Reconstitution of functional mRNA-protein complexes in a rabbit reticulocyte cell-free translation system

Development of Artificial Cell Models Using Microfluidic Technology and Synthetic Biology

Giant lipid vesicles or liposomes are primarily composed of phospholipids and form a lipid bilayer structurally similar to that of the cell membrane. These vesicles, like living cells, are 5-100 μm in diameter and can be easily observed using an optical microscope. As their biophysical and biochemical properties are similar to those of the cell membrane, they serve as model cell membranes for the investigation of the biophysical or biochemical properties of the lipid bilayer, as well as its dynamics and structure. Investigation of membrane protein functions and enzyme reactions has revealed the presence of soluble or membrane proteins integrated in the giant lipid vesicles. Recent developments in microfluidic technologies and synthetic biology have enabled the development of well-defined artificial cell models with complex reactions based on the giant lipid vesicles. In this review, using microfluidics, the formations of giant lipid vesicles with asymmetric lipid membranes or complex structures have been described. Subsequently, the roles of these biomaterials in the creation of artificial cell models including nanopores, ion channels, and other membrane and soluble proteins have been discussed. Finally, the complex biological functions of giant lipid vesicles reconstituted with various types of biomolecules has been communicated. These complex artificial cell models contribute to the production of minimal cells or protocells for generating valuable or rare biomolecules and communicating between living cells and artificial cell models.

Control of translation and miRNA-dependent repression by a novel poly(A) binding protein, hnRNP-Q

The heterogeneous nuclear ribonucleoprotein Q2 competitively binds mRNA poly(A) tails to regulate translational and miRNA-related functions of PABP.

Translation control often operates via remodeling of messenger ribonucleoprotein particles. The poly(A) binding protein (PABP) simultaneously interacts with the 3′ poly(A) tail of the mRNA and the eukaryotic translation initiation factor 4G (eIF4G) to stimulate translation. PABP also promotes miRNA-dependent deadenylation and translational repression of target mRNAs. We demonstrate that isoform 2 of the mouse heterogeneous nuclear protein Q (hnRNP-Q2/SYNCRIP) binds poly(A) by default when PABP binding is inhibited. In addition, hnRNP-Q2 competes with PABP for binding to poly(A) in vitro. Depleting hnRNP-Q2 from translation extracts stimulates cap-dependent and IRES-mediated translation that is dependent on the PABP/poly(A) complex. Adding recombinant hnRNP-Q2 to the extracts inhibited translation in a poly(A) tail-dependent manner. The displacement of PABP from the poly(A) tail by hnRNP-Q2 impaired the association of eIF4E with the 5′ m⁷G cap structure of mRNA, resulting in the inhibition of 48S and 80S ribosome initiation complex formation. In mouse fibroblasts, silencing of hnRNP-Q2 stimulated translation. In addition, hnRNP-Q2 impeded let-7a miRNA-mediated deadenylation and repression of target mRNAs, which require PABP. Thus, by competing with PABP, hnRNP-Q2 plays important roles in the regulation of global translation and miRNA-mediated repression of specific mRNAs.

The regulation of mRNA translation and stability is of paramount importance for almost every cellular function. In eukaryotes, the poly(A) binding protein (PABP) is a central regulator of both global and mRNA-specific translation. PABP simultaneously interacts with the 3′ poly(A) tail of the mRNA and the eukaryotic translation initiation factor 4G (eIF4G). These interactions circularize the mRNA and stimulate translation. PABP also regulates specific mRNAs by promoting miRNA-dependent deadenylation and translational repression. A key step in understanding PABP's functions is to identify factors that affect its association with the poly(A) tail. Here we show that the cytoplasmic isoform of the mouse heterogeneous nuclear ribonucleoprotein Q (hnRNP-Q2/SYNCRIP), which exhibits binding preference to poly(A), interacts with the poly(A) tail by default when PABP binding is inhibited. In addition, hnRNP-Q2 competes with PABP for binding to the poly(A) tail. Depleting hnRNP-Q2 stimulates translation in cell-free extracts and in cultured cells, in agreement with its function as translational repressor. In addition, hnRNP-Q2 impeded miRNA-mediated deadenylation and repression of target mRNAs, which requires PABP. Thus, competition from hnRNP-Q2 provides a novel mechanism by which multiple functions of PABP are regulated. This regulation could play important roles in various biological processes, such as development, viral infection, and human disease.

