Translation Initiation Research Articles

A modified method for isolation of total RNA from leaves of sweetpotato (Ipomoea batatas (L.) Lam.)

ABSTRACT Sweetpotato (Ipomoea batatas (L.) Lam.), a dicotyledonous plant belonging to the Convolvulaceae family, is the world’s sixth most important food crop cultivated for its tubers which are rich in carbohydrates. Polysaccharide and polyphenol content are high in sweetpotato, which can negatively interfere with isolating high quality nucleic acid. This study aims to determine a rapid and reliable method for total RNA extraction from sweetpotato leaves. Three procedures using Cetyltrimethylammonium bromide–Lithium Chloride (CTAB- LiCl), TRIzol and TRIzol method with modifications were carried out in 100 mg of ground tissue. The quantity and quality of the isolated RNA were evaluated using a microvolume spectrophotometer at A260/280 and A260/230 and 1% agarose gel electrophoresis. The TRIzol method with modifications showed more intact RNA when compared to the other two methods with ratios of 1.862 ± 0.02 at A260/280 and 2.027 ± 0.02 at A260/230. RNA isolated was then subjected to DNase treatment and converted to cDNA by reverse-transcriptase-PCR. Internal control genes reported for sweetpotato, alpha-tubulin and translation initiation factor (eIF) were amplified successfully from the cDNA. Considering that only a few transcriptomic studies have been done on sweetpotato, which aid in crop improvement strategies, this method is ideal for total RNA isolation from sweetpotato leaves.

Translation elongation defects activate the Caenorhabditis elegans ZIP-2 bZIP transcription factor-mediated toxin defense.

The Caenorhabditis elegans bZIP transcription factor ZIP-2 is activated by toxins or mutations that inhibit translational elongation. The zip-2 DNA-binding protein is encoded in a downstream main open reading frame (mORF), but under normal translation elongation conditions only an upstream overlapping oORF -1 frameshifted from mORF is translated. Mutations or toxins that slow translational elongation, but not inhibitors of translational initiation or termination, activate ZIP-2. An mORF initiation codon mutation does not disrupt the normal zip-2 response to translational elongation defects, suggesting that zip-2 activation does not depend on this ATG. An mORF early termination mutant can be activated by strong translation elongation inhibition, suggesting that translation initiated upstream on oORF +1 frameshifts when elongation is inhibited to the mORF reading frame downstream of the stop codon to activate a fused oORF/mORF ZIP-2 transcription factor. The protein and DNA sequences of zip-2 oORF and mORF are conserved across the Caenorhabditis, suggesting selection for particular codons sensitive to translational elongation defects. Mutations that disrupt the oORF initiation codon constitutively activate zip-2, but not if the mORF initiation codon is also mutant, showing that zip-2 oORF competes with mORF for translational initiation. oORF initiation codon mutation-activated zip-2 slows C. elegans growth, and this slow growth is suppressed by a zip-2 null mutation. A zip-2 null mutant also strongly suppresses the growth arrest caused by translational elongation inhibitors. Thus, ZIP-2 is both a sensor of translational elongation attack, and a defense regulatory output via its activation of response genes.

Galeterone monotherapy in advanced pancreatic ductal adenocarcinoma: Results from a phase two trial.

