Translation Initiation Signals Research Articles

Dual Luciferase Reporter Assay in Schizosaccharomyces pombe.

Here, I describe the methods to perform dual luciferase reporter assay in Schizosaccharomyces pombe. The experiment requires the generation of a reporter plasmid construct, with firefly luciferase gene controlled under the genetic element of interest (such as transcriptional promoter or translation initiation signal preceded by a defined promoter) and Renilla luciferase gene expressed under a fixed promoter. S. pombe transformants carrying the plasmids with varied control elements are grown in a selective medium and chilled on ice. Small amounts of cells are pelleted and subjected to the commercially available dual luciferase assay.

Differential Selection for Translation Efficiency Shapes Translation Machineries in Bacterial Species.

Different bacterial species have dramatically different generation times, from 20-30 min in Escherichia coli to about two weeks in Mycobacterium leprae. The translation machinery in a cell needs to synthesize all proteins for a new cell in each generation. The three subprocesses of translation, i.e., initiation, elongation, and termination, are expected to be under stronger selection pressure to optimize in short-generation bacteria (SGB) such as Vibrio natriegens than in the long-generation Mycobacterium leprae. The initiation efficiency depends on the start codon decoded by the initiation tRNA, the optimal Shine-Dalgarno (SD) decoded by the anti-SD (aSD) sequence on small subunit rRNA, and the secondary structure that may embed the initiation signals and prevent them from being decoded. The elongation efficiency depends on the tRNA pool and codon usage. The termination efficiency in bacteria depends mainly on the nature of the stop codon and the nucleotide immediately downstream of the stop codon. By contrasting SGB with long-generation bacteria (LGB), we predict (1) SGB to have more ribosome RNA operons to produce ribosomes, and more tRNA genes for carrying amino acids to ribosomes, (2) SGB to have a higher percentage of genes using AUG as the start codon and UAA as the stop codon than LGB, (3) SGB to exhibit better codon and anticodon adaptation than LGB, and (4) SGB to have a weaker secondary structure near the translation initiation signals than LGB. These differences between SGB and LGB should be more pronounced in highly expressed genes than the rest of the genes. We present empirical evidence in support of these predictions.

Pulsatile Leucine Administration during Continuous Enteral Feeding Enhances Skeletal Muscle Mechanistic Target of Rapamycin Complex 1 Signaling and Protein Synthesis in a Preterm Piglet Model

BackgroundContinuous feeding does not elicit an optimal anabolic response in skeletal muscle but is required for some preterm infants. We reported previously that intermittent intravenous pulses of leucine (Leu; 800 μmol Leu·kg–1·h–1 every 4 h) to continuously fed pigs born at term promoted mechanistic target of rapamycin complex 1 (mTORC1) activation and protein synthesis in skeletal muscle. ObjectivesThe aim was to determine the extent to which intravenous Leu pulses activate mTORC1 and enhance protein synthesis in the skeletal muscle of continuously fed pigs born preterm. MethodsPigs delivered 10 d preterm was advanced to full oral feeding >4 d and then assigned to 1 of the following 4 treatments for 28 h: 1) ALA (continuous feeding; pulsed with 800 μmol alanine·kg–1·h–1 every 4 h; n = 8); 2) L1× (continuous feeding; pulsed with 800 μmol Leu·kg–1·h–1 every 4 h; n = 7); 3) L2× (continuous feeding; pulsed with 1600 μmol Leu·kg–1·h–1 every 4 h; n = 8); and 4) INT (intermittent feeding every 4 h; supplied with 800 μmol alanine·kg–1 per feeding; n = 7). Muscle protein synthesis rates were determined with L-[2H5-ring]Phenylalanine. The activation of insulin, amino acid, and translation initiation signaling pathways were assessed by Western blot. ResultsPeak plasma Leu concentrations were 134% and 420% greater in the L2× compared to the L1× and ALA groups, respectively (P < 0.01). Protein synthesis was greater in the L2× than in the ALA and L1× groups in both the longissimus dorsi and gastrocnemius muscles (P < 0.05) but not different from the INT group (P > 0.10). Amino acid signaling upstream and translation initiation signaling downstream of mTORC1 largely corresponded to the differences in protein synthesis. ConclusionsIntravenous Leu pulses potentiate mTORC1 activity and protein synthesis in the skeletal muscles of continuously fed preterm pigs, but the amount required is greater than in pigs born at term.

