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1.
Nat Commun ; 15(1): 3945, 2024 May 10.
Artículo en Inglés | MEDLINE | ID: mdl-38730238

RESUMEN

Proline-rich antimicrobial peptides (PrAMPs) inhibit bacterial protein biosynthesis by binding to the polypeptide exit tunnel (PET) near the peptidyl transferase center. Api137, an optimized derivative of honeybee PrAMP apidaecin, inhibits protein expression by trapping release factors (RFs), which interact with stop codons on ribosomes to terminate translation. This study uses cryo-EM, functional assays and molecular dynamic (MD) simulations to show that Api137 additionally occupies a second binding site near the exit of the PET and can repress translation independently of RF-trapping. Api88, a C-terminally amidated (-CONH2) analog of Api137 (-COOH), binds to the same sites, occupies a third binding pocket and interferes with the translation process presumably without RF-trapping. In conclusion, apidaecin-derived PrAMPs inhibit bacterial ribosomes by multimodal mechanisms caused by minor structural changes and thus represent a promising pool for drug development efforts.


Asunto(s)
Péptidos Catiónicos Antimicrobianos , Simulación de Dinámica Molecular , Ribosomas , Ribosomas/metabolismo , Péptidos Catiónicos Antimicrobianos/metabolismo , Péptidos Catiónicos Antimicrobianos/química , Péptidos Catiónicos Antimicrobianos/farmacología , Biosíntesis de Proteínas , Sitios de Unión , Microscopía por Crioelectrón , Escherichia coli/metabolismo , Escherichia coli/genética , Escherichia coli/efectos de los fármacos , Factores de Terminación de Péptidos/metabolismo , Factores de Terminación de Péptidos/química , Factores de Terminación de Péptidos/genética , Unión Proteica , Péptidos Antimicrobianos/química , Péptidos Antimicrobianos/metabolismo , Péptidos Antimicrobianos/farmacología
2.
Genes (Basel) ; 15(4)2024 Mar 29.
Artículo en Inglés | MEDLINE | ID: mdl-38674371

RESUMEN

The adaptor protein 4 (AP-4) constitutes a conserved hetero-tetrameric complex within the family of adaptor protein (AP) complex, crucial for the signal-mediated trafficking of integral membrane proteins. Mutations affecting all subunits of the AP-4 complex have been linked to autosomal-recessive cerebral palsy and a complex hereditary spastic paraparesis (HSP) phenotype. Our report details the case of a 14-year-old boy born to consanguineous parents, presenting psychomotor delay, severe intellectual disability, microcephaly, and trigonocephaly. Despite a history of febrile seizures, subsequent years were devoid of seizures, with normal EEG. Exome sequencing revealed pathogenic variants in both the AP4B1 and ERF genes. Significantly, the patient exhibited features associated with AP4B1 mutations, including distinctive traits such as cranial malformations. The ERF gene variant, linked to craniosynostosis, likely contributes to the observed trigonocephaly. This case represents the initial documentation of a concurrent mutation in the AP4B1 and ERF genes, underscoring the critical role of exome analysis in unraveling complex phenotypes. Understanding these complex genotypes offers valuable insights into broader syndromic conditions, facilitating comprehensive patient management.


Asunto(s)
Complejo 4 de Proteína Adaptadora , Mutación , Factores de Terminación de Péptidos , Fenotipo , Proteínas Represoras , Humanos , Masculino , Adolescente , Factores de Terminación de Péptidos/genética , Complejo 4 de Proteína Adaptadora/genética , Discapacidad Intelectual/genética , Discapacidad Intelectual/patología , Secuenciación del Exoma , Microcefalia/genética , Microcefalia/patología , Craneosinostosis/genética , Craneosinostosis/patología
3.
Nature ; 626(8001): 1125-1132, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38355796

RESUMEN

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.


Asunto(s)
Proteínas Bacterianas , Respuesta al Choque por Frío , Factores de Terminación de Péptidos , Biosíntesis de Proteínas , Psychrobacter , Proteínas Ribosómicas , Ribosomas , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Proteínas Bacterianas/ultraestructura , Factor Tu de Elongación Peptídica/química , Factor Tu de Elongación Peptídica/metabolismo , Factor Tu de Elongación Peptídica/ultraestructura , Proteínas Ribosómicas/química , Proteínas Ribosómicas/genética , Proteínas Ribosómicas/metabolismo , Proteínas Ribosómicas/ultraestructura , Ribosomas/química , Ribosomas/metabolismo , Ribosomas/ultraestructura , Psychrobacter/química , Psychrobacter/genética , Psychrobacter/metabolismo , Psychrobacter/ultraestructura , Microscopía por Crioelectrón , Factores de Terminación de Péptidos/química , Factores de Terminación de Péptidos/genética , Factores de Terminación de Péptidos/metabolismo , Factores de Terminación de Péptidos/ultraestructura
4.
PLoS Genet ; 20(2): e1011194, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38422160