744 Background: Advanced pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with limited treatment options. Dysregulated MAPK and PI3K signaling in PDAC activates the eukaryotic translational initiation complex, promoting cell growth, chemoresistance and metastatic spread (PMID 25593033). Galeterone, a novel steroidal anti-androgen, downregulates critical mediators of this complex including Mnk1/2 and phosphorylated eIF4E, thereby blocking epithelial-to-mesenchymal transition and NF-kB activity. In-vitro, galeterone exhibits anti-tumor activity both alone and in combination with gemcitabine and slows tumor growth in a MiaPaCa-2 xenograft murine model (PMID 28881737). We present results of the monotherapy arm from an ongoing phase two trial evaluating galeterone +/- gemcitabine for patients with advanced PDAC. Methods: Patients with locally advanced or metastatic PDAC, an ECOG performance status of 0-2 and adequate organ function, who progressed on two prior lines of systemic therapy were eligible. Galeterone was administered orally at 2550mg daily and gemcitabine intravenously at 1000mg/m 2 weekly for three weeks on 28-day cycle. The primary endpoint was radiographic response rate per RECIST v1.1 and secondary endpoints included progression-free survival (PFS), overall survival (OS) and safety. We used a Simon’s optimal two-stage design with a null hypothesis of p 0 =0.05 and one-sided alternative of p 1 =0.20 with an early stopping rule for futility in each arm. Due to poor accrual and no signal of activity, the galeterone alone arm closed after enrollment of four patients. Results: Four patients were evaluable for the primary endpoint. Ages ranged from 43 to 68. Two patients were male and two were female. Two patients were white and two were black; one patient was Hispanic/Latino. All patients had ECOG PS of 1. No patients had a radiographic response; the best response was progressive disease (PD). PFS from cycle 1 day 1 ranged from 0.9 – 1.7 months and overall survival between 1.8 – 3.6 months. The only treatment-related adverse events (TRAEs) were grade 1 dizziness and grade 3 fatigue in one patient each. There were no treatment-related serious adverse events. No patients required dose modification or discontinued due to TRAEs. Conclusions: Galeterone showed no clinical activity, but with a favorable safety profile, as a single-agent in heavily pre-treated patients with advanced PDAC. Activation of the Mnk-eIF4E axis mediates chemoresistance in PDAC and galeterone may prove more efficacious with gemcitabine. This combination arm is currently open to enrollment. Clinical trial information: NCT04098081 . Clinical outcomes with galeterone monotherapy in PDAC. Pt # Age Prior lines of Therapy Time on Treatment (days) Best Response PFS (months) OS(months) 1 68 4 46 PD 1.5 3.6 2 59 2 54 PD 1.7 3.8 3 55 2 47 PD 1.4 2 4 43 2 35 PD 0.9 1.8

EIF2α phosphorylation-ATF4 axis-mediated transcriptional reprogramming mitigates mitochondrial impairment during ER stress.

Eukaryotic translation initiation factor 2α (eIF2α) phosphorylation, which regulates all 3 unfolded protein response pathways, helps maintain cellular homeostasis and overcome endoplasmic reticulum (ER) stress through transcriptional and translational reprogramming. However, transcriptional regulation of mitochondrial homeostasis by eIF2α phosphorylation during ER stress is not fully understood. Here, we report that the eIF2α phosphorylation-activating transcription factor 4 (ATF4) axis is required for the expression of multiple transcription factors, including nuclear factor erythroid 2-related factor 2and its target genes responsible for mitochondrial homeostasis during ER stress. eIF2α phosphorylation-deficient (A/A) cells displayed dysregulated mitochondrial dynamics and mitochondrial DNA replication, decreased expression of oxidative phosphorylation complex proteins, and impaired mitochondrial functions during ER stress. ATF4 overexpression suppressed impairment of mitochondrial homeostasis in A/A cells during ER stress by promoting the expression of downstream transcription factors and their target genes. Our findings underscore the importance of the eIF2α phosphorylation-ATF4 axis for maintaining mitochondrial homeostasis through transcriptional reprogramming during ER stress.