Branched-chain amino acid supplementation does not enhance lean tissue accretion in low birth weight neonatal pigs, despite lower Sestrin2 expression in skeletal muscle.

Postnatal muscle growth is impaired in low birth weight (L) neonatal pigs. Leucine supplementation has been established as a dietary intervention to enhance muscle growth in growing animals. The aim of this study was to investigate the efficacy of supplementing L neonatal pig formulas with branched-chain amino acids (B) to enhance the rate of protein accretion. Twenty-four 3-day old pigs were divided into two groups low (L) and normal birth weight (N) based on weight at birth. Pigs were assigned to a control (C) or 1% branched-chain amino acids (B) formulas, and fed at 250mL·kg body weight -1·d-1 for 28 d. Body weight of pigs in the L group was less than those in the N group (P < 0.01). However, fractional body weight was greater for L pigs compared with their N siblings from day 24 to 28 of feeding regardless of formula (P < 0.01). In addition, feed efficiency (P < 0.0001) and efficiently of protein accretion (P < 0.0001) were greater for L than N pigs regardless of supplementation. Pigs fed the B formula had greater plasma leucine, isoleucine, and valine concentrations compared with those fed the C formula (P < 0.05). Longissimus dorsi Sestrin2 protein expression was less for pigs in the L group compared with those in the N group (P < 0.01), but did not result in a corresponding increase in translation initiation signaling. Longissimus dorsi mRNAexpression of BCAT2 was less for LB pigs compared with those in the LC group, and was intermediate for NC and NB pigs (P < 0.05). Hepatic mRNA expression of BCKDHA was greater for pigs in the L compared with those in the N groups (P < 0.05). However, plasma branched-chain keto-acid concentration was reduced for C compared with those in the B group (P < 0.05). These data suggest that branched-chain amino acid supplementation does not improve lean tissue accretion of low and normal birth weight pigs, despite a reduction in Sestrin2 expression in skeletal muscle of low birth weight pigs. The modest improvement in fractional growth rate of low birth weight pigs compared with their normal birth weight siblings was likely due to a more efficient dietary protein utilization.

The molecular basis of the Fragile X syndrome

This analysis aimed to clarify the molecular basis of fragile X syndrome and explain the role of genetic material in the genetic disease's development and treatment. Fragile X syndrome is an X-linked mutation inheritance disorder. The mutated gene is called FMR-1. This is important for normal brain development and synaptic plasticity, which was verified and recognized in 1991, and this has become a hope for more clarification. FMR1 influences the translation of messenger RNA (mRNA), but identifying functional targets was complex and directly related to translational control and showed that dysregulated translation initiation signaling was observed for the FMR1 gene in the FMR1 knockout mouse model of FXS.&#x0D; Because of the epigenetic alteration, such as hypermethylated at the DNA promoter region, and chromatin modification, such as H3K9 methylation, the FMR1 gene can be imprinted. Still, their mechanisms of aberrant epigenetic marks play a role in the etiology of many neurodevelopmental disorders, some of which we still do not fully understand and need to show more. The opportunities for epigenetic markers to map and alter epigenetic marks and the potential for therapies based on epigenetics and noncoding manipulation. For neurodevelopmental and behavioral conditions, including mental retardation, autism, anxiety, and mood disturbance, FMR1 loss of control is a model.&#x0D; Most studies have focused on the new and effective approach for Fragile X syndrome, which is Gene therapy is unarguably the definitive way to treat and possibly cure genetic diseases. Many of them are under clinical trial, but more studies, such as the CRISPR/Cas9-based method, should be approved. Adeno-associated viral (AAV) vectors are highly effective for generating models. Most research is used in the mouse model of fragile X syndrome, where AAVs have been used to express fragile X mental retardation protein (FMRP), which is missing or highly reduced in the disorder. The vast expansions need southern blotting in myotonic dystrophy. Fragile X is diagnosed by a form of Southern blotting that relies on the size and the FRAXA gene's methylation status. Almost always, genetic testing is performed by PCR. The few Southern blotting uses include checking for significant destructive gene rearrangements and complete mutations of fragile X and myotonic dystrophy. Expansions suppress the expression of closely adjacent genes, causing loss of function. A named FMRI (fragile-X mental retardation syndrome) gene cDNA probe. Some unique molecular mechanisms, such as CGG expansion in Fragile-X syndrome, can make a particular sequence change in a gene far more probable than any other change.

