A crystallographic study of human NONO (p54(nrb)): overcoming pathological problems with purification, data collection and noncrystallographic symmetry

Non-POU domain-containing octamer-binding protein (NONO, a.k.a. p54(nrb)) is a central player in nuclear gene regulation with rapidly emerging medical significance. NONO is a member of the highly conserved Drosophila behaviour/human splicing (DBHS) protein family, a dynamic family of obligatory dimeric nuclear regulatory mediators. However, work with the NONO homodimer has been limited by rapid irreversible sample aggregation. Here, it is reported that L-proline stabilizes purified NONO homodimers, enabling good-quality solution small-angle X-ray structure determination and crystallization. NONO crystallized in the apparent space group P21 with a unique axis (b) of 408.9 Å and with evidence of twinning, as indicated by the cumulative intensity distribution L statistic, suggesting the possibility of space group P1. Structure solution by molecular replacement shows a superhelical arrangement of six NONO homodimers (or 12 in P1) oriented parallel to the long axis, resulting in extensive noncrystallographic symmetry. Further analysis revealed that the crystal was not twinned, but the collected data suffered from highly overlapping reflections that obscured the L-test. Optimized data collection on a new crystal using higher energy X-rays, a smaller beam width and an increased sample-to-detector distance produced non-overlapping reflections to 2.6 Å resolution. The steps taken to analyse and overcome this series of practical difficulties and to produce a biologically informative structure are discussed.

(1)H, (15)N and (13)C chemical shift assignments of the La motif and RRM1 from human LARP6

We report here the nearly complete (1)H, (15)N and (13)C resonance assignment of the La motif and RNA recognition motif 1 of human LARP6, an RNA binding protein involved in regulating collagen synthesis.

Rest perfusion abnormalities in hypertrophic cardiomyopathy: correlation with myocardial fibrosis and risk factors for sudden cardiac death

Aim

To measure the prevalence of abnormal rest perfusion in a population of consecutive patients with known hypertrophic cardiomyopathy (HCM) referred for cardiovascular MRI (CMR), and to assess any associations between abnormal rest perfusion and the presence, pattern, and severity of myocardial scar and the presence of risk factors for sudden death.

Materials and methods

Eighty consecutive patients with known HCM referred for CMR underwent functional imaging, rest first-pass perfusion, and late gadolinium enhancement (LGE).

Results

Thirty percent of the patients had abnormal rest perfusion, all of them corresponding to areas of mid-myocardial LGE and to a higher degree of segmental hypertrophy. Rest perfusion abnormalities correlated with more extensive and confluent LGE. The subgroup of patients with myocardial fibrosis and rest perfusion abnormalities (fibrosis+/perfusion+) had more than twice the incidence of episodes of non-sustained ventricular tachycardia on Holter monitoring in comparison to patients with myocardial fibrosis and normal rest perfusion (fibrosis+/perfusion–) and patients with no fibrosis and normal rest perfusion (fibrosis–/perfusion–).

Conclusions

First-pass perfusion CMR identifies abnormal rest perfusion in a significant proportion of patients with HCM. These abnormalities are associated with the presence and distribution of myocardial scar and the degree of hypertrophy. Rest perfusion abnormalities identify patients with increased incidence of episodes of non-sustained ventricular tachycardia on Holter monitoring, independently from the presence of myocardial fibrosis.

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30% of patients with HCM have perfusion abnormalities related to scar.

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No rest perfusion abnormalities were observed in areas of viable myocardium.

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Scar-related perfusion abnormalities were associated with the incidence of NSVT.