Knowledge translation initiatives at the Transitional Pain Service: insights from healthcare provider outreach and patient education

Evidence-based treatment of chronic pain requires a multidisciplinary approach grounded in the biopsychosocial model. Implementing this approach within health systems relies on its acceptance by both healthcare providers and patients. While pioneering multidisciplinary pain clinics can serve as a model for implementation, a systematic effort is needed to share knowledge effectively and broadly. In the current paper we provide an overview of the knowledge translation initiatives undertaken at our Transitional Pain Service (TPS) at Toronto General Hospital, a state-of-the-art multidisciplinary pain program established in 2014 for patients at risk of developing chronic pain after surgery. The TPS team strives to enhance acceptance of this model of care among patients and providers, facilitate the establishment of similar clinics, and promote patient understanding of the integrated multidisciplinary pain care approach. Guided by the Knowledge to Action (KTA) framework, knowledge translation activities undertaken by our TPS team include clinician training, resources and outreach activities for providers, and patient education. Resource development was preceded by consultation and needs assessment among patients and providers and feedback from both groups was incorporated as part of the development process. The tailored resources were disseminated via the TPS clinic website and monitoring of online usage enables continuous evaluation of engagement. Barriers to engagement with the resources were examined through patient surveys and staff interviews. Based on these activities, we offer insights gained by our team throughout the knowledge translation process and provide recommendations for other clinical teams who wish to undertake similar initiatives.

Cys-tRNAj as a Second Translation Initiator for Priming Proteins with Cysteine in Bacteria

Cys-tRNAj as a Second Translation Initiator for Priming Proteins with Cysteine in Bacteria

PEBP1 amplifies mitochondrial dysfunction-induced integrated stress response.

Mitochondrial dysfunction is involved in numerous diseases and the aging process. The integrated stress response (ISR) serves as a critical adaptation mechanism to a variety of stresses, including those originating from mitochondria. By utilizing mass spectrometry-based cellular thermal shift assay (MS-CETSA), we uncovered that phosphatidylethanolamine-binding protein 1 (PEBP1), also known as Raf kinase inhibitory protein (RKIP), is thermally stabilized by stresses which induce mitochondrial ISR. Depletion of PEBP1 impaired mitochondrial ISR activation by reducing eukaryotic translation initiation factor 2α (eIF2α) phosphorylation and subsequent ISR gene expression, which was independent of PEBP1's role in inhibiting the RAF/MEK/ERK pathway. Consistently, overexpression of PEBP1 potentiated ISR activation by heme-regulated inhibitor (HRI) kinase, the principal eIF2α kinase in the mitochondrial ISR pathway. Real-time interaction analysis using luminescence complementation in live cells revealed an interaction between PEBP1 and eIF2α, which was disrupted by eIF2α S51 phosphorylation. These findings suggest a role for PEBP1 in amplifying mitochondrial stress signals, thereby facilitating an effective cellular response to mitochondrial dysfunction. Therefore, PEBP1 may be a potential therapeutic target for diseases associated with mitochondrial dysfunction.

Post-transcriptional regulation of aromatic amino acid metabolism by GcvB small RNA in Escherichia coli.

Escherichia coli synthesizes aromatic amino acids (AAAs) through the common pathway to produce the precursor, chorismate, and the three terminal pathways to convert chorismate into Phe, Tyr, and Trp. E. coli also imports exogenous AAAs through five transporters. GcvB small RNA post-transcriptionally regulates more than 50 genes involved in amino acid uptake and biosynthesis in E. coli, but the full extent of GcvB regulon is still underestimated. This study examined all genes involved in AAA biosynthesis and transport using translation reporter assay and qRT-PCR analysis. In addition to previously verified targets, aroC, aroP, and trpE, we identified new target genes that were significantly repressed by GcvB primarily via the R1 seed region. Exceptionally, GcvB strongly inhibits the expression of aroG, which encodes the major isozyme of the first reaction in the common pathway, through direct base pairing between the aroG translation initiation region and the GcvB R3 seed sequence. RNase E mediates the degradation of target mRNAs except aroC and aroP via its C-terminal domain. GcvB overexpression prolongs the lag phase and reduces the growth rate in minimal media supplemented with AAAs and confers resistance to an antibiotic compound, azaserine, by repressing AAA transporters.IMPORTANCEE. coli strains have been genetically modified in relevant transcription factors and biosynthetic enzymes for industrial use in the fermentative production of aromatic amino acids (AAAs) and their derivative compounds. This study focuses on GcvB small RNA, a global regulator of amino acid metabolism in E. coli, and identifies new GcvB targets involved in AAA biosynthesis and uptake. GcvB represses the expression of the first and last enzymes of the common pathway and the first enzymes of Trp and Phe terminal pathways. GcvB also limits import of AAAs. This paper documents the impact of RNA-mediated regulation on AAA metabolism in E. coli.