The prokaryotic activity of the IGR IRESs is mediated by ribosomal protein S1.

Internal ribosome entry sites (IRESs) are RNA elements capable of initiating translation on an internal portion of a messenger RNA. The intergenic region (IGR) IRES of the Dicistroviridae virus family folds into a triple pseudoknot tertiary structure, allowing it to recruit the ribosome and initiate translation in a structure dependent manner. This IRES has also been reported to drive translation in Escherichia coli and to date is the only described translation initiation signal that functions across domains of life. Here we show that unlike in the eukaryotic context the tertiary structure of the IGR IRES is not required for prokaryotic ribosome recruitment. In E. coli IGR IRES translation efficiency is dependent on ribosomal protein S1 in conjunction with an AG-rich Shine-Dalgarno-like element, supporting a model where the translational activity of the IGR IRESs is due to S1-mediated canonical prokaryotic translation.

Prematurity Attenuates Skeletal Muscle Anabolism of Neonatal Pigs Independently of Birth Weight

ObjectivesPremature infants are at risk for postnatal growth failure that reduces lifelong lean mass. We have shown previously that preterm birth blunts the feeding-induced activation of the mechanistic target of rapamycin (mTOR) signaling pathway, translation initiation, and protein synthesis in skeletal muscle of neonatal pigs. Considering that body weight can vary widely at birth, we sought to separate the effect of prematurity from birth weight on the anabolic response to feeding. MethodsPigs were delivered by cesarean section at preterm (103 d) or term (112 d) gestation and fed parenterally for 4 d. On day 4, pigs were fasted for 4 h and were either fasted one additional hour or fed by oral gavage, yielding four groups: 1) preterm fasted (PT-FAST); 2) preterm fed (PT-FED); 3) term fasted (T-FAST); and 4) term fed (T-FED). All pigs were injected with a flooding dose of L-[4-3H]Phe to determine fractional protein synthesis rates and euthanized 60 min after feeding or the additional fast. Pigs were stratified by birth weight such that the highest birth weight preterm pigs were compared with the lowest birth weight term pigs (n = 10–13 per group). ResultsDespite similar birth weight in preterm and term pigs (1035 vs 993 ± 54 g, P > 0.10), relative weight gain of preterm was 33% lower than term pigs (22.0 vs. 32.9 ± 1.6 g·kg–1·d–1, P < 0.001). Longissimus dorsi (LD), gastrocnemius, and diaphragm protein synthesis rates were not different between PT-FAST and T-FAST groups. Gastrocnemius protein synthesis was 18% lower in PT-FED than T-FED group (P < 0.01), but protein synthesis was not different between PT-FED and T-FED groups in LD and diaphragm muscles. The abundance of the active eIF4E·eIF4G complex and phosphorylation of 4E-BP1 and S6K1, readouts of mTOR activation and translation initiation signaling, were increased after feeding in all muscles (P < 0.001). Translation initiation signaling was lower in LD and gastrocnemius muscles in PT-FED than T-FED groups (P < 0.05) but was not different in diaphragm muscle (P > 0.10). ConclusionsThese findings imply that prematurity, independent of birth weight, blunts mTOR activation and protein synthesis after feeding. The blunted anabolic response to feeding likely underpins postnatal growth failure often observed in infants born preterm. Funding SourcesNIH and USDA.

Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA.

SARS-CoV-2 is a novel positive-sense single-stranded RNA virus from the Coronaviridae family (genus Betacoronavirus), which has been established as causing the COVID-19 pandemic. The genome of SARS-CoV-2 is one of the largest among known RNA viruses, comprising of at least 26 known protein-coding loci. Studies thus far have outlined the coding capacity of the positive-sense strand of the SARS-CoV-2 genome, which can be used directly for protein translation. However, it has been recently shown that transcribed negative-sense viral RNA intermediates that arise during viral genome replication from positive-sense viruses can also code for proteins. No studies have yet explored the potential for negative-sense SARS-CoV-2 RNA intermediates to contain protein-coding loci. Thus, using sequence and structure-based bioinformatics methodologies, we have investigated the presence and validity of putative negative-sense ORFs (nsORFs) in the SARS-CoV-2 genome. Nine nsORFs were discovered to contain strong eukaryotic translation initiation signals and high codon adaptability scores, and several of the nsORFs were predicted to interact with RNA-binding proteins. Evolutionary conservation analyses indicated that some of the nsORFs are deeply conserved among related coronaviruses. Three-dimensional protein modeling revealed the presence of higher order folding among all putative SARS-CoV-2 nsORFs, and subsequent structural mimicry analyses suggest similarity of the nsORFs to DNA/RNA-binding proteins and proteins involved in immune signaling pathways. Altogether, these results suggest the potential existence of still undescribed SARS-CoV-2 proteins, which may play an important role in the viral lifecycle and COVID-19 pathogenesis.

BDK knockout skeletal muscle satellite cells exhibit enhanced protein translation initiation signal in response to BCAA in vitro

We examined the effects of branched-chain amino acids (BCAAs) and electrical pulse stimulation (EPS) on the mTORC1 pathway in muscle satellite cells (MSCs) isolated from branched-chain α-keto acid dehydrogenase kinase (BDK) knockout (KO) mice in vitro. MSCs were isolated from BDK KO and wild-type (WT) mice, proliferated, and differentiated into myotubes. BCAA stimulation increased the phosphorylation of p70 S6 kinase (p70S6K), a marker of protein translation initiation, in MSCs from WT and BDK KO mice, but the rate of the increase was higher in MSCs isolated from BDK KO mice. Contrarily, there was no difference in the increase in p70S6K phosphorylation by EPS. Acute BDK knockdown in MSCs from WT mice using shRNA decreased p70S6K phosphorylation in response to BCAA stimulation. Collectively, the susceptibility of mTORC1 to BCAA stimulation was elevated by chronic, but not acute, enhancement of BCAA catabolism.

Abstract 12496: Plasma Growth Factors and Hormones Drive Constitutive Translation of a Broad-Spectrum Proteome in Circulating Platelets via Stimulation of Translation Initiation Signal Pathways, Necessary for Rapid Hemostasis

Introduction: The ability of anucleate platelets to translate nascent protein from their inherited mRNAs was first demonstrated in 1967. Later studies supported these findings, but translation quickly ceased in washed ex vivo platelets, leading to a general presumption that platelet translation is not robust, and thus of limited biological significance. Agonist stimulation promotes platelet protein translation, and recent profiling studies confirmed &gt;6000 inherited mRNAs in polysomes, associated with inducible translation of cognate protein products in thrombin-stimulated human platelets. However, relevance of post-activation translation - a slow, rate-limiting step in cell response - to rapid hemostasis is not clear. Platelets express the requisite components and show broad ribosome occupancy of mRNAs under resting conditions. Hypothesis: Plasma-borne growth factors/hormones (GFH) drive constitutive translation in circulating platelets to modulate reactivity. Methods: We employed metabolic labeling of newly synthesized proteins by bio-orthogonal non-canonical amino acid tagging in plasma-starved human platelets fed back with autologous plasma or isolated GFH (VEGF, IGF-1, insulin, EGF, HMGB1), coupled with translation initiation signaling and functional tests. Results: We found that platelets undergo constitutive translation of a broad-spectrum translatome dependent on plasma or GFH exposure. Platelets freshly isolated from platelet-rich plasma showed homeostatic activation of translation initiation signaling, evidenced by phosphorylation of p38/ERK upstream kinases, essential intermediate MNK1/2, and downstream effectors eIF4E/4E-BP1. Plasma starvation led to a steady loss of phosphorylation of this pathway, which was fully restored within 5 min stimulation by either plasma or most GFH. Inhibition of translation with puromycin or cycloheximide suppressed thrombin-induced integrin GPIIb/IIIa activation, P-selectin exposure, and platelet aggregation in vitro , and delayed platelet clot retraction. Transfusion of puromycin or MNK inhibitor eFT-508 resulted in delayed hemostasis in a tail bleed assay in mice. Conclusions: Constitutive plasma GFH-driven translation supports hemostatic platelet function.

