole resistance) make resistant cells intolerant to norvaline, a chemical analog of leucine that is mistakenly used by tavaborole-resistant cells for protein synthesis. We then show that tavaborole-sensitive cells quickly outcompete tavaborole-resistant cells in the presence of norvaline due to the amplified cost of the molecular defect of tavaborole resistance. This finding illustrates that understanding molecular mechanisms of drug resistance allows us to effectively amplify even small evolutionary vulnerabilities of resistant cells to potentially enhance or enable adaptive therapies by accelerating posttreatment competition between resistant and susceptible cells.


Assuntos
Evolução Biológica , Resistência a Medicamentos , Antibacterianos/farmacologia , Farmacorresistência Bacteriana , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Variação Genética , Modelos Moleculares , Conformação Proteica , Relação Estrutura-Atividade
10.
Mol Biol Evol ; 37(1): 124-133, 2020 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-31501901

RESUMO

Eukaryotic cells are divided into the nucleus and the cytosol, and, to enter the nucleus, proteins typically possess short signal sequences, known as nuclear localization signals (NLSs). Although NLSs have long been considered as features unique to eukaryotic proteins, we show here that similar or identical protein segments are present in ribosomal proteins from the Archaea. Specifically, the ribosomal proteins uL3, uL15, uL18, and uS12 possess NLS-type motifs that are conserved across all major branches of the Archaea, including the most ancient groups Microarchaeota and Diapherotrites, pointing to the ancient origin of NLS-type motifs in the Archaea. Furthermore, by using fluorescence microscopy, we show that the archaeal NLS-type motifs can functionally substitute eukaryotic NLSs and direct the transport of ribosomal proteins into the nuclei of human cells. Collectively, these findings illustrate that the origin of NLSs preceded the origin of the cell nucleus, suggesting that the initial function of NLSs was not related to intracellular trafficking, but possibly was to improve recognition of nucleic acids by cellular proteins. Overall, our study reveals rare evolutionary intermediates among archaeal cells that can help elucidate the sequence of events that led to the origin of the eukaryotic cell.


Assuntos
Proteínas Arqueais/química , Evolução Biológica , Células Eucarióticas , Sinais de Localização Nuclear , Proteínas Ribossômicas/química , Motivos de Aminoácidos , Sequência de Aminoácidos , Animais , Humanos
11.
Nucleic Acids Res ; 47(4): 2089-2100, 2019 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-30520988

RESUMO

During protein synthesis, ribosomes discriminate chirality of amino acids and prevent incorporation of D-amino acids into nascent proteins by slowing down the rate of peptide bond formation. Despite this phenomenon being known for nearly forty years, no structures have ever been reported that would explain the poor reactivity of D-amino acids. Here we report a 3.7Å-resolution crystal structure of a bacterial ribosome in complex with a D-aminoacyl-tRNA analog bound to the A site. Although at this resolution we could not observe individual chemical groups, we could unambiguously define the positions of the D-amino acid side chain and the amino group based on chemical restraints. The structure reveals that similarly to L-amino acids, the D-amino acid binds the ribosome by inserting its side chain into the ribosomal A-site cleft. This binding mode does not allow optimal nucleophilic attack of the peptidyl-tRNA by the reactive α-amino group of a D-amino acid. Also, our structure suggests that the D-amino acid cannot participate in hydrogen-bonding with the P-site tRNA that is required for the efficient proton transfer during peptide bond formation. Overall, our work provides the first mechanistic insight into the ancient mechanism that helps living cells ensure the stereochemistry of protein synthesis.