A distinct FMRP polysomal population at an advanced stage of mammalian erythropoiesis

The fragile-X syndrome is a mental disorder caused by the absence of FMRP (the Fragile-X Mental Retardation Protein). While FMRP is found to be associated with the ribosomal components, its precise translational function remains to be defined. Here we report that FMRP is not found with the abundant free polysomes of the reticulocyte lysate, but rather with a heavy ribonucleoprotein complex sedimenting over 400S. This unusual distribution of FMRP at an advanced stage of mammalian erythropoiesis may unveil the discrete role of FMRP in translation.

Why, when and how does the poly(A) tail shorten during mRNA translation?

1. The length of the poly(A) tail at the 3'-end of mRNA may control protein synthesis by bringing the 3'-end in close proximity to the 5'-end of the noncoding region as well as increasing the duration of mRNA translation by its binding to the poly(A) binding protein. 2. The rate-limiting step in the decay of the body of the message is the shortening of a long poly(A) tail during mRNA translation. The shortening of the poly(A) tail occurs during pre-elongation in the protein synthesis cycle. 3. The shortening of the poly(A) tail during mRNA translation may not involve RNase activity, however poly(A) binding protein seems to play a role, at least in part, in shortening of the poly(A) tail.

Brain non-adenylated mRNAs

Most eukaryotic messenger RNA (mRNA) species contain a 3'-poly(A) tract. The histone mRNAs are a notable exception although a subclass of histone-encoding mRNAs is polyadenylated. A class of mRNAs lacking a poly(A) tail would be expected to be less stable than poly(A)+ mRNAs and might, like the histones, have a half-life that varied in response to changes in the intracellular milieu. Brain mRNA exhibits an unusually high degree of sequence complexity; studies published ten years ago suggested that a large component of this complexity might be present in a poly(A)- mRNA population that was expressed postnatally. The question of the existence of a complex class of poly(A)- brain mRNAs is particularly tantalizing in light of the heterogeneity of brain cells and the possibility that the stability of these poly(A)- mRNAs might vary with changes in synaptic function, changing hormonal stimulation or with other modulations of neuronal function. The mRNA complexity analyses, although intriguing, did not prove the existence of the complex class of poly(A)- brain mRNAs. The observed mRNA complexity could have resulted from a variety of artifacts, discussed in more detail below. Several attempts have been made to clone members of this class of mRNA. This search for specific poly(A)- brain mRNAs has met with only limited success. Changes in mRNA polyadenylation state do occur in brain in response to specific physiologic stimuli; however, both the role of polyadenylation and de-adenylation in specific neuronal activities and the existence and significance of poly(A)- mRNAs in brain remain unclear.

Identification of proteins associating with poly(A)-binding-protein mRNA

Synthesis of poly(A)-binding protein is regulated at the translational level. We have investigated the binding of proteins to this mRNA on the premise that the protein(s) of the mRNP complex may be involved in regulating the expression of the mRNA. We found the first 243 nucleotides of the 5' untranslated region to contain sequences essential for RNP formation. A large, single-stranded bulge structure encompassing stretches rich in adenine nucleotides and a potential stem-loop domain appear to be the primary sites for protein binding. Removal of the 243-nucleotide segment results in a drastic reduction in protein binding and a concomitant increase in translational efficiency in vitro. We suggest that proteins binding to this region, including poly(A)-binding protein itself, may be essential for regulating translation of this mRNA.