Synergic interplay of the La motif, RRM1 and the interdomain linker of LARP6 in the recognition of collagen mRNA expands the RNA binding repertoire of the La module

The La-related proteins (LARPs) form a diverse group of RNA-binding proteins characterized by the possession of a composite RNA binding unit, the La module. The La module comprises two domains, the La motif (LaM) and the RRM1, which together recognize and bind to a wide array of RNA substrates. Structural information regarding the La module is at present restricted to the prototypic La protein, which acts as an RNA chaperone binding to 3' UUUOH sequences of nascent RNA polymerase III transcripts. In contrast, LARP6 is implicated in the regulation of collagen synthesis and interacts with a specific stem-loop within the 5' UTR of the collagen mRNA. Here, we present the structure of the LaM and RRM1 of human LARP6 uncovering in both cases considerable structural variation in comparison to the equivalent domains in La and revealing an unprecedented fold for the RRM1. A mutagenic study guided by the structures revealed that RNA recognition requires synergy between the LaM and RRM1 as well as the participation of the interdomain linker, probably in realizing tandem domain configurations and dynamics required for substrate selectivity. Our study highlights a considerable complexity and plasticity in the architecture of the La module within LARPs.

Mechanism and consequence of the autoactivation of p38α mitogen-activated protein kinase promoted by TAB1

p38α mitogen-activated protein kinase (p38α) is activated by a variety of mechanisms, including autophosphorylation initiated by TGFβ-activated kinase 1 binding protein 1 (TAB1) during myocardial ischemia and other stresses. Chemical-genetic approaches and coexpression in mammalian, bacterial and cell-free systems revealed that mouse p38α autophosphorylation occurs in cis by direct interaction with TAB1(371-416). In isolated rat cardiac myocytes and perfused mouse hearts, TAT-TAB1(371-416) rapidly activates p38 and profoundly perturbs function. Crystal structures and characterization in solution revealed a bipartite docking site for TAB1 in the p38α C-terminal kinase lobe. TAB1 binding stabilizes active p38α and induces rearrangements within the activation segment by helical extension of the Thr-Gly-Tyr motif, allowing autophosphorylation in cis. Interference with p38α recognition by TAB1 abolishes its cardiac toxicity. Such intervention could potentially circumvent the drawbacks of clinical pharmacological inhibitors of p38 catalytic activity.

The association of a La module with the PABP-interacting motif PAM2 is a recurrent evolutionary process that led to the neofunctionalization of La-related proteins

La-related proteins (LARPs) are largely uncharacterized factors, well conserved throughout evolution. Recent reports on the function of human LARP4 and LARP6 suggest that these proteins fulfill key functions in mRNA metabolism and/or translation. We report here a detailed evolutionary history of the LARP4 and 6 families in eukaryotes. Genes coding for LARP4 and 6 were duplicated in the common ancestor of the vertebrate lineage, but one LARP6 gene was subsequently lost in the common ancestor of the eutherian lineage. The LARP6 gene was also independently duplicated several times in the vascular plant lineage. We observed that vertebrate LARP4 and plant LARP6 duplication events were correlated with the acquisition of a PABP-interacting motif 2 (PAM2) and with a significant reorganization of their RNA-binding modules. Using isothermal titration calorimetry (ITC) and immunoprecipitation methods, we show that the two plant PAM2-containing LARP6s (LARP6b and c) can, indeed, interact with the major plant poly(A)-binding protein (PAB2), while the third plant LARP6 (LARP6a) is unable to do so. We also analyzed the RNA-binding properties and the subcellular localizations of the two types of plant LARP6 proteins and found that they display nonredundant characteristics. As a whole, our results support a model in which the acquisition by LARP4 and LARP6 of a PAM2 allowed their targeting to mRNA 3' UTRs and led to their neofunctionalization.