Assuntos
Peptídeos/química , Biossíntese de Proteínas/genética , Aminoacil-RNA de Transferência/química , Ribossomos/química , Aminoácidos/química , Aminoácidos/genética , Sítios de Ligação/genética , Domínio Catalítico/genética , Cristalografia por Raios X , Ligação de Hidrogênio , Peptídeos/genética , Aminoacil-RNA de Transferência/genética , Ribossomos/genética
12.
Proc Natl Acad Sci U S A ; 115(49): E11505-E11512, 2018 12 04.
Artigo em Inglês | MEDLINE | ID: mdl-30455292

RESUMO

Intracellular organisms, such as obligate parasites and endosymbionts, typically possess small genomes due to continuous genome decay caused by an environment with alleviated natural selection. Previously, a few species with highly reduced genomes, including the intracellular pathogens Mycoplasma and Microsporidia, have been shown to carry degenerated editing domains in aminoacyl-tRNA synthetases. These defects in the protein synthesis machinery cause inaccurate translation of the genetic code, resulting in significant statistical errors in protein sequences that are thought to help parasites to escape immune response of a host. In this study we analyzed 10,423 complete bacterial genomes to assess conservation of the editing domains in tRNA synthetases, including LeuRS, IleRS, ValRS, ThrRS, AlaRS, and PheRS. We found that, while the editing domains remain intact in free-living species, they are degenerated in the overwhelming majority of host-restricted bacteria. Our work illustrates that massive genome erosion triggered by an intracellular lifestyle eradicates one of the most fundamental components of a living cell: the system responsible for proofreading of amino acid selection for protein synthesis. This finding suggests that inaccurate translation of the genetic code might be a general phenomenon among intercellular organisms with reduced genomes.


Assuntos
Bactérias/genética , Bactérias/metabolismo , Sequência de Aminoácidos , Aminoácidos , Sequência Conservada , Regulação Bacteriana da Expressão Gênica/fisiologia , Biossíntese de Proteínas , Domínios Proteicos , Edição de RNA
13.
Proc Natl Acad Sci U S A ; 115(27): E6245-E6253, 2018 07 03.
Artigo em Inglês | MEDLINE | ID: mdl-29915081

RESUMO

Microsporidia are parasitic fungi-like organisms that invade the interior of living cells and cause chronic disorders in a broad range of animals, including humans. These pathogens have the tiniest known genomes among eukaryotic species, for which they serve as a model for exploring the phenomenon of genome reduction in obligate intracellular parasites. Here we report a case study to show an apparent effect of overall genome reduction on the primary structure and activity of aminoacyl-tRNA synthetases, indispensable cellular proteins required for protein synthesis. We find that most microsporidian synthetases lack regulatory and eukaryote-specific appended domains and have a high degree of sequence variability in tRNA-binding and catalytic domains. In one synthetase, LeuRS, an apparent sequence degeneration annihilates the editing domain, a catalytic center responsible for the accurate selection of leucine for protein synthesis. Unlike accurate LeuRS synthetases from other eukaryotic species, microsporidian LeuRS is error-prone: apart from leucine, it occasionally uses its near-cognate substrates, such as norvaline, isoleucine, valine, and methionine. Mass spectrometry analysis of the microsporidium Vavraia culicis proteome reveals that nearly 6% of leucine residues are erroneously replaced by other amino acids. This remarkably high frequency of mistranslation is not limited to leucine codons and appears to be a general property of protein synthesis in microsporidian parasites. Taken together, our findings reveal that the microsporidian protein synthesis machinery is editing-deficient, and that the proteome of microsporidian parasites is more diverse than would be anticipated based on their genome sequences.


Assuntos
Aminoacil-tRNA Sintetases , Proteínas Fúngicas , Genoma Fúngico , Microsporida , Biossíntese de Proteínas/fisiologia , Aminoacil-tRNA Sintetases/genética , Aminoacil-tRNA Sintetases/metabolismo , Proteínas Fúngicas/biossíntese , Proteínas Fúngicas/genética , Microsporida/genética , Microsporida/metabolismo , RNA Fúngico/genética , RNA Fúngico/metabolismo , RNA de Transferência/genética , RNA de Transferência/metabolismo
14.
Mol Biol Evol ; 35(7): 1588-1598, 2018 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-29529322