RESUMEN

Misfolded proteins are usually refolded to their functional conformations or degraded by quality control mechanisms. When misfolded proteins evade quality control, they can be sequestered to specific sites within cells to prevent the potential dysfunction and toxicity that arises from protein aggregation. Btn2 and Hsp42 are compartment-specific sequestrases that play key roles in the assembly of these deposition sites. Their exact intracellular functions and substrates are not well defined, particularly since heat stress sensitivity is not observed in deletion mutants. We show here that Btn2 and Hsp42 are required for tolerance to oxidative stress conditions induced by exposure to hydrogen peroxide. Btn2 and Hsp42 act to sequester oxidized proteins into defined PQC sites following ROS exposure and their absence leads to an accumulation of protein aggregates. The toxicity of protein aggregate accumulation causes oxidant sensitivity in btn2 hsp42 sequestrase mutants since overexpression of the Hsp104 disaggregase rescues oxidant tolerance. We have identified the Sup35 translation termination factor as an in vivo sequestrase substrate and show that Btn2 and Hsp42 act to suppress oxidant-induced formation of the yeast [PSI+] prion, which is the amyloid form of Sup35. [PSI+] prion formation in sequestrase mutants does not require IPOD (insoluble protein deposit) localization which is the site where amyloids are thought to undergo fragmentation and seeding to propagate their heritable prion form. Instead, both amorphous and amyloid Sup35 aggregates are increased in btn2 hsp42 mutants consistent with the idea that prion formation occurs at multiple intracellular sites during oxidative stress conditions in the absence of sequestrase activity. Taken together, our data identify protein sequestration as a key antioxidant defence mechanism that functions to mitigate the damaging consequences of protein oxidation-induced aggregation.


Asunto(s)
Priones , Proteínas de Saccharomyces cerevisiae , Agregado de Proteínas/genética , Priones/genética , Priones/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Chaperonas Moleculares/genética , Chaperonas Moleculares/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Estrés Oxidativo/genética , Amiloide/metabolismo , Oxidantes/farmacología , Oxidantes/metabolismo , Factores de Terminación de Péptidos/genética , Factores de Terminación de Péptidos/metabolismo
5.
Nat Chem Biol ; 20(5): 605-614, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38267667

RESUMEN

In response to environmental changes, cells flexibly and rapidly alter gene expression through translational controls. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is downregulated in response to an excess amount of boric acid in the environment through upstream open reading frames (uORFs) that consist of only AUG and stop codons. However, the molecular details of how this minimum uORF controls translation of the downstream main ORF in a boric acid-dependent manner have remained unclear. Here, by combining ribosome profiling, translation complex profile sequencing, structural analysis with cryo-electron microscopy and biochemical assays, we show that the 80S ribosome assembled at AUG-stop migrates into the subsequent RNA segment, followed by downstream translation initiation, and that boric acid impedes this process by the stable confinement of eukaryotic release factor 1 on the 80S ribosome on AUG-stop. Our results provide molecular insight into translation regulation by a minimum and environment-responsive uORF.


Asunto(s)
Ácidos Bóricos , Biosíntesis de Proteínas , Ribosomas , Ribosomas/metabolismo , Ácidos Bóricos/química , Factores de Terminación de Péptidos/metabolismo , Factores de Terminación de Péptidos/química , Factores de Terminación de Péptidos/genética , Microscopía por Crioelectrón , Sistemas de Lectura Abierta , Codón de Terminación , Arabidopsis/metabolismo , Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/genética
6.
Cell Rep ; 42(7): 112809, 2023 07 25.
Artículo en Inglés | MEDLINE | ID: mdl-37450369

RESUMEN

Abscisic acid (ABA) is involved in lateral root (LR) development, but how ABA signaling interacts with auxin signaling to regulate LR formation is not well understood. Here, we report that ABA-responsive ERF1 mediates the crosstalk between ABA and auxin signaling to regulate Arabidopsis LR emergence. ABI3 is a negative factor in LR emergence and transcriptionally activates ERF1 by binding to its promoter, and reciprocally, ERF1 activates ABI3, which forms a regulatory loop that enables rapid signal amplification. Notably, ABI3 physically interacts with ERF1, reducing the cis element-binding activities of both ERF1 and ABI3 and thus attenuating the expression of ERF1-/ABI3-regulated genes involved in LR emergence and ABA signaling, such as PIN1, AUX1, ARF7, and ABI5, which may provide a molecular rheostat to avoid overamplification of auxin and ABA signaling. Taken together, our findings identify the role of the ABI3-ERF1 module in mediating crosstalk between ABA and auxin signaling in LR emergence.