RNA chaperone activity of human La protein is mediated by variant RNA recognition motif

La proteins are conserved factors in eukaryotes that bind and protect the 3' trailers of pre-tRNAs from exonuclease digestion via sequence-specific recognition of UUU-3'OH. La has also been hypothesized to assist pre-tRNAs in attaining their native fold through RNA chaperone activity. In addition to binding polymerase III transcripts, human La has also been shown to enhance the translation of several internal ribosome entry sites and upstream ORF-containing mRNA targets, also potentially through RNA chaperone activity. Using in vitro FRET-based assays, we show that human and Schizosaccharomyces pombe La proteins harbor RNA chaperone activity by enhancing RNA strand annealing and strand dissociation. We use various RNA substrates and La mutants to show that UUU-3'OH-dependent La-RNA binding is not required for this function, and we map RNA chaperone activity to its RRM1 motif including a noncanonical α3-helix. We validate the importance of this α3-helix by appending it to the RRM of the unrelated U1A protein and show that this fusion protein acquires significant strand annealing activity. Finally, we show that residues required for La-mediated RNA chaperone activity in vitro are required for La-dependent rescue of tRNA-mediated suppression via a mutated suppressor tRNA in vivo. This work delineates the structural elements required for La-mediated RNA chaperone activity and provides a basis for understanding how La can enhance the folding of its various RNA targets.

Analysis of the interaction with the hepatitis C virus mRNA reveals an alternative mode of RNA recognition by the human La protein

Human La protein is an essential factor in the biology of both coding and non-coding RNAs. In the nucleus, La binds primarily to 3' oligoU containing RNAs, while in the cytoplasm La interacts with an array of different mRNAs lacking a 3' UUU(OH) trailer. An example of the latter is the binding of La to the IRES domain IV of the hepatitis C virus (HCV) RNA, which is associated with viral translation stimulation. By systematic biophysical investigations, we have found that La binds to domain IV using an RNA recognition that is quite distinct from its mode of binding to RNAs with a 3' UUU(OH) trailer: although the La motif and first RNA recognition motif (RRM1) are sufficient for high-affinity binding to 3' oligoU, recognition of HCV domain IV requires the La motif and RRM1 to work in concert with the atypical RRM2 which has not previously been shown to have a significant role in RNA binding. This new mode of binding does not appear sequence specific, but recognizes structural features of the RNA, in particular a double-stranded stem flanked by single-stranded extensions. These findings pave the way for a better understanding of the role of La in viral translation initiation.

Resonance assignment of nsp7α from arterivirus

The (1)H, (15)N and (13)C resonance assignment of nsp7α, a non-structural protein of unknown function from the equine arteritis virus, is reported.

La-related protein 4 binds poly(A), interacts with the poly(A)-binding protein MLLE domain via a variant PAM2w motif, and can promote mRNA stability

The conserved RNA binding protein La recognizes UUU-3'OH on its small nuclear RNA ligands and stabilizes them against 3'-end-mediated decay. We report that newly described La-related protein 4 (LARP4) is a factor that can bind poly(A) RNA and interact with poly(A) binding protein (PABP). Yeast two-hybrid analysis and reciprocal immunoprecipitations (IPs) from HeLa cells revealed that LARP4 interacts with RACK1, a 40S ribosome- and mRNA-associated protein. LARP4 cosediments with 40S ribosome subunits and polyribosomes, and its knockdown decreases translation. Mutagenesis of the RNA binding or PABP interaction motifs decrease LARP4 association with polysomes. Several translation and mRNA metabolism-related proteins use a PAM2 sequence containing a critical invariant phenylalanine to make direct contact with the MLLE domain of PABP, and their competition for the MLLE is thought to regulate mRNA homeostasis. Unlike all ∼150 previously analyzed PAM2 sequences, LARP4 contains a variant PAM2 (PAM2w) with tryptophan in place of the phenylalanine. Binding and nuclear magnetic resonance (NMR) studies have shown that a peptide representing LARP4 PAM2w interacts with the MLLE of PABP within the affinity range measured for other PAM2 motif peptides. A cocrystal of PABC bound to LARP4 PAM2w shows tryptophan in the pocket in PABC-MLLE otherwise occupied by phenylalanine. We present evidence that LARP4 expression stimulates luciferase reporter activity by promoting mRNA stability, as shown by mRNA decay analysis of luciferase and cellular mRNAs. We propose that LARP4 activity is integrated with other PAM2 protein activities by PABP as part of mRNA homeostasis.