RESUMO

Ribosomal proteins are indispensable components of a living cell, and yet their structures are remarkably diverse in different species. Here we use manually curated structural alignments to provide a comprehensive catalog of structural variations in homologous ribosomal proteins from bacteria, archaea, eukaryotes, and eukaryotic organelles. By resolving numerous ambiguities and errors of automated structural and sequence alignments, we uncover a whole new class of structural variations that reside within seemingly conserved segments of ribosomal proteins. We then illustrate that these variations reflect an apparent adaptation of ribosomal proteins to the specific environments and lifestyles of living species. Finally, we show that most of these structural variations reside within nonglobular extensions of ribosomal proteins-protein segments that are thought to promote ribosome biogenesis by stabilizing the proper folding of ribosomal RNA. We show that although the extensions are thought to be the most ancient peptides on our planet, they are in fact the most rapidly evolving and most structurally and functionally diverse segments of ribosomal proteins. Overall, our work illustrates that, despite being long considered as slowly evolving and highly conserved, ribosomal proteins are more complex and more specialized than is generally recognized.


Assuntos
Archaea/química , Bactérias/química , Eucariotos/química , Proteínas Ribossômicas/química , Sequência de Aminoácidos , Estrutura Terciária de Proteína
15.
Phys Chem Chem Phys ; 21(33): 18386-18392, 2019 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-31403642

RESUMO

Post-combustion carbon capture by amine scrubbing is the most frequently used process to remove CO2 from pulverized coal-fired power plants and also biogas flue gas streams. The quest for novel absorbents for CO2 capture with improved properties requires insight into the properties of the CO2-loaded mixed solutions. A comparative molecular dynamics study of the product state solutions, with chemically-bound CO2 of standard monoethanolamine (MEA) and the new alternative 4-diethylamino-2-butanol (DEAB) at various CO2-loadings yields solvent properties in good agreement with experimental data. The concentration of all post-reaction species in solution was based on experimental equilibria distributions. The data generated provide detailed insight into the properties of reactive mixed alkanolamine solutions. The liquid structure of aqueous MEA solutions undergoes only minor changes when absorbing CO2. The diffusion coefficients of all molecular species, however, decrease significantly with increasing CO2-loadings. The large hydrophobic clusters formed in the reactant state by DEAB molecules in water prior to CO2 binding significantly decrease in size and structure upon CO2 absorption. The diffusion coefficients of all components decrease with increasing CO2-loading, whereas the pre-reaction alkanolamine DEAB shows an increase in diffusion coefficient. This structural and kinetic information supports the molecular design and further development of novel compounds and provides data for a global process simulation and optimization.

16.
Int J Mol Sci ; 20(8)2019 Apr 19.
Artigo em Inglês | MEDLINE | ID: mdl-31010123

RESUMO

In the past two decades, tRNA molecules and their corresponding aminoacyl-tRNA synthetases (aaRS) have been extensively used in synthetic biology to genetically encode post-translationally modified and unnatural amino acids. In this review, we briefly examine one fundamental requirement for the successful application of tRNA/aaRS pairs for expanding the genetic code. This requirement is known as "orthogonality"-the ability of a tRNA and its corresponding aaRS to interact exclusively with each other and avoid cross-reactions with additional types of tRNAs and aaRSs in a given organism.


