The KH domain mediates RNA binding in a wide range of proteins. Here we investigate the RNA-binding properties of two abundant RNA-binding proteins, ␣CP-2KL and heterogeneous nuclear ribonucleoprotein (hnRNP) K. These proteins constitute the major poly(C) binding activity in mammalian cells, are closely related on the basis of the structures and positioning of their respective triplicated KH domains, and have been implicated in a variety of post-transcriptional controls. By using SELEX, we have obtained sets of high affinity RNA targets for both proteins. The primary and secondary structures necessary for optimal protein binding were inferred in each case from SELEX RNA sequence comparisons and confirmed by mutagenesis and structural mapping. The target sites for ␣CP-2KL and hnRNP K were both enriched for cytosine bases and were presented in a single-stranded conformation. In contrast to these shared characteristics, the optimal target sequence for hnRNP K is composed of a single short "Cpatch" compatible with recognition by a single KH domain whereas that for ␣CP-2KL encompassed three such C-patches suggesting more extensive interactions. The binding specificities of the respective SELEX RNAs were confirmed by testing their interactions with native proteins in cell extracts, and the importance of the secondary structure in establishing an optimized ␣CP-2KL-binding site was supported by comparison of SELEX target structure with that of the native human ␣-globin 3-untranslated region. These data indicate that modes of macromolecular interactions of arrayed KH domains can differ even among closely related KH proteins and that binding affinities are substantially dependent on the presentation of the target site within the RNA secondary structure.Post-transcriptional controls play an important role in the determination of gene expression. The controls over RNA splicing, transport, localization, translation, and/or stability either contribute to or are the major component(s) of gene modulation during development (1). These controls are often mediated via interactions between specific mRNA sequences and/or structures and corresponding trans-acting RNA-binding proteins (2, 3). In several cases such interactions have been described in detail and emphasize the importance of primary and higher order structural RNA motifs (4 -9). The number and variety of RNA-binding proteins reported in the literature are rapidly expanding. Some of these RNA-binding proteins, such as those associated with heterogenous nuclear RNA, show low sequence specificity, suggesting general packaging functions (3, 10). Others demonstrate high level RNA-binding specificity suggesting circumscribed functions in gene control. Examples of the latter group of proteins include cytosolic iron-response element-binding protein (6, 11), human immunodeficiency virus Rev response element-binding protein (8), and the sex-lethal alternative-splicing factor (13). RNA-binding proteins, like their DNA-binding protein counterparts, tend to be modular in structure wit...

The hok/sok system of plasmid R1, which mediates plasmid stabilization via killing of plasmid-free segregants, encodes two genes: hok and sok. The hok gene product is a potent cell-killing protein. The expression of hok is regulated post-transcriptionally by the sok gene-encoded repressor, an antisense RNA complementary to the hok mRNA leader region. We show here that the hok mRNA is very stable, while the sok RNA decays rapidly. We also observe a new hok mRNA species which is 70 nucleotides shorter in the 3'-end than the full-length hok transcript. The appearance of the truncated hok mRNA was found to be regulated by the sok antisense RNA. Furthermore, the presence of the truncated hok mRNA was found to be correlated with efficient expression of the Hok protein. On the basis of these findings, we propose an extended model in order to explain the killing of plasmid-free segregants by the hok/sok system.

The hok/sok system of plasmid R1, which mediates plasmid stabilization by killing of plasmid‐free segregants, codes for two RNA species, Hok mRNA and Sok antisense RNA. The lethal expression of hok is inhibited post‐transcriptionally by the 67 nt Sok‐RNA. In this paper, we analyse the secondary structure of Sok‐RNA and the binding of Sok‐RNA to Hok mRNA in vitro. The reaction between the two RNAs leads to the formation of a complete duplex in which Sok‐RNA is hybridized over its entire length to Hok mRNA. The second‐order rate constant of duplex formation was determined to be approximately 1 × 10(5) M‐1s‐1. Mutations in the 5′‐end single‐stranded leader of Sok‐RNA severely reduced the binding rate to wt Hok mRNA, whereas loop mutations in Sok‐RNA had no such effect. The reduced binding rates were paralleled by abolished in vivo regulatory properties. These results suggest that, unlike in other well‐characterized antisense/target RNA systems, the initial recognition reaction between Sok‐RNA and Hok mRNA takes place between the single‐stranded 5′‐end of Sok‐RNA and the complementary region in Hok mRNA, without the involvement of an antisense loop in the initial binding step. Furthermore, the finding that Sok‐RNA competes with the 3′‐end of full‐length Hok mRNA for binding to the mok translational initiation region adds to the complexity of killer gene regulation.

The gene systems hok/sok of R1, srnB of F and pnd of R483 mediate plasmid maintenance by killing of plasmid‐free segregants. Translation of the very stable mRNAs encoding the killer proteins is regulated by small unstable antisense RNAs. The differential decay rates of the inhibitory antisense RNAs and the mRNAs encoding the killer proteins is the basis for the onset of killer mRNA translation in newborn plasmid‐free segregants and the killing of these cells. We have suggested previously that this requires that the killer mRNAs occur in two forms. A translationally inactive form was proposed to be converted into a 3′‐truncated, translationally active mRNA. In the presence of the antisense RNA, translation from this killer mRNA should be inhibited. In this communication we present in vivo and in vitro evidence that support this model. The requirement for 3′‐processing for killer gene expression is demonstrated. By using in vitro techniques it is shown that full‐length Hok mRNA is translationally inactive, whereas a 3′‐end truncated version of the Hok mRNA is translationally active. In vitro secondary structure probing suggests that the 3′‐end of the full‐length Hok mRNA folds back onto the translational initiation region of the mok gene and thereby inhibits translation of the mRNA. By inference we conclude that the Pnd and SrnB mRNAs are regulated by a similar mechanism.

The CD40/CD40L axis plays a central role in the generation of humoral immune responses and is an attractive target for treating autoimmune diseases in the clinic. Here, we report the generation and clinical results of a CD40L binding protein, VIB4920, which lacks an Fc domain, therefore avoiding platelet-related safety issues observed with earlier monoclonal antibody therapeutics that targeted CD40L. VIB4920 blocked downstream CD40 signaling events, resulting in inhibition of human B cell activation and plasma cell differentiation, and did not induce platelet aggregation in preclinical studies. In a phase 1 study in healthy volunteers, VIB4920 suppressed antigen-specific IgG in a dose-dependent fashion after priming and boosting with the T-dependent antigen, KLH. Furthermore, VIB4920 significantly reduced circulating Ki67+ dividing B cells, class-switched memory B cells, and a plasma cell gene signature after immunization. In a phase 1b proof-of-concept study in patients with rheumatoid arthritis, VIB4920 significantly decreased disease activity, achieving low disease activity or clinical remission in more than 50% of patients in the two higher-dose groups. Dose-dependent decreases in rheumatoid factor autoantibodies and Vectra DA biomarker score provide additional evidence that VIB4920 effectively blocked the CD40/CD40L pathway. VIB4920 demonstrated a good overall safety profile in both clinical studies. Together, these data demonstrate the potential of VIB4920 to significantly affect autoimmune disease and humoral immune activation and to support further evaluation of this molecule in inflammatory conditions.