Epidemiology and patterns of care of patients admitted to Italian Intensive Cardiac Care units: the BLITZ-3 registry

BACKGROUND

Intensive cardiac care units (ICCUs) have shifted from the observation of patients with myocardial infarction to the care of different acute cardiac diseases. However, few data on such an evolution are available.

METHODS AND RESULTS

From 7 to 20 April 2008, 6986 consecutive patients admitted to 81% of Italian ICCUs were prospectively enrolled. Patients observed were mainly elderly men (median age 72 years) with several co-morbidities. Most of them were triaged to ICCU from the emergency room, but 15% of admissions were transfer-in from other hospitals. Several diagnostic and therapeutic procedures were applied (78% had echocardiography and 35% coronary angiography) during the ICCU stay [median length 4 days, interquartile range (IQR) 2-5]. The discharge diagnosis was ST-elevation acute coronary syndrome (ACS) in 21%, non-ST-elevation ACS in 31%, acute heart failure (AHF) in 14% and other acute non-ACS, non-AHF cardiac diseases in 34%. Of those with ST-elevation ACS, 60% received reperfusion (15% fibrinolysis and 45% primary percutaneous coronary intervention). The overall in-ICCU crude mortality was 3.3%.

CONCLUSION

The BLITZ-3 survey provides a unique snapshot of current epidemiology and patterns of care of patients admitted to ICCUs. Although ACS still remains the most frequent admission diagnosis, the number of non-ACS patients is substantial. However, the correct standard of care for these non-ACS patients has to be defined.

Heterodimerization of the human RNase P/MRP subunits Rpp20 and Rpp25 is a prerequisite for interaction with the P3 arm of RNase MRP RNA

Rpp20 and Rpp25 are two key subunits of the human endoribonucleases RNase P and MRP. Formation of an Rpp20–Rpp25 complex is critical for enzyme function and sub-cellular localization. We present the first detailed in vitro analysis of their conformational properties, and a biochemical and biophysical characterization of their mutual interaction and RNA recognition. This study specifically examines the role of the Rpp20/Rpp25 association in the formation of the ribonucleoprotein complex. The interaction of the individual subunits with the P3 arm of the RNase MRP RNA is revealed to be negligible whereas the 1:1 Rpp20:Rpp25 complex binds to the same target with an affinity of the order of nM. These results unambiguously demonstrate that Rpp20 and Rpp25 interact with the P3 RNA as a heterodimer, which is formed prior to RNA binding. This creates a platform for the design of future experiments aimed at a better understanding of the function and organization of RNase P and MRP. Finally, analyses of interactions with deletion mutant proteins constructed with successively shorter N- and C-terminal sequences indicate that the Alba-type core domain of both Rpp20 and Rpp25 contains most of the determinants for mutual association and P3 RNA recognition.

Letter to the Editor: resonance assignment of SlyD from E. coli

SlyD from Escherichia coli is a peptidyl-prolyl cis-trans isomerase involved in [Ni-Fe] hydrogenase metallocentre assembly in bacteria. We present here the backbone and side chain assignments for E. coli SlyD.

Getting to the end of RNA: structural analysis of protein recognition of 5' and 3' termini

The specific recognition by proteins of the 5' and 3' ends of RNA molecules is an important facet of many cellular processes, including RNA maturation, regulation of translation initiation and control of gene expression by degradation and RNA interference. The aim of this review is to survey recent structural analyses of protein binding domains that specifically bind to the extreme 5' or 3' termini of RNA. For reasons of space and because their interactions are also governed by catalytic considerations, we have excluded enzymes that modify the 5' and 3' extremities of RNA. It is clear that there is enormous structural diversity among the proteins that have evolved to bind to the ends of RNA molecules. Moreover, they commonly exhibit conformational flexibility that appears to be important for binding and regulation of the interaction. This flexibility has sometimes complicated the interpretation of structural results and presents significant challenges for future investigations.