Asunto(s)
Proteínas de Arabidopsis , Arabidopsis , Factores de Terminación de Péptidos , Factores de Transcripción , Ácido Abscísico/metabolismo , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Regulación de la Expresión Génica de las Plantas , Ácidos Indolacéticos/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Factores de Terminación de Péptidos/genética , Factores de Terminación de Péptidos/metabolismo
7.
Biol Chem ; 404(8-9): 769-779, 2023 07 26.
Artículo en Inglés | MEDLINE | ID: mdl-37377370

RESUMEN

Mitochondria are the essential players in eukaryotic ATP production by oxidative phosphorylation, which relies on the maintenance and accurate expression of the mitochondrial genome. Even though the basic principles of translation are conserved due to the descendance from a bacterial ancestor, some deviations regarding translation factors as well as mRNA characteristics and the applied genetic code are present in human mitochondria. Together, these features are certain challenges during translation the mitochondrion has to handle. Here, we discuss the current knowledge regarding mitochondrial translation focusing on the termination process and the associated quality control mechanisms. We describe how mtRF1a resembles bacterial RF1 mechanistically and summarize in vitro and recent in vivo data leading to the conclusion of mtRF1a being the major mitochondrial release factor. On the other hand, we discuss the ongoing debate about the function of the second codon-dependent mitochondrial release factor mtRF1 regarding its role as a specialized termination factor. Finally, we link defects in mitochondrial translation termination to the activation of mitochondrial rescue mechanisms highlighting the importance of ribosome-associated quality control for sufficient respiratory function and therefore for human health.


Asunto(s)
Factores de Terminación de Péptidos , Biosíntesis de Proteínas , Humanos , Codón de Terminación/metabolismo , Especificidad por Sustrato , Factores de Terminación de Péptidos/genética , Factores de Terminación de Péptidos/metabolismo , Mitocondrias/metabolismo
8.
Mol Biol Evol ; 40(4)2023 04 04.
Artículo en Inglés | MEDLINE | ID: mdl-36952281

RESUMEN

Bifunctional stop codons that have both translation and termination functions in the same species are important for understanding the evolution and function of genetic codes in living organisms. Considering the high frequency of bifunctional codons but limited number of available genomes in ciliates, we de novo sequenced seven representative ciliate genomes to explore the evolutionary history of stop codons. We further propose a stop codon reassignment quantification method (stopCR) that can identify bifunctional codons and measure their frequencies in various eukaryotic organisms. Using our newly developed method, we found two previously undescribed genetic codes, illustrating the prevalence of bifunctional stop codons in ciliates. Overall, evolutionary genomic analyses suggest that gain or loss of reassigned stop codons in ciliates is shaped by their living environment, the eukaryotic release factor 1, and suppressor tRNAs. This study provides novel clues about the functional diversity and evolutionary history of stop codons in eukaryotic organisms.


Asunto(s)
Cilióforos , Factores de Terminación de Péptidos , Codón de Terminación , Factores de Terminación de Péptidos/genética , Cilióforos/genética , Código Genético , Secuencia de Bases
9.
Nature ; 613(7945): 751-758, 2023 01.
Artículo en Inglés | MEDLINE | ID: mdl-36631608

RESUMEN

Cognate tRNAs deliver specific amino acids to translating ribosomes according to the standard genetic code, and three codons with no cognate tRNAs serve as stop codons. Some protists have reassigned all stop codons as sense codons, neglecting this fundamental principle1-4. Here we analyse the in-frame stop codons in 7,259 predicted protein-coding genes of a previously undescribed trypanosomatid, Blastocrithidia nonstop. We reveal that in this species in-frame stop codons are underrepresented in genes expressed at high levels and that UAA serves as the only termination codon. Whereas new tRNAsGlu fully cognate to UAG and UAA evolved to reassign these stop codons, the UGA reassignment followed a different path through shortening the anticodon stem of tRNATrpCCA from five to four base pairs (bp). The canonical 5-bp tRNATrp recognizes UGG as dictated by the genetic code, whereas its shortened 4-bp variant incorporates tryptophan also into in-frame UGA. Mimicking this evolutionary twist by engineering both variants from B. nonstop, Trypanosoma brucei and Saccharomyces cerevisiae and expressing them in the last two species, we recorded a significantly higher readthrough for all 4-bp variants. Furthermore, a gene encoding B. nonstop release factor 1 acquired a mutation that specifically restricts UGA recognition, robustly potentiating the UGA reassignment. Virtually the same strategy has been adopted by the ciliate Condylostoma magnum. Hence, we describe a previously unknown, universal mechanism that has been exploited in unrelated eukaryotes with reassigned stop codons.