Proteins associated with the messenger ribonucleoprotein particle for the estrogen-regulated apolipoprotein II mRNA

The stability of the mRNA for apolipoprotein (apo) II is regulated by estrogen [Gordon et al. (1988) J. Biol. Chem. 263, 2625-2631]. On the hypothesis tha estrogen regulation of apoII mRNA stability is mediated through mRNA-protein interaction, we have examined the messenger ribonucleoprotein particle (mRNP) for apoII mRNA following release from chicken liver polyribosomes. Polyribosomes containing undegraded apoII mRNA were obtained when tissue was homogenized without detergent, and polyribosomes were isolated following simultaneous addition of detergent and magnesium to a 20000g supernatant. ApoII mRNP released by EDTA sedimented at 12-18 S in sucrose gradients, and banded at rho = 1.4 g/mL in CsCl isopycnic centrifugation, indicative of a 3:1 ratio of protein to mRNA. A fraction in which apoII mRNP was enriched to 40-50% of total mRNP was prepared by successive size fractionation steps on sucrose gradients. Proteins associated with sucrose gradient enriched apoII mRNP were examined by iodination of UV-cross-linked proteins followed by SDS-polyacrylamide gel electrophoresis. Comparisons of proteins in highly enriched apoII mRNP to proteins in mRNP from non-estrogen-treated rooster liver did not reveal any differences. This result suggests that the major proteins associated with apoII mRNA are mRNP proteins also associated with the bulk of liver mRNAs.

A 60-kDa protein from rabbit reticulocytes specifically recognizes the capped 5' end of beta-globin mRNA

The binding of proteins from rabbit reticulocyte lysate to in-vitro-generated beta-globin mRNA and its defined segments was investigated using ultraviolet-cross-linking experiments as well as gel-retardation assays. Under stringent conditions, only three proteins (72, 60 and 50 kDa) were found associated with full-length beta-globin mRNA at different positions. The 72-kDa protein is most likely the poly(A)-binding protein and binds, as expected, to the poly(A) tail, whereas the 50-kDa protein exhibits affinity for the trailer region of beta-globin mRNA. The binding region of the 60-kDa protein is located at the 5' end of beta-globin mRNA. The interaction of this protein is dependent on the presence of the 5' cap structure, as indicated by competition experiments using an uncapped beta-globin-mRNA leader segment. Further competition experiments with beta-globin mRNA, deleted in part in the leader region, suggest that, besides the cap structure, certain sequence elements are necessary for the interaction of the 60-kDa protein and the beta-globin mRNA leader.

Distribution and activity of alternatively spliced Alzheimer amyloid peptide precursor and scrapie PrP mRNAs on rat brain polysomes

Mammalian brains contain low levels of the Alzheimer amyloid precursor variants (AAPPs) and the normal form of the scrapie agent protease-resistant protein (PrPc); however, their mRNAs are readily detectable. To understand these discrepancies we have investigated some aspects of the translational regulation of these mRNAs. An accurate blot-hybridization procedure was developed to measure absolute amounts of mRNA. Rat brain contains the following mRNA levels (ng/g tissue) AAPP(695), 170; AAPP(751/770), 63; PrPc, 144; actin, 615; glyceraldehyde-3-phosphate dehydrogenase (G3PDH), 359; ferritin, 148. The method was also used to determine the distribution of mRNAs between translationally active polysomes and translationally inactive ribonucleoprotein protein particles (mRNPs). More than 90% of G3PDH and actin mRNAs were associated with polysomal RNA; whereas, ferritin light chain mRNA was predominantly (90%) in mRNP RNA. The degree of cross-contamination of mRNPs with polysomes was less than 10%. Probes specific for the scrapie PrP protein and the AAPP(695) splice junction revealed that 70% of these mRNAs were associated with polysomes. One-half of AAPP(751/770) mRNAs (which comprise 20-30% of all AAPP mRNA in brain) were found in polysomes. We conclude therefore that both scrapie and AAPP mRNAs are subject to translational regulation in rat brain. Evidence from in vitro translational experiments confirm the message distribution determined by blot hybridization and corroborate the hypothesis that AAPP is subject to partial post-transcriptional regulation. Nevertheless, the low tissue levels of AAPP and PrPc must result primarily from their relatively rapid turnover.