Role of endopeptidases in peptidoglycan synthesis mediated by alternative cross-linking enzymes in Escherichia coli.

Bacteria resist to the turgor pressure of the cytoplasm through a net-like macromolecule, the peptidoglycan, made of glycan strands connected via peptides cross-linked by penicillin-binding proteins (PBPs). We recently reported the emergence of β-lactam resistance resulting from a bypass of PBPs by the YcbB L,D-transpeptidase (LdtD), which form chemically distinct 3→3 cross-links compared to 4→3 formed by PBPs. Here we show that peptidoglycan expansion requires controlled hydrolysis of cross-links and identify among eight endopeptidase paralogues the minimum enzyme complements essential for bacterial growth with 4→3 (MepM) and 3→3 (MepM and MepK) cross-links. Purified Mep endopeptidases unexpectedly displayed a 4→3 and 3→3 dual specificity implying recognition of a common motif in the two cross-link types. Uncoupling of the polymerization of glycan chains from the 4→3 cross-linking reaction was found to facilitate the bypass of PBPs by YcbB. These results illustrate the plasticity of the peptidoglycan polymerization machinery in response to the selective pressure of β-lactams.

Read between the Lines: Diversity of Nontranslational Selection Pressures on Local Codon Usage.

Protein coding genes can contain specific motifs within their nucleotide sequence that function as a signal for various biological pathways. The presence of such sequence motifs within a gene can have beneficial or detrimental effects on the phenotype and fitness of an organism, and this can lead to the enrichment or avoidance of this sequence motif. The degeneracy of the genetic code allows for the existence of alternative synonymous sequences that exclude or include these motifs, while keeping the encoded amino acid sequence intact. This implies that locally, there can be a selective pressure for preferentially using a codon over its synonymous alternative in order to avoid or enrich a specific sequence motif. This selective pressure could—in addition to mutation, drift and selection for translation efficiency and accuracy—contribute to shape the codon usage bias. In this review, we discuss patterns of avoidance of (or enrichment for) the various biological signals contained in specific nucleotide sequence motifs: transcription and translation initiation and termination signals, mRNA maturation signals, and antiviral immune system targets. Experimental data on the phenotypic or fitness effects of synonymous mutations in these sequence motifs confirm that they can be targets of local selection pressures on codon usage. We also formulate the hypothesis that transposable elements could have a similar impact on codon usage through their preferred integration sequences. Overall, selection on codon usage appears to be a combination of a global selection pressure imposed by the translation machinery, and a patchwork of local selection pressures related to biological signals contained in specific sequence motifs.