Asunto(s)
Anticodón , Codón de Terminación , Células Eucariotas , Código Genético , Mutación , Factores de Terminación de Péptidos , ARN de Transferencia , Anticodón/química , Anticodón/genética , Anticodón/metabolismo , Cilióforos/genética , Codón de Terminación/genética , Código Genético/genética , Factores de Terminación de Péptidos/genética , Factores de Terminación de Péptidos/metabolismo , ARN de Transferencia/genética , ARN de Transferencia/metabolismo , ARN de Transferencia de Triptófano/genética , Saccharomyces cerevisiae/genética , ARN de Transferencia de Ácido Glutámico/genética , Trypanosoma brucei brucei/genética
10.
Viruses ; 14(10)2022 09 30.
Artículo en Inglés | MEDLINE | ID: mdl-36298715

RESUMEN

Yeast prions are protein-based transmissible elements, most of which are amyloids. The chaperone protein network in yeast is inexorably linked to the spreading of prions during cell division by fragmentation of amyloid prion aggregates. Specifically, the core "prion fragmentation machinery" includes the proteins Hsp104, Hsp70 and the Hsp40/J-domain protein (JDP) Sis1. Numerous novel amyloid-forming proteins have been created and examined in the yeast system and occasionally these amyloids are also capable of continuous Hsp104-dependent propagation in cell populations, forming synthetic prions. However, additional chaperone requirements, if any, have not been determined. Here, we report the first instances of a JDP-Hsp70 system requirement for the propagation of synthetic prions. We utilized constructs from a system of engineered prions with prion-forming domains (PrDs) consisting of a polyQ stretch interrupted by a single heterologous amino acid interspersed every fifth residue. These "polyQX" PrDs are fused to the MC domains of Sup35, creating chimeric proteins of which a subset forms synthetic prions in yeast. For four of these prions, we show that SIS1 repression causes prion loss in a manner consistent with Sis1's known role in prion fragmentation. PolyQX prions were sensitive to Sis1 expression levels to differing degrees, congruent with the variability observed among native prions. Our results expand the scope known Sis1 functionality, demonstrating that Sis1 acts on amyloids broadly, rather than through specific protein-protein interactions with individual yeast prion-forming proteins.


Asunto(s)
Priones , Proteínas de Saccharomyces cerevisiae , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Priones/química , Proteínas de Saccharomyces cerevisiae/química , Chaperonas Moleculares/metabolismo , Proteínas HSP70 de Choque Térmico/metabolismo , Amiloide/química , Proteínas Amiloidogénicas/metabolismo , Aminoácidos/metabolismo , Proteínas Recombinantes de Fusión/metabolismo , Proteínas de Choque Térmico/genética , Proteínas de Choque Térmico/metabolismo , Factores de Terminación de Péptidos/genética , Factores de Terminación de Péptidos/metabolismo
11.
Nat Commun ; 13(1): 6406, 2022 10 27.
Artículo en Inglés | MEDLINE | ID: mdl-36302763

RESUMEN

Translation termination requires release factors that read a STOP codon in the decoding center and subsequently facilitate the hydrolysis of the nascent peptide chain from the peptidyl tRNA within the ribosome. In human mitochondria eleven open reading frames terminate in the standard UAA or UAG STOP codon, which can be recognized by mtRF1a, the proposed major mitochondrial release factor. However, two transcripts encoding for COX1 and ND6 terminate in the non-conventional AGA or AGG codon, respectively. How translation termination is achieved in these two cases is not known. We address this long-standing open question by showing that the non-canonical release factor mtRF1 is a specialized release factor that triggers COX1 translation termination, while mtRF1a terminates the majority of other mitochondrial translation events including the non-canonical ND6. Loss of mtRF1 leads to isolated COX deficiency and activates the mitochondrial ribosome-associated quality control accompanied by the degradation of COX1 mRNA to prevent an overload of the ribosome rescue system. Taken together, these results establish the role of mtRF1 in mitochondrial translation, which had been a mystery for decades, and lead to a comprehensive picture of translation termination in human mitochondria.