Small molecule modulators of B56-PP2A restore 4E-BP function to suppress eIF4E-dependent translation in cancer cells.

Dysregulated eIF4E-dependent translation is a central driver of tumorigenesis and therapy resistance. eIF4E binding proteins (4E-BP1/2/3) are major negative regulators of eIF4E-dependent translation that are inactivated in tumors through inhibitory phosphorylation or downregulation. Previous studies have linked PP2A phosphatase(s) to activation of 4E-BP1. Here, we leveraged biased small molecule activators of PP2A (SMAPs) to explore the role of B56-PP2A(s) in 4E-BP regulation and the potential of B56-PP2A activation for restoring translational control in tumors. SMAP treatment promoted PP2A-dependent hypophosphorylation of 4E-BP1/2, supporting a role for B56-PP2As (e.g., B56α-PP2A) as 4E-BP phosphatases. Unexpectedly, SMAPs induced transcriptional upregulation of 4E-BP1 through a B56 PP2A→TFE3/TFEB→ATF4 axis. Cap-binding and co-immunoprecipitation assays showed that B56-PP2A(s) activation blocks assembly of the eIF4F translation initiation complex, and cap-dependent translation assays confirmed the translation inhibitory effects of SMAPs. Thus, B56-PP2A(s) orchestrate a translation repressive program involving transcriptional induction and activation of 4E-BP1. Notably, SMAPs promoted 4E-BP1-dependent apoptosis in tumor cells and potentiated 4E-BP1 function in the presence of ERK or mTOR inhibitors, agents that rely on inhibition of eIF4E-dependent translation for antitumor activity. These findings, combined with the ability of SMAPs to regulate 4E-BP1 in vivo, highlight the potential of PP2A activators for cancer therapy and overcoming therapy resistance.

Effects of Enterocytozoon hepatopenaei infection on intestinal immune defense and physiological processes of Penaeus vannamei

As the main pathogen causing growth retardation, EHP is considered to be mainly parasitic in the hepatopancreas of shrimp. However, the intestines of shrimp infected with EHP frequently exhibit syndromes such as jejunum and white midgut. Therefore, the challenge experiment was carried out in this study to compare the differences in intestinal histology, digestion and absorption, immune defense and oxidative stress of P. vannamei between the control group and EHP infection group. Histological analysis showed that EHP infection significantly damaged the intestine of the shrimp, including intestinal villus rupture and outer membrane impairment. Concurrently, EHP infection can trigger intestinal immune response, and the expression of key immune genes like Toll, myeloid differentiation factor, anti-lipopolysaccharide factor, and Relish was significantly enhanced, while the expression of IMD and alkaline phosphatase was suppressed. Additionally, antioxidant genes manganese superoxide dismutase, catalase, glutathione peroxidase, glutathione-S-transferase, and nuclear factor E2-related factor 2 were up-regulated to varying extents in EHP infection group, and the contents of lipid peroxides and malondialdehyde were heavily accumulated. Moreover, the expression levels of key genes involved in nutrient absorption, transport and synthesis, such as glucose transporter 1, Na+-K+ATPase, fatty acid synthase, acetyl-CoA carboxylase, rapamycin kinase, mTOR regulation-related protein, eukaryotic translation initiation factor 4E binding protein, ribosomal protein S6 kinase, were significantly up-regulated. However, the activities of amylase, lipase, and trypsin were inhibited in EHP infection group throughout the experiment. In summary, EHP infection damaged the intestine of P. vannamei, accompanied by immune response and oxidative stress. At the same time, nutrient transport and synthesis pathways were activated, while digestive enzyme activities were inhibited, indicating that in order to maintain survival, shrimps must accelerate material transport. Unfortunately, it remains in a state of nutrient deficiency that ultimately affects growth.