A snapshot of translation in Mycobacterium tuberculosis during exponential growth and nutrient starvation revealed by ribosome profiling

SummaryMycobacterium tuberculosis, which causes tuberculosis, can undergo prolonged periods of non-replicating persistence in the host. The mechanisms underlying this are not fully understood, but translational regulation is thought to play a role. A large proportion of mRNA transcripts expressed in M. tuberculosis lack canonical bacterial translation initiation signals, but little is known about the implications of this for fine-tuning of translation. Here, we perform ribosome profiling to characterize the translational landscape of M. tuberculosis under conditions of exponential growth and nutrient starvation. Our data reveal robust, widespread translation of non-canonical transcripts and point toward different translation initiation mechanisms compared to canonical Shine-Dalgarno transcripts. During nutrient starvation, patterns of ribosome recruitment vary, suggesting that regulation of translation in this pathogen is more complex than originally thought. Our data represent a rich resource for others seeking to understand translational regulation in bacterial pathogens.

Prematurity blunts the insulin- and amino acid-induced stimulation of translation initiation and protein synthesis in skeletal muscle of neonatal pigs.

Extrauterine growth restriction in premature infants is largely attributed to reduced lean mass accretion and is associated with long-term morbidities. Previously, we demonstrated that prematurity blunts the feeding-induced stimulation of translation initiation signaling and protein synthesis in skeletal muscle of neonatal pigs. The objective of the current study was to determine whether the blunted feeding response is mediated by reduced responsiveness to insulin, amino acids, or both. Pigs delivered by cesarean section preterm (PT; 103 days, n = 25) or at term (T; 112 days, n = 26) were subject to euinsulinemic-euaminoacidemic-euglycemic (FAST), hyperinsulinemic-euaminoacidemic-euglycemic (INS), or euinsulinemic-hyperaminoacidemic-euglycemic (AA) clamps four days after delivery. Indices of mechanistic target of rapamycin complex 1 (mTORC1) signaling and fractional protein synthesis rates were measured after 2 h. Although longissimus dorsi (LD) muscle protein synthesis increased in response to both INS and AA, the increase was 28% lower in PT than in T. Upstream of mTORC1, Akt phosphorylation, an index of insulin signaling, was increased with INS but was 40% less in PT than in T. The abundances of mTOR·RagA and mTOR·RagC, indices of amino acid signaling, increased with AA but were 25% less in PT than in T. Downstream of mTORC1, eIF4E·eIF4G abundance was increased by both INS and AA but attenuated by prematurity. These results suggest that preterm birth blunts both insulin- and amino acid-induced activation of mTORC1 and protein synthesis in skeletal muscle, thereby limiting the anabolic response to feeding. This anabolic resistance likely contributes to the high prevalence of extrauterine growth restriction in prematurity.NEW & NOTEWORTHY Extrauterine growth faltering is a major complication of premature birth, but the underlying cause is poorly understood. Our results demonstrate that preterm birth blunts both the insulin-and amino acid-induced activation of mTORC1-dependent translation initiation and protein synthesis in skeletal muscle, thereby limiting the anabolic response to feeding. This anabolic resistance likely contributes to the reduced accretion of lean mass and extrauterine growth restriction of premature infants.

Intermittent Bolus Feeding Enhances Organ Growth More Than Continuous Feeding in a Neonatal Piglet Model.

ABSTRACTBackgroundOrogastric tube feeding is frequently prescribed for neonates who cannot ingest food normally. In a piglet model of the neonate, greater skeletal muscle growth is sustained by upregulation of translation initiation signaling when nutrition is delivered by intermittent bolus meals, rather than continuously.ObjectivesThe objective of this study was to determine the long-term effects of feeding frequency on organ growth and the mechanism by which feeding frequency modulates protein anabolism in these organs.MethodsEighteen neonatal pigs were fed by gastrostomy tube the same amount of a sow milk replacer either by continuous infusion (CON) or on an intermittent bolus schedule (INT). After 21 d of feeding, the pigs were killed without interruption of feeding (CON; n = 6) or immediately before (INT-0; n = 6) or 60 min after (INT-60; n = 6) a meal, and fractional protein synthesis rates and activation indexes of signaling pathways that regulate translation initiation were measured in the heart, jejunum, ileum, kidneys, and liver.ResultsCompared with continuous feeding, intermittent feeding stimulated the growth of the liver (+64%), jejunum (+48%), ileum (+40%), heart (+64%), and kidney (+56%). The increases in heart, kidney, jejunum, and ileum masses were proportional to whole body lean weight gain, but liver weight gain was greater in the INT-60 than the CON, and intermediate for the INT-0 group. For the liver and ileum, but not the heart, kidney, and jejunum, INT-60 compared with CON pigs had greater fractional protein synthesis rates (22% and 48%, respectively) and was accompanied by an increase in ribosomal protein S6 kinase 1 and eukaryotic initiation factor 4E binding protein 1 phosphorylation.ConclusionsThese results suggest that intermittent bolus compared with continuous orogastric feeding enhances organ growth and that in the ileum and liver, intermittent feeding enhances protein synthesis by stimulating translation initiation.