Asunto(s)
Ciclooxigenasa 1 , Proteínas Mitocondriales , Ribosomas Mitocondriales , Factores de Terminación de Péptidos , Humanos , Codón de Terminación/genética , Codón de Terminación/metabolismo , Ribosomas Mitocondriales/metabolismo , Factores de Terminación de Péptidos/genética , Factores de Terminación de Péptidos/metabolismo , Biosíntesis de Proteínas , Control de Calidad , Ribosomas/genética , Ribosomas/metabolismo , Proteínas Mitocondriales/genética , Proteínas Mitocondriales/metabolismo , Ciclooxigenasa 1/genética
12.
J Biol Chem ; 298(8): 102143, 2022 08.
Artículo en Inglés | MEDLINE | ID: mdl-35714774

RESUMEN

Prion-like self-perpetuating conformational conversion of proteins is involved in both transmissible neurodegenerative diseases in mammals and non-Mendelian inheritance in yeast. The transmissibility of amyloid-like aggregates is dependent on the stoichiometry of chaperones such as heat shock proteins (Hsps), including disaggregases. To provide the mechanistic underpinnings of the formation and persistence of prefibrillar amyloid seeds, we investigated the role of substoichiometric Hsp104 on the in vitro amyloid aggregation of the prion domain (NM-domain) of Saccharomyces cerevisiae Sup35. At low substoichiometric concentrations, we show Hsp104 exhibits a dual role: it considerably accelerates the formation of prefibrillar species by shortening the lag phase but also prolongs their persistence by introducing unusual kinetic halts and delaying their conversion into mature amyloid fibers. Additionally, Hsp104-modulated amyloid species displayed a better seeding capability compared to NM-only amyloids. Using biochemical and biophysical tools coupled with site-specific dynamic readouts, we characterized the distinct structural and dynamical signatures of these amyloids. We reveal that Hsp104-remodeled amyloidogenic species are compositionally diverse in prefibrillar aggregates and are packed in a more ordered fashion compared to NM-only amyloids. Finally, we show these Hsp104-remodeled, conformationally distinct NM aggregates display an enhanced autocatalytic self-templating ability that might be crucial for phenotypic outcomes. Taken together, our results demonstrate that substoichiometric Hsp104 promotes compositional diversity and conformational modulations during amyloid formation, yielding effective prefibrillar seeds that are capable of driving prion-like Sup35 propagation. Our findings underscore the key functional and pathological roles of substoichiometric chaperones in prion-like propagation.


Asunto(s)
Proteínas de Choque Térmico , Factores de Terminación de Péptidos , Priones , Proteínas de Saccharomyces cerevisiae , Amiloide/química , Proteínas Amiloidogénicas/metabolismo , Proteínas de Choque Térmico/genética , Proteínas de Choque Térmico/metabolismo , Chaperonas Moleculares/metabolismo , Factores de Terminación de Péptidos/genética , Factores de Terminación de Péptidos/metabolismo , Priones/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo
13.
Mol Biol (Mosk) ; 56(2): 206-226, 2022.
Artículo en Ruso | MEDLINE | ID: mdl-35403616

RESUMEN

The review discusses the role that proteins interacting with the translation termination factors eRF1 and eRF3 play in the control of protein synthesis and prionization. These proteins interact not only with each other, but also with many other proteins involved in controlling the efficiency of translation termination, and associate translation termination with other cell processes. The termination of translation is directly related not only to translation re-initiation and ribosome recycling, but also to mRNA stability and protein quality control. This connection is ensured by the interaction of eRF1 and eRF3 with proteins participating in various cell metabolic processes, such as mRNA transport from the nucleus into the cytoplasm (Dbp5/DDX19 and Gle1), ribosome recycling (Rli1/ABCE1), mRNA degradation (Upf proteins), and translation initiation (Pab1/PABP). In addition to genetic control, there is epigenetic control of translation termination. This mechanism is associated with prion polymerization of the Sup35 protein to form the [PSI^(+)] prion. The maintenance of the [PSI^(+)] prion, like other yeast prions, requires the operation of a system of molecular chaperones and protein sorting factors. The review considers in detail the interaction of the translation termination factors with proteins involved in various cellular processes.