Pharmacological Dissection Identifies Retatrutide Overcomes the Therapeutic Barrier of Obese TNBC Treatments through Suppressing the Interplay between Glycosylation and Ubiquitylation of YAP.

Triple-negative breast cancer (TNBC) in obese patients remains challenging. Recent studies have linked obesity to an increased risk of TNBC and malignancies. Through multiomic analysis and experimental validation, a dysfunctional Eukaryotic Translation Initiation Factor 3 Subunit H (EIF3H)/Yes-associated protein (YAP) proteolytic axis is identified as a pivotal junction mediating the interplay between cancer-associated adipocytes and the response to anti-cancer drugs in TNBC. Mechanistically, cancer-associated adipocytes drive metabolic reprogramming resulting in an upregulated hexosamine biosynthetic pathway (HBP). This aberrant upregulation of HBP promotes YAP O-GlcNAcylation and the subsequent recruitment of EIF3H deubiquitinase, which stabilizes YAP, thus promoting tumor growth and chemotherapy resistance. It is found that Retatrutide, an anti-obesity agent, inhibits HBP and YAP O-GlcNAcylation leading to increased YAP degradation through the deprivation of EIF3H-mediated deubiquitylation of YAP. In preclinical models of obese TNBC, Retatrutide downregulates HBP, decreases YAP protein levels, and consequently decreases tumor size and enhances chemotherapy efficacy. This effect is particularly pronounced in obese mice bearing TNBC tumors. Overall, these findings reveal a critical interplay between adipocyte-mediated metabolic reprogramming and EIF3H-mediated YAP proteolytic control, offering promising therapeutic strategies to mitigate the adverse effects of obesity on TNBC progression.

Translational activators align mRNAs at the small mitoribosomal subunit for translation initiation.

Mitochondrial gene expression is essential for oxidative phosphorylation. Mitochondrial-encoded mRNAs are translated by dedicated mitochondrial ribosomes (mitoribosomes), whose regulation remains elusive. In the baker's yeast Saccharomyces cerevisiae , nuclear-encoded mitochondrial translational activators (TAs) facilitate transcript-specific translation by a yet unknown mechanism. Here, we investigated the function of TAs containing RNA-binding pentatricopeptide repeats (PPRs) using selective mitoribosome profiling and cryo-EM structural analysis. These analyses revealed that TAs exhibit strong selectivity for mitoribosomes initiating on their target transcripts. Moreover, TA-mitoribosome footprints indicated that TAs recruit mitoribosomes proximal to the start codon. Two cryo-EM structures of mRNA-TA complexes bound to post-initiation/pre-elongation-stalled mitoribosomes revealed the general mechanism of TA action. Specifically, the TAs bind to structural elements in the 5' UTR of the client mRNA as well as to the mRNA channel exit to align the mRNA in the small subunit during initiation. Our findings provide a mechanistic basis for understanding how mitochondria achieve transcript-specific translation initiation without relying on general sequence elements to position mitoribosomes at start codons.

Selection of initiator tRNA and start codon by mammalian mitochondrial initiation factor 3 in leaderless mRNA translation.