Establishment of a Recombinant AAV2/HBoV1 Vector Production System in Insect Cells.

We have previously developed an rAAV2/HBoV1 vector in which a recombinant adeno-associated virus 2 (rAAV2) genome is pseudopackaged into a human bocavirus 1 (HBoV1) capsid. Recently, the production of rAAV2/HBoV1 in human embryonic kidney (HEK) 293 cells has been greatly improved in the absence of any HBoV1 nonstructural proteins (NS). This NS-free production system yields over 16-fold more vectors than the original production system that necessitates NS expression. The production of rAAV with infection of baculovirus expression vector (BEV) in the suspension culture of Sf9 insect cells is highly efficient and scalable. Since the replication of the rAAV2 genome in the BEV system is well established, we aimed to develop a BEV system to produce the rAAV2/HBoV1 vector in Sf9 cells. We optimized the usage of translation initiation signals of the HBoV1 capsid proteins (Cap), and constructed a BEV Bac-AAV2Rep-HBoV1Cap, which expresses the AAV2 Rep78 and Rep52 as well as the HBoV1 VP1, VP2, and VP3 at the appropriate ratios. We found that it is sufficient as a trans helper to the production of rAAV2/HBoV1 in Sf9 cells that were co-infected with the transfer Bac-AAV2ITR-GFP-luc that carried a 5.4-kb oversized rAAV2 genome with dual reporters. Further study found that incorporation of an HBoV1 small NS, NP1, in the system maximized the viral DNA replication and thus the rAAV2/HBoV1 vector production at a level similar to that of the rAAV2 vector in Sf9 cells. However, the transduction potency of the rAAV2/HBoV1 vector produced from BEV-infected Sf9 cells was 5–7-fold lower in polarized human airway epithelia than that packaged in HEK293 cells. Transmission electron microscopy analysis found that the vector produced in Sf9 cells had a high percentage of empty capsids, suggesting the pseudopackage of the rAAV2 genome in HBoV1 capsid is not as efficient as in the capsids of AAV2. Nevertheless, our study demonstrated that the rAAV2/HBoV1 can be produced in insect cells with BEVs at a comparable yield to rAAV, and that the highly efficient expression of the HBoV1 capsid proteins warrants further optimization.

Prematurity blunts the feeding-induced stimulation of translation initiation signaling and protein synthesis in muscle of neonatal piglets.

Postnatal growth of lean mass is commonly blunted in preterm infants and may contribute to short- and long-term morbidities. To determine whether preterm birth alters the protein anabolic response to feeding, piglets were delivered at term or preterm, and fractional protein synthesis rates (Ks) were measured at 3 days of age while fasted or after an enteral meal. Activation of signaling pathways that regulate protein synthesis and degradation were determined. Relative body weight gain was lower in preterm than in term. Gestational age at birth (GAB) did not alter fasting plasma glucose or insulin, but when fed, plasma insulin and glucose rose more slowly, and reached peak value later, in preterm than in term. Feeding increased Ks in longissimus dorsi (LD) and gastrocnemius muscles, heart, pancreas, and kidney in both GAB groups, but the response was blunted in preterm. In diaphragm, lung, jejunum, and brain, feeding increased Ks regardless of GAB. Liver Ks was greater in preterm than term and increased with feeding regardless of GAB. In all tissues, changes in 4EBP1, S6K1, and PKB phosphorylation paralleled changes in Ks. In LD, eIF4E·eIF4G complex formation, phosphorylation of TSC2, mTOR, and rpS6, and association of mammalian target of rapamycin (mTOR1) complex with RagA, RagC, and Rheb were increased by feeding and blunted by prematurity. There were no differences among groups in LD protein degradation markers. Our results demonstrate that preterm birth reduces weight gain and the protein synthetic response to feeding in muscle, pancreas, and kidney, and this is associated with blunted insulin- and/or amino acid-induced translation initiation signaling.