Assuntos
Aminoacil-tRNA Sintetases/genética , Código Genético , RNA de Transferência/genética , Aminoacil-tRNA Sintetases/química , Engenharia Genética , RNA de Transferência/química , Biologia Sintética
17.
EMBO Rep ; 17(12): 1776-1784, 2016 12.
Artigo em Inglês | MEDLINE | ID: mdl-27827794

RESUMO

Proline is an amino acid with a unique cyclic structure that facilitates the folding of many proteins, but also impedes the rate of peptide bond formation by the ribosome. As a ribosome substrate, proline reacts markedly slower when compared with other amino acids both as a donor and as an acceptor of the nascent peptide. Furthermore, synthesis of peptides with consecutive proline residues triggers ribosome stalling. Here, we report crystal structures of the eukaryotic ribosome bound to analogs of mono- and diprolyl-tRNAs. These structures provide a high-resolution insight into unique properties of proline as a ribosome substrate. They show that the cyclic structure of proline residue prevents proline positioning in the amino acid binding pocket and affects the nascent peptide chain position in the ribosomal peptide exit tunnel. These observations extend current knowledge of the protein synthesis mechanism. They also revise an old dogma that amino acids bind the ribosomal active site in a uniform way by showing that proline has a binding mode distinct from other amino acids.


Assuntos
Peptídeos/metabolismo , Prolina/metabolismo , Biossíntese de Proteínas , Ribossomos/química , Sequência de Aminoácidos , Cristalografia por Raios X , Escherichia coli/genética , Modelos Moleculares , Peptídeos/química , Prolina/química , Ligação Proteica , RNA de Transferência de Prolina/metabolismo , Ribossomos/metabolismo
18.
Nucleic Acids Res ; 44(10): 4978-87, 2016 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-27079977

RESUMO

Cisplatin is a widely prescribed anticancer drug, which triggers cell death by covalent binding to a broad range of biological molecules. Among cisplatin targets, cellular RNAs remain the most poorly characterized molecules. Although cisplatin was shown to inactivate essential RNAs, including ribosomal, spliceosomal and telomeric RNAs, cisplatin binding sites in most RNA molecules are unknown, and therefore it remains challenging to study how modifications of RNA by cisplatin contributes to its toxicity. Here we report a 2.6Å-resolution X-ray structure of cisplatin-modified 70S ribosome, which describes cisplatin binding to the ribosome and provides the first nearly atomic model of cisplatin-RNA complex. We observe nine cisplatin molecules bound to the ribosome and reveal consensus structural features of the cisplatin-binding sites. Two of the cisplatin molecules modify conserved functional centers of the ribosome-the mRNA-channel and the GTPase center. In the mRNA-channel, cisplatin intercalates between the ribosome and the messenger RNA, suggesting that the observed inhibition of protein synthesis by cisplatin is caused by impaired mRNA-translocation. Our structure provides an insight into RNA targeting and inhibition by cisplatin, which can help predict cisplatin-binding sites in other cellular RNAs and design studies to elucidate a link between RNA modifications by cisplatin and cisplatin toxicity.


Assuntos
Antineoplásicos/química , Cisplatino/química , RNA Ribossômico/química , Ribossomos/química , Adenina/química , Antibacterianos/química , Antineoplásicos/metabolismo , Sítios de Ligação , Cisplatino/metabolismo , Cumarínicos/química , Cristalografia por Raios X , Guanina/química , Modelos Moleculares , Inibidores da Síntese de Ácido Nucleico/química , RNA Ribossômico/metabolismo , Ribossomos/metabolismo
19.
Int J Mol Sci ; 19(12)2018 Dec 19.
Artigo em Inglês | MEDLINE | ID: mdl-30572624