The mammalian mitochondrial protein synthesis system produces 13 essential subunits of oxidative phosphorylation (OXPHOS) complexes. Translation initiation in mammalian mitochondria is characterized by the use of leaderless messenger RNAs (mRNAs) and non-AUG start codons, where the proofreading function of IF-3mt still remains elusive. Here, we developed a reconstituted mammalian mitochondrial translation system using in vitro transcribed and native mitochondrial transfer RNAs (tRNAs) to investigate IF-3mt's proofreading function. Similar to bacterial IF-3, IF-3mt permits an initiator tRNA to participate in initiation by discriminating the three G-C pairs in its anticodon stem, and by the cognate interactions of its anticodon with the AUG start codon. As a result, IF-3mt promotes the accurate initiation of leaderless mRNAs. Nevertheless, IF-3mt can also facilitate initiation from the non-AUG(AUA) start codon through its unique N- and C-terminal extensions, in concert with the 5-methylcytidine (m5C) or 5-formylcytidine (f5C) modification at the anticodon wobble position of mt-tRNAMet. This is partly because the IF-3mt-specific N- and C-terminal extensions and the KKGK-motif favor leaderless mRNA initiation and relax non-AUG start codon discrimination. Analyses of IF-3mt-depleted human cells revealed that IF-3mt indeed participates in translating the open reading frames (ORFs) of leaderless mRNAs, as well as the internal ORFsof dicistronic mRNAs.

Role of Ribosomal Protein bS1 in Orthogonal mRNA Start Codon Selection.

In many bacteria, the location of the mRNA start codon is determined by a short ribosome binding site sequence that base pairs with the 3'-end of 16S rRNA (rRNA) in the 30S subunit. Many groups have changed these short sequences, termed the Shine-Dalgarno (SD) sequence in the mRNA and the anti-Shine-Dalgarno (ASD) sequence in 16S rRNA, to create "orthogonal" ribosomes to enable the synthesis of orthogonal polymers in the presence of the endogenous translation machinery. However, orthogonal ribosomes are prone to SD-independent translation. Ribosomal protein bS1, which binds to the 30S ribosomal subunit, is thought to promote translation initiation by shuttling the mRNA to the ribosome. Thus, a better understanding of how the SD and bS1 contribute to start codon selection could help efforts to improve the orthogonality of ribosomes. Here, we engineered the Escherichia coli ribosome to prevent binding of bS1 to the 30S subunit and separate the activity of bS1 binding to the ribosome from the role of the mRNA SD sequence in start codon selection. We find that ribosomes lacking bS1 are slightly less active than wild-type ribosomes in vitro. Furthermore, orthogonal 30S subunits lacking bS1 do not have an improved orthogonality. Our findings suggest that mRNA features outside the SD sequence and independent of binding of bS1 to the ribosome likely contribute to start codon selection and the lack of orthogonality of present orthogonal ribosomes.

An alternatively translated isoform of PPARG proposes AF-1 domain inhibition as an insulin sensitization target.

PPARγ is the pharmacological target of thiazolidinediones (TZDs), potent insulin sensitizers that prevent metabolic disease morbidity but are accompanied by side effects such as weight gain, in part due to non-physiological transcriptional agonism. Using high throughput genome engineering, we targeted nonsense mutations to every exon of PPARG, finding an ATG in Exon 2 (chr3:12381414, CCDS2609 c.A403) that functions as an alternative translational start site. This downstream translation initiation site gives rise to a PPARγ protein isoform (M135), preferentially generated from alleles containing nonsense mutations upstream of c.A403. PPARγ M135 retains the DNA and ligand binding domains of full-length PPARγ but lacks the N-terminal AF-1 domain. Despite being truncated, PPARγ M135 shows increased transactivation of target genes, but only in the presence of agonists. Accordingly, human missense mutations disrupting AF-1 domain function actually increase agonist-induced cellular PPARγ activity compared to wild-type (WT), and carriers of these AF-1 disrupting variants are protected from metabolic syndrome. Thus, we propose the existence of PPARγ M135 as a fully functional, alternatively translated isoform that may be therapeutically generated to treat insulin resistance-related disorders.

Yeast Eukaryotic Initiation Factor 4B Remodels the MRNA Entry Site on the Small Ribosomal Subunit.