Binding of globin mRNA, beta-globin mRNA segments and RNA homopolymers by immobilized protein of polysomal globin messenger ribonucleoprotein

The binding of rabbit globin mRNA, in-vitro-generated beta-globin mRNA segments, and RNA homopolymers by proteins of rabbit reticulocyte polysomal messenger ribonucleoproteins (mRNP) after SDS gel electrophoresis and electroblotting was examined. The polysomal mRNP proteins have a higher affinity for mRNA than for rRNA and tRNA while having a higher affinity for polypurine than polypyrimidine homopolymers. Binding experiments with synthetic poly(A) and with segments of beta-globin mRNA transcribed from a cDNA in vitro revealed a set of polysomal mRNP proteins which preferentially bind the poly(A)-free beta-globin mRNA. A protein of Mr 90,000 binds specifically the 3'-nontranslated trailer of the poly(A)-free beta-globin mRNA and not the poly(A)-containing globin mRNA. Another set of proteins preferentially binds poly(A). The latter group of proteins contains a prominent species of Mr 72,000, which is most likely the rabbit poly(A)-binding protein. Three polysomal mRNP proteins which bound rabbit globin mRNA did not bind preferentially any of the other RNA probes used.

Growth factor regulated expression of poly(A)+ binding protein messenger RNA

A 72,000 mol wt protein designated PABP binds to the poly(A)+ track of messenger RNAs with high affinity and has been suggested to play an important role in mRNA metabolism in eucaryotic cells. We have employed a human PABP cDNA probe to study the expression of this gene at the mRNA level in BALB/c3T3 mouse cells under different growth conditions and in exponentially growing HeLa cells throughout the cell division cycle. We describe experiments which establish that in BALB/c3T3 cells the expression of this gene is growth factor regulated. Moreover, the gene behaves like a primary response gene in that its induction in quiescent cells does not require the prior synthesis of other growth factor-regulated proteins. In exponentially growing HeLa cells PABP mRNA is expressed throughout the cell division cycle indicating that the expression of this gene is not limited to a specific phase of the cell cycle.

Characterization of mouse reticulocyte free globin mRNP

Globin messenger ribonucleoprotein particles (free and polysomal) from mouse reticulocyte lysates were characterized for their mRNA composition, translational activity as well as the proteins in direct contact with them. In contrast to the homogeneous single-peak distribution of rabbit and duck reticulocyte free mRNPs, mouse free mRNP particles were heterogeneously dispersed on the sucrose density gradient into two major domains called region I and region II. Region I appeared enriched with alpha-globin mRNP and region II with beta-globin mRNP. mRNP from both regions was translationally active. Examination of lysates prepared from beta-thalassemic mice revealed a reduction of translatable beta minor mRNP within region I, supporting the hypothesis of a compensatory recruitment of beta minor free mRNP into polysomes in beta-thalassemic mice.

Growth-related expression of a 72,000 molecular weight poly(A)+ mRNA binding protein

In this communication, we have studied a 72,000 mol w (p72) host protein which reacts with a mouse monoclonal antibody (PAb6) directed against antigenic determinants on the Simian virus 40 (SV40) large T antigen protein that map 5' of 0.42 map units on the viral genome. The p72 protein is an abundant basic (pI greater than 7) cytoplasmic protein found in both SV40-transformed and untransformed parental cells and in cell lines derived from normal human and tumor tissue. By two-dimensional gel analysis and Western blot analysis the p72 protein identified by PAb6 is indistinguishable from the 72,000 mol w protein PABP associated with the poly(A)+ tract of cytoplasmic messenger RNA molecules. In normal human peripheral blood mononuclear cells stimulated to proliferate with the T-cell-specific mitogenic lectin phytohemagglutinin the synthesis and cytoplasmic accumulation of p72 occurs very early during the G0----G1-phase transition. The p72 protein is also expressed in proliferating and differentiated human promyelocytic HL60 cells indicating that the expression of this protein is not strictly limited to cycling cells.

The poly(A)-binding protein facilitates in vitro translation of poly(A)-rich mRNA

To investigate the role of the 73-kDa poly(A)-binding protein in protein synthesis, the effect of the addition of homo-polyribonucleotides on the translation of polyadenylated and non-adenylated mRNA was studied in the rabbit reticulocyte lysate. Poly(A) was found to be the most effective polynucleotide in inhibiting duck-globin mRNA translation, whereas it had no effect on the translation of polyribosomal duck-globin mRNP, or on the endogenous synthesis of the rabbit reticulocyte lysate. The translation of poly(A)-free mRNA was not affected by the addition of poly(A). Furthermore, we found that the inhibiting effect of poly(A) can be reversed by addition of purified poly(A)-binding protein. It is thus likely that the 73-kDa poly(A)-binding protein is an essential factor necessary for poly(A)-rich mRNA translation.