Asunto(s)
Priones , Proteínas de Saccharomyces cerevisiae , ARN Helicasas DEAD-box/metabolismo , Proteínas de Transporte Nucleocitoplasmático/metabolismo , Terminación de la Cadena Péptídica Traduccional/genética , Factores de Terminación de Péptidos/genética , Factores de Terminación de Péptidos/metabolismo , Proteínas de Unión a Poli(A)/metabolismo , Priones/genética , Priones/metabolismo , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo
14.
Proteins ; 90(7): 1468-1473, 2022 07.
Artículo en Inglés | MEDLINE | ID: mdl-35194850

RESUMEN

The heterologous overexpression states of prion proteins play a critical role in understanding the mechanisms of prion-related diseases. We report herein the identification of soluble monomer and complex states for a bakers' yeast prion, Sup35, when expressed in Escherichia coli. Two peaks are apparent with the elution of His-tagged Sup35 by imidazole from a Ni2+ affinity column. Peak I contains Sup35 in both monomer and aggregated states. Sup35 aggregate is abbreviated as C-aggregate and includes a non-fibril complex comprising Sup35 aggregate-HSP90-Dna K, ATP synthase ß unit (chain D), 30S ribosome subunit, and Omp F. The purified monomer and C-aggregate can remain stable for an extended period of time. Peak II contains Sup35 also in both monomer and aggregated (abbreviated as S-aggregate) states, but the aggregated states are caused by the formation of inter-Sup35 disulfide bonds. This study demonstrates that further assembly of Sup35 non-fibril C-aggregate can be interrupted by the chaperone repertoire system in E. coli.


Asunto(s)
Priones , Proteínas de Saccharomyces cerevisiae , Escherichia coli/genética , Escherichia coli/metabolismo , Factores de Terminación de Péptidos/genética , Factores de Terminación de Péptidos/metabolismo , Priones/química , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/química
15.
Mol Biol Evol ; 39(1)2022 01 07.
Artículo en Inglés | MEDLINE | ID: mdl-34751397

RESUMEN

In bacteria stop codons are recognized by one of two class I release factors (RF1) recognizing TAG, RF2 recognizing TGA, and TAA being recognized by both. Variation across bacteria in the relative abundance of RF1 and RF2 is thus hypothesized to select for different TGA/TAG usage. This has been supported by correlations between TAG:TGA ratios and RF1:RF2 ratios across multiple bacterial species, potentially also explaining why TAG usage is approximately constant despite extensive variation in GC content. It is, however, possible that stop codon trends are determined by other forces and that RF ratios adapt to stop codon usage, rather than vice versa. Here, we determine which direction of the causal arrow is the more parsimonious. Our results support the notion that RF1/RF2 ratios become adapted to stop codon usage as the same trends, notably the anomalous TAG behavior, are seen in contexts where RF1:RF2 ratios cannot be, or are unlikely to be, causative, that is, at 3'untranslated sites never used for translation termination, in intragenomic analyses, and across archaeal species (that possess only one RF1). We conclude that specifics of RF biology are unlikely to fully explain TGA/TAG relative usage. We discuss why the causal relationships for the evolution of synonymous stop codon usage might be different from those affecting synonymous sense codon usage, noting that transitions between TGA and TAG require two-point mutations one of which is likely to be deleterious.


Asunto(s)
Bacterias , Uso de Codones , Codón de Terminación , Factores de Terminación de Péptidos , Bacterias/genética , Composición de Base , Factores de Terminación de Péptidos/genética
16.
Genes (Basel) ; 12(12)2021 12 19.
Artículo en Inglés | MEDLINE | ID: mdl-34946968

RESUMEN

Protein synthesis (translation) is one of the fundamental processes occurring in the cells of living organisms. Translation can be divided into three key steps: initiation, elongation, and termination. In the yeast Saccharomyces cerevisiae, there are two translation termination factors, eRF1 and eRF3. These factors are encoded by the SUP45 and SUP35 genes, which are essential; deletion of any of them leads to the death of yeast cells. However, viable strains with nonsense mutations in both the SUP35 and SUP45 genes were previously obtained in several groups. The survival of such mutants clearly involves feedback control of premature stop codon readthrough; however, the exact molecular basis of such feedback control remain unclear. To investigate the genetic factors supporting the viability of these SUP35 and SUP45 nonsense mutants, we performed whole-genome sequencing of strains carrying mutant sup35-n and sup45-n alleles; while no common SNPs or indels were found in these genomes, we discovered a systematic increase in the copy number of the plasmids carrying mutant sup35-n and sup45-n alleles. We used the qPCR method which confirmed the differences in the relative number of SUP35 and SUP45 gene copies between strains carrying wild-type or mutant alleles of SUP35 and SUP45 genes. Moreover, we compare the number of copies of the SUP35 and SUP45 genes in strains carrying different nonsense mutant variants of these genes as a single chromosomal copy. qPCR results indicate that the number of mutant gene copies is increased compared to the wild-type control. In case of several sup45-n alleles, this was due to a disomy of the entire chromosome II, while for the sup35-218 mutation we observed a local duplication of a segment of chromosome IV containing the SUP35 gene. Taken together, our results indicate that gene amplification is a common mechanism of adaptation to nonsense mutations in release factor genes in yeast.