Eukaryotic Initiation Factor 4 (eIF4) is a group of factors that activates mRNA for translation and recruit 43S preinitiation complex (PIC) to the mRNA 5' end, forming the 48S PIC. The eIF4 factors include mRNA 5' cap-binding protein eIF4E, ATP-dependent RNA helicase eIF4A, and scaffold protein eIF4G, which anchors eIF4A and eIF4E. Another eIF4 factor, eIF4B, stimulates the RNA helicase activity of eIF4A and facilitates mRNA recruitment. However, the mechanisms by which eIF4B binds the 40S ribosomal subunit and promotes mRNA recruitment remain poorly understood. Using cryo-Eletron Microscopy (cryo-EM), we obtained a map of the yeast 40S ribosomal subunit in a complex with eIF4B (40S-eIF4B complex). An extra density, tentatively assigned to yeast eIF4B, was observed near the mRNA entry channel of the 40S, contacting ribosomal proteins uS10, uS3, and eS10 as well as rRNA helix h16. Predictive modeling of the 40S-eIF4B complex suggests that the N-terminal domain of eIF4B binds near the mRNA entry channel, overlapping with the extra density observed in the 40S-eIF4B map. The partially open conformation of 40S in the 40S-eIF4B map is incompatible with eIF3j binding observed in the 48S PIC. Additionally, the extra density at the mRNA entry channel poses steric hindrance for eIF3g binding in the 48S PIC. Thus, structural insights suggest that eIF4B facilitates the release of eIF3j and the relocation of the eIF3b-g-i module during mRNA recruitment, thereby advancing our understanding of eIF4B's role in translation initiation.

Generation of ribosomal protein S1 mutants for improving of expression of difficult to translate mRNAs

Metagenomes present a source for novel enzymes, but under 1% of environmental microbes are cultivatable. Because of its useful properties, Escherichia coli has been used as a host organism in functional genomic screens. However, due to differing expression machineries in the expression host compared to the source organism of the DNA sequences, screening outcomes can be biased. Here, we focused on one of the limiting processes—translation initiation. To that end, we created an operon-like screening system in E. coli to select mutants of the ribosomal protein S1 with more relaxed sequence requirements for 5’-untranslated regions of mRNAs. We created two mutation libraries of the ribosomal protein S1, one covering domains 3 and 4 (D3-D4) and the second covering domains 3 to 5 (D3-D5). Most mutants from library D3-D4 proofed to be specific for a particular UTR sequence and improved only expression from a single construct. Only mutant 3 from library D3-D4 led to increased expression of four different reporters improving fluorescence levels by up to 21%. Mutants isolated from D3-D5 library led up to 90% higher expression compared to the control, though the mutants with highest improvements exhibited a specialist phenotype. The most promising mutant, mutant 4, exhibited a generalist phenotype and showed increased expression in all six reporter strains compared to the control. This could indicate the potential for a more promiscuous translation initiation of metagenomic sequences in E. coli although at the price of smaller increases compared to specialist mutants.Key points• An operon-like selection system allowed to isolate generalist and specialist S1 mutants.• S1 mutants improved translation of mRNAs with 5'-UTRs from metagenomic sequences.• Use of S1 mutants could increase coverage from metagenomic libraries in functional screens.

The translation initiation factor eIF2 is phosphorylated to inhibit protein translation through reactive oxygen species under nutrient deficiencies in Arabidopsis

Nitrogen (N), phosphorus (P) or potassium (K) deficiency in plants can lead to a decrease in amino acid and protein synthesis. However, it is unknown how protein translation gets repressed during macronutrient deficiencies. Previous research has shown that general control non-depressible 1 (GCN1) cooperate with GCN2 to phosphorylate the alpha subunit of eukaryotic translation initiation factor (eIF2α). In this study, we observed phosphorylation of eIF2α under N, P, and K deficiencies, which was found to be lost in gcn1. Mutant gcn1 displayed higher sensitivity to macronutrient deficiencies compared to the wild-type (WT). The evidence of in situ reactive oxygen species (ROS) accumulation in leaves indicated that macronutrient starvation triggers ROS production. Treatment with Dimethylthiourea (DMTU), a ROS scavenger, eliminated ROS and reversed eIF2α phosphorylation induced by nutrient deficiency. Moreover, it was discovered that protein translation was reduced under N or K deficiency in the WT but not in gcn1, whereas under P deprivation, protein translation was reduced in both the WT and gcn1. We additionally found that DMTU can partially recover translation inhibition under N or K deprivation. Taken together, it is concluded that GCN1-GCN2-eIF2α pathway is regulated by ROS and is essential for plant survival under macronutrient starvation conditions.