Photocrosslinking of proteins to maternal mRNA in Xenopus oocytes

Ultraviolet irradiation was used to covalently crosslink poly(A) RNA and associated proteins in Xenopus oocytes and reticulocytes. Each cell type contained similar as well as unique crosslinked proteins. The somatic cells contained a single 78-kDa 3' poly(A) tract binding protein while oocyte poly(A), however, was bound by this protein and at least three additional proteins. Based on the mass of poly(A) RNA, oocytes in their earliest stages of growth contained crosslinked proteins that were generally more prevalent than in fully grown oocytes. An investigation of possible messenger RNA-specific proteins was undertaken by a series of RNA injection experiments. Two radiolabeled SP6-derived mRNAs were injected into oocytes; the first, globin mRNA, assembled into polysomes, while the second, a maternal mRNA termed G10, entered a nontranslating ribonucleoprotein compartment. Following the induction of oocyte maturation, additional globin mRNA was recruited onto polysomes while G10 mRNA remained a nontranslating mRNP. The proteins that can be crosslinked to these injected mRNAs were detected by 32P nucleotide transfer. Each mRNA associated with shared as well as unique proteins, some of which were detected only in mature oocytes. The possible function of these proteins is discussed.

Inhibition of rabbit beta-globin synthesis by complementary oligonucleotides: identification of mRNA sites sensitive to inhibition

We tested the effects of a series of synthetic oligonucleotides (hybridons) complementary to the 5' noncoding and coding regions of rabbit beta-globin mRNA on endogenous protein synthesis in a rabbit reticulocyte cell-free translation system. With highly purified hybridons inhibition was completely specific for beta-globin. The sites most sensitive to inhibition are the beginning of the 5' noncoding region and a sequence including the initiation codon and several upstream bases. The region between these was relatively insensitive to inhibition. The sites of maximum sensitivity coincide with known protein binding sites, suggesting that hybridons exert their effects in part by blocking the binding of proteins required for translation. Their effectiveness seems related to the ease with which they are displaced by ribosomes.

Purification and properties of a protein component of messenger ribonucleoprotein particles that shares a common epitope with eucaryotic elongation factor Tu

A 62-kDa polypeptide, which reacts with antibodies directed against a peptide corresponding to a portion of the amino-terminal structure of eucaryotic elongation factor Tu (eEF-Tu), was purified from the 0.5 M NaCl wash of rabbit reticulocyte polysomes. Previous work has shown that this polypeptide is a constituent of messenger ribonucleoprotein particles (mRNPs) from a variety of mammalian cell types [Greenberg, J.R. and Carroll, E. C. (1985) Mol. Cell Biol. 5, 342-351]. The purified polypeptide bound mRNA as well as rRNA using a nitrocellulose-filter assay. The same nitrocellulose-filter assay failed to detect binding to GTP. Using a competition-binding assay, it was established that the purified polypeptide interacts with poly(U) and poly(G) but not with poly(A). This preference for synthetic polynucleotides was the same as found for eEF-Tu [Slobin, L.I. (1983) J. Biol. Chem. 258, 4895-4900]. Furthermore, treatment of the purified RNA-binding protein with trypsin resulted in a rapid cleavage of two peptide bonds resulting in fragments of 60 kDa and 53 kDa. Trypsin also cleaves eEF-Tu rapidly at two bonds resulting in two large polypeptide fragments [Slobin, L.I., Clark, R.V. & Olson, M.O.J. (1981) Biochemistry 20, 5761-5767]. The amino acid sequence of the first 39 residues of the purified RNA-binding protein was determined and found to possess no homology to eEF-Tu.

Eukaryotic elongation factor Tu is present in mRNA-protein complexes

By two-dimensional gel electrophoresis, partial peptide mapping, and antibody binding we have shown that eukaryotic elongation factor Tu is in close contact with mRNA in rabbit reticulocytes. It can be crosslinked to mRNA by irradiating both polysomes and 40-80 S mRNA-protein complexes with short-wave UV light. To our knowledge this is the first case in which a known translation factor has been shown to be associated with mRNA in native ribonucleoproteins.