Asunto(s)
Amplificación de Genes , Factores de Terminación de Péptidos/genética , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/crecimiento & desarrollo , Adaptación Fisiológica , Cromosomas Fúngicos/genética , Codón sin Sentido , Saccharomyces cerevisiae/genética , Secuenciación Completa del Genoma
17.
Int J Mol Sci ; 22(23)2021 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-34884817

RESUMEN

Calcium deficiency usually causes accelerated quality deterioration in postharvest fruit, whereas the underlining mechanism is still unclear. Here, we report that calcium deficiency induced the development of bitter pit on the surface of apple peels compared with the healthy appearance in control apples during postharvest storage. Physiological analysis indicates that calcium-deficient peels contained higher levels of superoxide anion (O2•-), malondialdehyde (MDA), total phenol, flavonoid contents and polyphenol oxidase (PPO) activity, and reduced calcium, H2S production, anthocyanin, soluble protein content, and peroxidase (POD) activity compared with those in calcium-sufficient peels. The principal component analysis (PCA) results show that calcium content, ROS, and H2S production were the main factors between calcium-deficient and calcium-sufficient apple peels. Transcriptome data indicated that four calmodulin-like proteins (CMLs), seven AP2/ERFs, and three bHLHs transcripts were significantly differentially expressed in calcium-deficient apple peels. RT-qPCR and correlation analyses further revealed that CML5 expression was significantly positively correlated with the expression of ERF2/17, bHLH2, and H2S production related genes. In addition, transcriptional co-activation of CML5 by ERF2 and bHLH2 was demonstrated by apple transient expression assays and dual-luciferase reporter system experiments. Therefore, these findings provide a basis for studying the molecular mechanism of postharvest quality decline in calcium-deficient apples and the potential interaction between Ca2+ and endogenous H2S.


Asunto(s)
Sulfuro de Hidrógeno/metabolismo , Malus/metabolismo , Proteínas de Plantas/metabolismo , Especies Reactivas de Oxígeno/metabolismo , Transcriptoma , Antocianinas/metabolismo , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/genética , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/metabolismo , Calcio/metabolismo , Proteínas de Unión al Calcio/genética , Proteínas de Unión al Calcio/metabolismo , Catecol Oxidasa/metabolismo , Flavonoides/metabolismo , Almacenamiento de Alimentos , Frutas/genética , Frutas/metabolismo , Malus/genética , Factores de Terminación de Péptidos/genética , Factores de Terminación de Péptidos/metabolismo , Fenoles/metabolismo , Fenotipo , Proteínas de Plantas/genética , Análisis de Componente Principal
18.
Genetics ; 219(2)2021 10 02.
Artículo en Inglés | MEDLINE | ID: mdl-34849884

RESUMEN

[PSI+] is a prion of Saccharomyces cerevisiae Sup35, an essential ribosome release factor. In [PSI+] cells, most Sup35 is sequestered into insoluble amyloid aggregates. Despite this depletion, [PSI+] prions typically affect viability only modestly, so [PSI+] must balance sequestering Sup35 into prions with keeping enough Sup35 functional for normal growth. Sis1 is an essential J-protein regulator of Hsp70 required for the propagation of amyloid-based yeast prions. C-terminally truncated Sis1 (Sis1JGF) supports cell growth in place of wild-type Sis1. Sis1JGF also supports [PSI+] propagation, yet [PSI+] is highly toxic to cells expressing only Sis1JGF. We searched extensively for factors that mitigate the toxicity and identified only Sis1, suggesting Sis1 is uniquely needed to protect from [PSI+] toxicity. We find the C-terminal substrate-binding domain of Sis1 has a critical and transferable activity needed for the protection. In [PSI+] cells that express Sis1JGF in place of Sis1, Sup35 was less soluble and formed visibly larger prion aggregates. Exogenous expression of a truncated Sup35 that cannot incorporate into prions relieved [PSI+] toxicity. Together our data suggest that Sis1 has separable roles in propagating Sup35 prions and in moderating Sup35 aggregation that are crucial to the balance needed for the propagation of what otherwise would be lethal [PSI+] prions.