Age‑related changes in endoplasmic reticulum stress response‑associated protein expression in rat tibial nerves.

In age-related peripheral neurodegeneration, changes in the promotion or inhibition of endoplasmic reticulum (ER) stress response related to the ubiquitin-proteasome degradation system (UPS), autophagy and apoptosis signaling factors during aging remain unclear. In the present study, the expression of ER stress response signaling-related protein factors was examined in tibial nerves during aging in rats. Tibial nerves were extracted from continuously housed rats at 20, 50, 70, 90 and 105 weeks of age. Expression of factors associated with ER stress-related degradation, including X-box binding protein 1 (XBP1s), eukaryotic translation initiation factor 2 subunit 1 (eIF2α), Beclin-1 (Becn1), and Caspase-3 (Casp3); ER stress-related repair, including binding immunoglobulin protein [also known as 78 kDa glucose-regulated protein (BiP/GRP78)], protein disulfide isomerase (PDI), brain-derived neurotrophic factor (BDNF) and the inflammatory cytokine IL6, was assessed by western blotting of tibial nerves from rats in each age group. Expression of XBP1s and Becn1, which promote UPS and autophagy, decreased significantly after 50 weeks of age. However, expression of eIF2α and Casp3, which inhibit new protein biosynthesis and promote apoptosis, increased significantly after 50 weeks. Expression of BiP/GRP78 and PDI, which are refolding factors for denatured proteins, showed a significant decrease after 50 (or 70) weeks of age. The expression of BDNF, a ligand protein for the repair cascade, showed a significant increase after 70 weeks of age, while that of IL6 increased significantly after 50 weeks of age. These results indicate that ER stress-related degradation (UPS and autophagy) and refolding repair functions are reduced in rat tibial nerves after 50 weeks, followed by enhanced apoptosis and inflammation. These findings shed light on the progression of age-related peripheral neurodegeneration in rats.

RAB3GAP2 dysregulation in adult T-cell leukemia/lymphoma (ATLL) compared to acute lymphoblastic leukemia (ALL): a molecular perspective

Adult T-cell leukemia/lymphoma (ATLL) is a type of blood cancer related to human T-cell lymphotropic virus type 1 (HTLV-1). The principal aim of this study was to investigate cellular processes related to innate immune response, intracellular protein transport, and translational initiation regulation in individuals afflicted with ATLL and Acute lymphoblastic leukemia (ALL). Whole blood samples and peripheral blood mononuclear cells were collected from 10 viral ATLL patients and 10 ALL subjects. Real-time quantitative PCR was then performed to quantify mRNA expression levels of SMC6, FANCM, EIF4H, WDR7, RAB3GAP2, and IFN α/β. The study revealed some distinctions between ATLL and ALL patients. Particularly, RAB3GAP2 level (P = 0.028) was found to be elevated in ATLL patients compared to ALL. Conversely, expression levels of IFN-β (P = 0.31), SMC6 (P = 0.68), WDR7 (P = 0.43), EIF4H (P = 0.38), and FANCM (P = 0.57) were diminished in ATLL patients in contrast to ALL. These proteins play a pivotal role in both translation and immune activation, suggesting a potential correlation between the observed disparities and the virus-mediated progression of cancer. However, it is worth noting that the expression differences in FANCM, EIF4H, SMC6, and WDR7 between ATLL and ALL were minimal. This proposes that the underlying molecular mechanisms governing ATLL and ALL may largely overlap concerning these cellular processes. However, considerable increased expression of RAB3GAP2 was observed in ATLL compared to ALL.