Identification of the proteins in direct contact with duck globin mRNA

Proteins in direct contact with translationally active and repressed duck globin mRNA were determined by irradiating blood or lysates with ultraviolet light. Cross-linked proteins from polyribosomes and free mRNP particles were 14C-labeled by reductive methylation and identified on SDS-polyacrylamide gels upon autoradiography. Results indicate that ten cross-linked proteins are common to both polysomal and free mRNP, however, a 44 kDa protein appears to be specific for repressed mRNP particles. Furthermore, the notable lack of cross-linked proteins in the 20-30 kDa range in free mRNP supports the view that the characteristic low molecular mass 'prosomal' proteins, previously found associated with translationally repressed duck globin free mRNP [(1984) EMBO J. 3, 29-34], do not interact directly with the mRNA molecule.

Eukaryotic initiation factor 4A stimulates translation in microinjected Xenopus oocytes

The injection of heterologous mRNA into fully grown Xenopus oocytes results not only in the synthesis of the heterologous protein but also in a reciprocal decrease in the synthesis of endogenous proteins. This indicates that injected and endogenous mRNAs compete for some component which is rate-limiting for translation in oocytes. We have attempted to identify this rate-limiting translational component. We find that heterologous and homologous polysomes compete with endogenous mRNAs as effectively as naked mRNA, indicating that polysomes do not contain detectable levels of the rate-limiting factor. In addition, we have used micrococcal nuclease digestion and a mRNA-specific oligonucleotide to destroy the mRNA component of polysomes. The remaining polysome factors, when injected into oocytes, failed to stimulate translation. When several eukaryotic translation initiation factors were injected into oocytes, initiation factor 4A consistently increased general oocyte protein synthesis by about twofold. It is possible that the availability of eIF-4A in oocytes is a key factor in limiting the overall rate of protein synthesis.

Identification and characterization of developmentally regulated mRNP proteins of Dictyostelium discoideum

The isolation of poly(A)+ polysomal and nonpolysomal RNPs by oligo(dT)-cellulose chromatography has led to the identification of more than 20 polypeptides that bind to the poly(A)+ mRNA in growing Dictyostelium cells. Most of these polypeptides were identified in experiments using short-wave UV light (254 nm) to crosslink specifically bound proteins to the RNA. Digestion of the RNPs with ribonucleases A and T1 prior to their application to oligo(dT)-cellulose permitted the isolation of the 3' poly(A)-protein complexes. In polysomal RNPs, two major polypeptides, with molecular weights of 31,000 (p31) and 31,500 (p31.5), are bound to poly(A). These proteins can also be purified from cytoplasmic extracts by affinity chromatography on poly(A)-Sepharose. Partial proteolytic digestion of p31 and p31.5 indicates that they are closely related. The UV-crosslinking experiments established that p31 and p31.5 bind to the non-poly(A) segments of mRNA as well. In nonpolysomal RNPs, p31 and a polypeptide with a molecular weight of 29,500 (p29.5) are the major species associated with poly(A). Partial proteolytic digestion of p29.5 indicates that it is closely related to p31 and p31.5. Only small amounts of p29.5 were observed in the polysomal poly(A)-protein complexes. Early in Dictyostelium development, when cellular translation activity is sharply reduced, most of the p29.5, p31 and p31.5 present is selectively degraded. These observations are consistent with a translational role for these proteins.

The storage of globin mRNA during the inhibition of protein synthesis by heme deprivation

The inhibition of protein synthesis in reticulocytes and their lysates caused by heme-deprivation is reversible on restoration of an optimal heme concentration. Inhibition is accompanied by the disaggregation of polyribosomes and the accumulation of components of the translational mechanism. By determining the fate of labeled globin 9S mRNA added to an unfractionated reticulocyte lysate cell-free system, we find that normal cellular mRNA accumulates during inhibition in 20S and 48S complexes and in a complex which sediments just ahead of the 80S ribosome dimer OD260 peak (designated as greater than or equal to 80S complex)1. The 20S and greater than 80S complexes are the major pools of stored mRNA which is readily translated if optimal heme conditions are restored. In the 48S complex, however, the mRNA remains non-functional, and the complex is abortive, probably as a result of deacylation of the Met.tRNAf.