The interaction of the Escherichia coli protein SlyD with nickel ions illuminates the mechanism of regulation of its peptidyl-prolyl isomerase activity

The sensitive to lysis D (SlyD) protein from Escherichia coli is related to the FK506-binding protein family, and it harbours both peptidyl-prolyl cis-trans isomerase (PPIase) and chaperone-like activity, preventing aggregation and promoting the correct folding of other proteins. Whereas a functional role of SlyD as a protein-folding catalyst in vivo remains unclear, SlyD has been shown to be an essential component for [Ni-Fe]-hydrogenase metallocentre assembly in bacteria. Interestingly, the isomerase activity of SlyD is uniquely modulated by nickel ions, which possibly regulate its functions in response to external stimuli. In this work, we investigated the solution structure of SlyD and its interaction with nickel ions, enabling us to gain insights into the molecular mechanism of this regulation. We have revealed that the PPIase module of SlyD contains an additional C-terminal alpha-helix packed against the catalytic site of the domain; unexpectedly, our results show that the interaction of SlyD with nickel ions entails participation of the novel structural features of the PPIase domain, eliciting structural alterations of the catalytic pocket. We suggest that such conformational rearrangements upon metal binding underlie the ability of nickel ions to regulate the isomerase activity of SlyD.

NMR assignment of the N-terminal region of human La free and in complex with RNA

(1)H, (15)N and (13)C chemical shift assignments are presented for the N-terminal region of human La protein, in the apo and 5'-UUUU RNA-bound state. Secondary structure analysis shows conformational changes in the interdomain linker upon complex formation.

Structural analysis reveals conformational plasticity in the recognition of RNA 3' ends by the human La protein

The eukaryotic La protein recognizes the 3' poly(U) sequences of nascent RNA polymerase III transcripts to assist folding and maturation. The 3' ends of such RNAs are bound by the N-terminal domain of La (LaNTD). We have solved the crystal structures of four LaNTD:RNA complexes, each containing a different single-stranded RNA oligomer, and compared them to the structure of a previously published LaNTD:RNA complex containing partially duplex RNA. The presence of purely single-stranded RNA in the binding pocket at the interface between the La motif and RRM domains allows significantly closer contact with the 3' end of the RNA. Comparison of the different LaNTD:RNA complexes identifies a conserved set of interactions with the last two nucleotides at the 3' end of the RNA ligand that are key to binding. Strikingly, we also observe two alternative conformations of bound ssRNA, indicative of an unexpected degree of plasticity in the modes of RNA binding.

Primary angioplasty and routine utilization of thrombus aspiration devices: feasibility and results in a consecutive series of 486 patients

BACKGROUND

Primary percutaneous transluminal coronary angioplasty (PTCA) is the treatment of choice for acute ST-segment elevation myocardial infarction (STEMI) in high-volume centres with experienced operators, but is often limited by a suboptimal microvascular perfusion due to distal embolization and impaired myocardial perfusion. The present study investigates whether routine use of thrombus aspiration (TA) devices is feasible in daily practice, along with its safety and effectiveness.

METHODS

This study is based on a series of 486 consecutive STEMI patients treated at our single institution by the same three operators (from 2001 to 2005). They underwent primary PTCA with or without TA according to these angiographic features: infarct related artery (IRA) diameter>or=3 mm; thrombotic occlusion or angiographic evidence of thrombus; absence of severe proximal tortuosity or calcification. We evaluate the efficacy of TA in terms of procedural success, coronary thrombolysis in myocardial infarction (TIMI) flow, myocardial blush grade (MBG), resolution>or=50% of ST segment elevation, and clinical events during hospital stay and at 6-month follow-up.