RESUMO

Microsporidia are fungi-like parasites that have the smallest known eukaryotic genome, and for that reason they are used as a model to study the phenomenon of genome decay in parasitic forms of life. Similar to other intracellular parasites that reproduce asexually in an environment with alleviated natural selection, Microsporidia experience continuous genome decay that is driven by Muller's ratchet-an evolutionary process of irreversible accumulation of deleterious mutations that lead to gene loss and the miniaturization of cellular components. Particularly, Microsporidia have remarkably small ribosomes in which the rRNA is reduced to the minimal enzymatic core. In this study, we analyzed microsporidian ribosomes to study an apparent impact of Muller's ratchet on structure of RNA and protein molecules in parasitic forms of life. Through mass spectrometry of microsporidian proteome and analysis of microsporidian genomes, we found that massive rRNA reduction in microsporidian ribosomes appears to annihilate the binding sites for ribosomal proteins eL8, eL27, and eS31, suggesting that these proteins are no longer bound to the ribosome in microsporidian species. We then provided an evidence that protein eS31 is retained in Microsporidia due to its non-ribosomal function in ubiquitin biogenesis. Our study illustrates that, while Microsporidia carry the same set of ribosomal proteins as non-parasitic eukaryotes, some ribosomal proteins are no longer participating in protein synthesis in Microsporidia and they are preserved from genome decay by having extra-ribosomal functions. More generally, our study shows that many components of parasitic cells, which are identified by automated annotation of pathogenic genomes, may lack part of their biological functions due to continuous genome decay.


Assuntos
Espaço Intracelular/parasitologia , Microsporídios/metabolismo , Parasitos/metabolismo , Ribossomos/metabolismo , Sequência de Aminoácidos , Animais , Sítios de Ligação , Evolução Biológica , Proteínas de Protozoários/química , Proteínas de Protozoários/metabolismo , RNA Ribossômico/metabolismo , Proteínas Ribossômicas/metabolismo
20.
Eur J Nutr ; 53(3): 723-9, 2014 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-23975326

RESUMO

PURPOSE: Small fat droplets infused into the gut reduce food intake and hunger more than bigger ones, at levels as low as 6 g, and these effects are hypothesized to occur via satiety hormones such as cholecystokinin. It is, however, unknown whether the effect of droplet size would persist after oral consumption. It is also unknown whether an even smaller droplet size can affect hunger and food intake and at what minimum amount of fat. Therefore, the aim of the study was to test the effect of very fine fat droplets on satiety and food intake in two different quantities. METHODS: In a balanced-order 4-way crossover design, 24 volunteers consumed a fat-free meal replacement drink with either 5 or 9 g oil (rapeseed) and either 3 or 0.1 µm droplet size. Appetite scores and plasma cholecystokinin levels (in n = 12 subset) were measured for 180 min, when food intake was assessed during an ad libitum meal. Data were analyzed by ANCOVA, followed by Dunnett's test and paired t test. The behavior of the emulsions was also characterized in a simulated gastrointestinal model. RESULTS: Despite faster in vitro lipolysis of the smallest droplets, neither droplet size nor fat amount affected satiety or food intake. From t = 45-150 min, cholecystokinin response was 50% higher (P < 0.05) after the 0.1 versus 3 µm, but only with 9 g fat. CONCLUSION: When this particular fat at these amounts is delivered in a meal replacement drink, droplet size does not influence appetite or food intake. This effect is independent of the amount of fat or plasma cholecystokinin changes.


Assuntos
Bebidas , Desjejum , Colecistocinina/sangue , Gorduras na Dieta/uso terapêutico , Alimentos Especializados , Sobrepeso/dietoterapia , Regulação para Cima , Adulto , Bebidas/efeitos adversos , Bebidas/análise , Índice de Massa Corporal , Colecistocinina/metabolismo , Estudos Cross-Over , Dieta Redutora/efeitos adversos , Dieta Redutora/métodos , Gorduras na Dieta/administração & dosagem , Gorduras na Dieta/efeitos adversos , Gorduras na Dieta/metabolismo , Digestão , Método Duplo-Cego , Emulsões , Ácidos Graxos Monoinsaturados , Feminino , Alimentos Especializados/efeitos adversos , Alimentos Especializados/análise , Humanos , Masculino , Pessoa de Meia-Idade , Países Baixos , Sobrepeso/sangue , Óleos de Plantas/administração & dosagem , Óleos de Plantas/efeitos adversos , Óleos de Plantas/metabolismo , Óleos de Plantas/uso terapêutico , Óleo de Brassica napus , Resposta de Saciedade , Adulto Jovem
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