Optimizing Phage Translation Initiation

Phage as an anti-bacterial agent must be efficient in killing bacteria, and consequently needs to replicate efficiently. Protein production is a limiting step in replication in almost all forms of life, including phages. Efficient protein production depends on the efficiency of translation initiation, elongation and termination, with translation initiation often being rate limiting. Initiation signals such as Shine-Dalgarno (SD) sequences and start codon are decoded by anti-SD sequences and initiation tRNA, respectively. While the decoding machinery cannot be readily modified, the signals can be engineered to increase the efficiency of their decoding. Here I review our understanding of the translation machinery to facilitate the engineering of optimal translation initiation signals for facilitating the design of phage protein-coding genes, including 1) accurate characterization of the 3’ end of 16S rRNA by using RNA-Seq data, 2) identification of the optimal SD/aSD interaction, and 3) reduction of secondary structure in sequences flanking the start codon.

The effect of mesenchymal stem cells' secretome on lung cancer progression is contingent on their origin: primary or metastatic niche

The fatality of non-small-cell lung cancer (NSCLC) and the role of the cancer microenvironment in its resistance to therapy are long recognized. Accumulating data allocate a significant role for mesenchymal stem cells (MSCs) in the malignant environment. Previously, we have demonstrated that MSCs from NSCLC metastatic bone marrow (BM) niche deleteriously affected NSCLC cells. Here, we have decided to examine the effect of MSCs from the primary niche of the lung (healthy or adjacent to tumor) on NSCLC phenotype. We cultured NSCLC cell lines with healthy/NSCLC lung-MSCs conditioned media (secretome) and showed elevation in cells' MAPKs and translation initiation signals, proliferation, viability, death, and migration. We also established enhanced autophagy and epithelial to mesenchymal transition processes. Moreover, we observed that MSCs from tumor adjacent sites (pathological niche) exhibited a more profound effect than MSCs from healthy lung tissue. Our findings underscore the capacity of the lung-MSCs to modulate NSCLC phenotype. Interestingly, both tumor adjacent (pathological) and distant lung-MSCs (healthy) promoted the NSCLC's TI, proliferation, migration, and epithelial to mesenchymal transition, yet the pathological MSCs displayed a greater affect. In conclusion, by comparing the effects of normal lung-MSCs, NSCLC adjacent MSCs, and BM-MSCs, we have established that the primary and metastatic niches display opposite and critical effects that promote the cancerous systemic state. Specifically, the primary site MSCs promote the expansion of the malignant clone and its dispersion, whereas the metastatic site MSCs facilitates the cells re-seeding. We suggest that sabotaging the cross-talk between MSCs and NSCLC affords effective means to inhibit lung cancer progression and will require different targeting strategies in accordance with niche/disease stage.This study demonstrates that lung mesenchymal stem cells promote non-small cell lung cancer proliferation and migration in a MAPK/translation initiation/autophagy-dependent manner. The authors describe how primary and metastatic niches display opposite and critical effects, both crucial to cancer progression.

Visualizing translation by ensemble cryo‐EM

Translation of mRNA is a key step of gene expression regulation and a therapeutic target. Translation is governed by ribosome dynamics. To visualize the translational machinery in action, we determine high‐resolution ensembles of structures by cryo‐EM. I will discuss how this approach provides insights into the essential aspects of gene expression, such as translation initiation, translation fidelity and ribosome‐induced stress signaling.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.