In-vitro dual binding activity of a evolutionarily related subgroup of hnRNP proteins

The citrullinated/native index of autoantibodies against hnRNP-DL predicts an individual "window of treatment success" in RA patients

BACKGROUND

There is a need for biomarker to identify patients "at risk" for rheumatoid arthritis (risk-RA) and to better predict the therapeutic response and in this study we tested the hypothesis that novel native and citrullinated heterogeneous nuclear ribonucleoprotein (hnRNP)-DL autoantibodies could be possible biomarkers.

METHODS

Using protein macroarray and ELISA, epitope recognition against hnRNP-DL was analysed in sera from different developed RA disease and diagnosed SLE patients. Toll-like receptor (TLR) 7/9 and myeloid differentiation primary response gene 88 (MyD88)-dependency were studied in sera from murine disease models. HnRNP-DL expression in cultivated cells and synovial tissue was analysed by indirect immunofluorescence, immunoblot and immunohistochemistry.

RESULTS

HnRNP-DL was highly expressed in stress granules, citrullinated in the rheumatoid joint and targeted by autoantibodies either as native or citrullinated proteins in patient subsets with different developed RA disease. Structural citrullination dependent epitopes (SCEs) of hnRNP-DL were detected in 58% of the SLE patients although 98% of these sera were α-CCP-2-negative. To obtain a specific citrullinated signal value, we subtracted the native antibody value from the citrullinated signal. The citrullinated/native index of autoantibodies against hnRNP-DL (CNDL-Index) was identified as a new value for an "individual window of treatment success" in early RA and for the detection of RF IgM/α-CCP-2 seronegative RA patients (24-46%). Negative CNDL-index was found in SLE patients, risk-RA and early RA cohorts such as EIRA where the majority of these patients are DAS28-responders to methotrexate (MTX) treatment (87%). High positive CNDL-values were associated with more severe RA, shared epitope and parenchymal changes in the lung. Specifically, native α-hnRNP-DL is TLR7/9-dependent, associated with pain and ROC analysis revealed an association to initial MTX or etanercept treatment response, especially in seronegative RA patients.

CONCLUSION

CNDL-index defines people at risk to develop RA and the "window of treatment success" thereby closing the sensitivity gap in RA.

Two-timing zinc finger transcription factors liaising with RNA

Classical zinc fingers (ZFs) are one of the most common protein domains in higher eukaryotes and have been known for almost 30 years to act as sequence-specific DNA-binding domains. This knowledge has come, however, from the study of a small number of archetypal proteins, and a larger picture is beginning to emerge that ZF functions are far more diverse than originally suspected. Here, we review the evidence that a subset of ZF proteins live double lives, binding to both DNA and RNA targets and frequenting both the cytoplasm and the nucleus. This duality can create an important additional level of gene regulation that serves to connect transcriptional and post-transcriptional control.

Characterization of a Cryptosporidium parvum protein that binds single-stranded G-strand telomeric DNA

We have initiated a project to characterize telomere-associated proteins of Cryptosporidium parvum. Searching public databases with C. parvum expressed sequence tag (EST) sequences revealed one EST sequence that is highly similar to Gbp1p of Chlamydomonas reinhardtii (Cr Gbp1p), a protein that binds single-stranded telomeric DNA. This EST was used to clone a gene encoding a 198 amino acids long protein (CpGbp). Sequence analysis suggested that CpGbp contains two RNA recognition motif (RRMs) domains linked with a short hinge region. RT-PCR analysis showed that the mRNA expression of CpGbp was up- and down-regulated significantly comparing to that of CpDNAPol, suggesting a potential role of CpGbp playing in the parasite's life cycle. In Western blot analysis, monoclonal antibody against recombinant CpGbp identified one band (approximately 23kDa) specifically from cell extracts of C. parvum sporozoites. Confocal microscopy analysis with anti-CpGbp antibody localized CpGbp proteins to the nucleus, consistent with its potential role in telomere length regulation. In electrophoretic mobility shift assays (EMSAs), recombinant CpGbp bound oligonucleotide TG3 that bears three copies of C. parvum telomeric DNA G-strand repeat "TTTAGG", but not C-strand or double-stranded telomeric DNA sequences. To map the binding domain and to define the binding site of CpGbp, we constructed four CpGbp deletion mutants and synthesized ten TG3 mutants and tested their binding affinities by EMSAs. We found that only the RRM domain at N-terminus has oligonucleotide-binding ability in vitro. And the minimal sequence necessary for CpGbp's binding is "GTTTAGGTTTAG". These data support the notion that CpGbp represents a C. parvum single-stranded telomeric DNA binding protein.

Telomere dynamics: the means to an end

Telomeres are among the most important structures in eukaryotic cells. Creating the physical ends of linear chromosomes, they play a crucial role in maintaining genome stability, control of cell division, cell growth and senescence. In vertebrates, telomeres consist of G-rich repetitive DNA sequences (TTAGGG)n and specific proteins, creating a specialized structure called the telosome that through mutual interactions with many other factors in the cell give rise to dynamic regulation of chromosome maintenance. In this review, we survey the structural and mechanistic aspects of telomere length regulation and how these processes lead to alterations in normal and immortal cell growth.

NRF IRES activity is mediated by RNA binding protein JKTBP1 and a 14-nt RNA element

The mRNA of human NF-kappaB repressing factor (NRF) contains a long 5'-untranslated region (UTR) that directs ribosomes to the downstream start codon by a cap-independent mechanism. Comparison of the nucleotide (nt) sequences of human and mouse NRF mRNAs reveals a high degree of identity throughout a fragment of 150 nt proximal to the start codon. Here, we show that this region constitutes a minimal internal ribosome entry segment (IRES) module. Enzymatic RNA structure analysis reveals a secondary structure model of the NRF IRES module. Point mutation analysis of the module determines a short, 14-nt RNA element (nt 640-653) as a mediator of IRES function. Purification of IRES binding cellular proteins and subsequent ESI/MS/MS sequence analysis led to identification of the RNA-binding protein, JKTBP1. EMSA experiments show that JKTBP1 binds upstream to the 14-nt RNA element in the NRF IRES module (nt 579-639). Over-expression of JKTBP1 significantly enhances activity of the NRF IRES module in dicistronic constructs. Moreover, siRNA experiments demonstrate that down-regulation of endogenous JKTBP1 decreases NRF IRES activity and the level of endogenous NRF protein. The data of this study show that JKTBP1 and the 14-nt element act independently to mediate NRF IRES activity.