Asunto(s)
Proteínas del Choque Térmico HSP40/metabolismo , Factores de Terminación de Péptidos/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas del Choque Térmico HSP40/química , Proteínas del Choque Térmico HSP40/genética , Factores de Terminación de Péptidos/genética , Dominios Proteicos , Proteostasis , Saccharomyces cerevisiae , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/genética
19.
Nat Commun ; 12(1): 5340, 2021 09 09.
Artículo en Inglés | MEDLINE | ID: mdl-34504068

RESUMEN

Free L-tryptophan (L-Trp) stalls ribosomes engaged in the synthesis of TnaC, a leader peptide controlling the expression of the Escherichia coli tryptophanase operon. Despite extensive characterization, the molecular mechanism underlying the recognition and response to L-Trp by the TnaC-ribosome complex remains unknown. Here, we use a combined biochemical and structural approach to characterize a TnaC variant (R23F) with greatly enhanced sensitivity for L-Trp. We show that the TnaC-ribosome complex captures a single L-Trp molecule to undergo termination arrest and that nascent TnaC prevents the catalytic GGQ loop of release factor 2 from adopting an active conformation at the peptidyl transferase center. Importantly, the L-Trp binding site is not altered by the R23F mutation, suggesting that the relative rates of L-Trp binding and peptidyl-tRNA cleavage determine the tryptophan sensitivity of each variant. Thus, our study reveals a strategy whereby a nascent peptide assists the ribosome in detecting a small metabolite.


Asunto(s)
Escherichia coli/genética , Regulación Bacteriana de la Expresión Génica , Iniciación de la Cadena Peptídica Traduccional , Ribosomas/genética , Triptófano/química , Sustitución de Aminoácidos , Sitios de Unión , Microscopía por Crioelectrón , Escherichia coli/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Modelos Moleculares , Mutación , Operón , Terminación de la Cadena Péptídica Traduccional , Factores de Terminación de Péptidos/genética , Factores de Terminación de Péptidos/metabolismo , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Aminoacil-ARN de Transferencia/genética , Aminoacil-ARN de Transferencia/metabolismo , Ribosomas/metabolismo , Ribosomas/ultraestructura , Triptófano/metabolismo
20.
Nucleic Acids Res ; 49(19): 11181-11196, 2021 11 08.
Artículo en Inglés | MEDLINE | ID: mdl-34591963

RESUMEN

eIF3j is one of the eukaryotic translation factors originally reported as the labile subunit of the eukaryotic translation initiation factor eIF3. The yeast homolog of this protein, Hcr1, has been implicated in stringent AUG recognition as well as in controlling translation termination and stop codon readthrough. Using a reconstituted mammalian in vitro translation system, we showed that the human protein eIF3j is also important for translation termination. We showed that eIF3j stimulates peptidyl-tRNA hydrolysis induced by a complex of eukaryotic release factors, eRF1-eRF3. Moreover, in combination with the initiation factor eIF3, which also stimulates peptide release, eIF3j activity in translation termination increases. We found that eIF3j interacts with the pre-termination ribosomal complex, and eRF3 destabilises this interaction. In the solution, these proteins bind to each other and to other participants of translation termination, eRF1 and PABP, in the presence of GTP. Using a toe-printing assay, we determined the stage at which eIF3j functions - binding of release factors to the A-site of the ribosome before GTP hydrolysis. Based on these data, we assumed that human eIF3j is involved in the regulation of translation termination by loading release factors into the ribosome.


Asunto(s)
Factor 3 de Iniciación Eucariótica/genética , Terminación de la Cadena Péptídica Traduccional , Factores de Terminación de Péptidos/genética , Proteína I de Unión a Poli(A)/genética , Ribosomas/genética , Animales , Sistema Libre de Células , Clonación Molecular , Escherichia coli/genética , Escherichia coli/metabolismo , Factor 3 de Iniciación Eucariótica/química , Factor 3 de Iniciación Eucariótica/metabolismo , Expresión Génica , Regulación de la Expresión Génica , Vectores Genéticos/química , Vectores Genéticos/metabolismo , Guanosina Trifosfato/metabolismo , Humanos , Hidrólisis , Modelos Moleculares , Factores de Terminación de Péptidos/metabolismo , Proteína I de Unión a Poli(A)/metabolismo , Unión Proteica , Conformación Proteica , Isoformas de Proteínas , Conejos , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Reticulocitos/química , Reticulocitos/metabolismo , Ribosomas/metabolismo , Transducción de Señal
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