RESULTS

A total of 486 primary PTCAs were performed, 217 (44.6%) with TA as a first device using RESCUE (n=65), EXPORT (n=140) and DIVER-CE (n=12) catheters. In 141 (65%) cases, macroscopic material was aspirated. The patients submitted to TA were more often males (84.7% versus 71.7%, P<0.05) and younger (age: 61.02+/-11.91 versus 64.47+/-10.59 years, P<0.01) than patients treated with traditional PTCA and the IRA was more frequently occluded at angiography (basal TIMI 0: 70.5% versus 47.9%). Application of the TA did not increase the complexity of the procedure (door-to-balloon times, minutes of fluoroscopy and amount of dye). TA alone was effective to restore TIMI 3 flow in 187 cases (86.2%) as a first device and in three other cases (1.4%) after predilatation with balloon. Direct stenting without predilatation was possible in 144 cases (66.4%) after TA. TA was not effective in 27 cases (12.4%) and this subgroup had both angiographic and clinical unfavourable results in comparison with the effective TA group (final TIMI 1 in 11.1% versus 0.5%, P<0.015; final MBG 1 in 55.5% versus 9.5%, P<0.001; lack of ST segment resolution>or=50% in 44.4% versus 7.9%, P<0.001; in-hospital mortality 14.8% versus 2.6%, P<0.05 and mortality at 6 months 18.5% versus 3.1%, P<0.05). In the whole TA population, final TIMI 3 flow was achieved in 203 cases (93.5%), final MBG 3 in 145 cases (66.8%) and ST segment resolution>or=50% in 185 cases (85.2%), in-hospital mortality was 4.1% and cumulative mortality at 6-month follow-up was 5.5%.

CONCLUSIONS

In our case series, 486 consecutive unselected patients with STEMI were treated in a primary PTCA high-volume centre using TA devices. Our study demonstrates that, in STEMI patients treated with primary PTCA, a routine strategy with TA before angioplasty guided by angiographic selection criteria is feasible in almost 50% of cases, is safe and effective, does not increase procedural time and offers good results in terms of tissue perfusion, both epicardial (TIMI flow) and myocardial (MBG, ST regression). When successfully performed, TA identifies a population with favourable in-hospital and 6-month outcome.

A terminal affair: 3'-end recognition by the human La protein

The La protein, an autoantigen in rheumatic disease, orchestrates several aspects of the metabolism of noncoding RNA molecules. More than 20 years ago it was shown that La primarily binds the 3' UUU-OH tails of nascent transcripts of RNA polymerase III. A recent study now reveals how the structure of the amino-terminal domain of the human La protein achieves specific 3'-end recognition.

Structure of the eukaryotic initiation factor (eIF) 5 reveals a fold common to several translation factors

Eukaryotic initiation factor 5 (eIF5) plays multiple roles in translation initiation. Its N-terminal domain functions as a GTPase-activator protein (GAP) for GTP bound to eIF2, while its C-terminal region nucleates the interactions between multiple translation factors, including eIF1, which acts to inhibit GTP hydrolysis or P(i) release, and the beta subunit of eIF2. These proteins and the events in which they participate are critical for the accurate recognition of the correct start codon during translation initiation. Here, we report the three-dimensional solution structure of the N-terminal domain of human eIF5, comprising two subdomains, both reminiscent of nucleic-acid-binding modules. The N-terminal subdomain contains the "arginine finger" motif that is essential for GAP function but which, unusually, resides in a partially disordered region of the molecule. This implies that a conformational reordering of this portion of eIF5 is likely to occur upon formation of a competent complex for GTP hydrolysis, following the appropriate activation signal. Interestingly, the N-terminal subdomain of eIF5 reveals an alpha/beta fold structurally similar to both the archaeal orthologue of the beta subunit of eIF2 and, unexpectedly, to eIF1. These results reveal a novel protein fold common to several factors involved in related steps of translation initiation. The implications of these observations are discussed in terms of the mechanism of translation initiation.