Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2

In actively translating 80S ribosomes the ribosomal protein eS7 of the 40S subunit is monoubiquitinated by the E3 ligase Not4 and deubiquitinated by Otu2 upon ribosomal subunit recycling. Despite its importance for translation efficiency the exact role and structural basis for this translational reset is poorly understood. Here, structural analysis by cryo-electron microscopy of native and reconstituted Otu2-bound ribosomal complexes reveals that Otu2 engages 40S subunits mainly between ribosome recycling and initiation stages. Otu2 binds to several sites on the intersubunit surface of the 40S that are not occupied by any other 40S-binding factors. This binding mode explains the discrimination against 80S ribosomes via the largely helical N-terminal domain of Otu2 as well as the specificity for mono-ubiquitinated eS7 on 40S. Collectively, this study reveals mechanistic insights into the Otu2-driven deubiquitination steps for translational reset during ribosome recycling/(re)initiation.

Disordered region of H3K9 methyltransferase Clr4 binds the nucleosome and contributes to its activity

Heterochromatin is a distinctive chromatin structure that is essential for chromosome segregation, genome stability and regulation of gene expression. H3K9 methylation (H3K9me), a hallmark of heterochromatin, is deposited by the Su(var)3-9 family of proteins; however, the mechanism by which H3K9 methyltransferases bind and methylate the nucleosome is poorly understood. In this work we determined the interaction of Clr4, the fission yeast H3K9 methyltransferase, with nucleosomes using nuclear magnetic resonance, biochemical and genetic assays. Our study shows that the Clr4 chromodomain binds the H3K9me3 tail and that both, the chromodomain and the disordered region connecting the chromodomain and the SET domain, bind the nucleosome core. We show that interaction of the disordered region with the nucleosome core is independent of H3K9me and contributes to H3K9me in vitro and in vivo. Moreover, we show that those interactions with the nucleosome core are contributing to de novo deposition of H3K9me and to establishment of heterochromatin.

Fuzzy Interactions Form and Shape the Histone Transport Complex

Protein transport into the nucleus is mediated by transport receptors. Import of highly charged proteins, such as histone H1 and ribosomal proteins, requires a dimer of two transport receptors. In this study, we determined the cryo-EM structure of the Imp7:Impβ:H1.0 complex, showing that the two importins form a cradle that accommodates the linker histone. The H1.0 globular domain is bound to Impβ, whereas the acidic loops of Impβ and Imp7 chaperone the positively charged C-terminal tail. Although it remains disordered, the H1 tail serves as a zipper that closes and stabilizes the structure through transient non-specific interactions with importins. Moreover, we found that the GGxxF and FxFG motifs in the Imp7 C-terminal tail are essential for Imp7:Impβ dimerization and H1 import, resembling importin interaction with nucleoporins, which, in turn, promote complex disassembly. The architecture of many other complexes might be similarly defined by rapidly exchanging electrostatic interactions mediated by disordered regions.

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Importin 7 and Importin β form a cradle to chaperone and transport histone H1

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Transient and non-specific electrostatic interactions form and shape the complex

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The H1 tail serves as a zipper that closes and stabilizes Imp7:Impβ:H1

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FxFG motifs in nucleoporins facilitate RanGTP-dependent disassembly of the complex

Preparative two-step purification of recombinant H1.0 linker histone and its domains

H1 linker histones are small basic proteins that have a key role in the formation and maintenance of higher-order chromatin structures. Additionally, many examples have shown that linker histones play an important role in gene regulation, modulated by their various subtypes and posttranslational modifications. Obtaining high amounts of very pure linker histones, especially for efficient antibody production, remains a demanding and challenging procedure. Here we present an easy and fast method to purify human linker histone H1.0 overexpressed in Escherichia coli, as well as its domains: N-terminal/globular domain and C-terminal intrinsically disordered domain. This purification protocol relies on a simple affinity chromatography step followed by cation exchange due to the highly basic properties of histone proteins. Therefore, this protocol can also be applied to other linker histones. Highly pure proteins in amounts sufficient for most biochemical experiments can be obtained. The functional quality of purified H1.0 histone and its domains has been confirmed by pull-down, gel-mobility shift assays and the nuclear import assay.

Structure-function relationships of two paralogous single-stranded DNA-binding proteins from Streptomyces coelicolor: implication of SsbB in chromosome segregation during sporulation

The linear chromosome of Streptomyces coelicolor contains two paralogous ssb genes, ssbA and ssbB. Following mutational analysis, we concluded that ssbA is essential, whereas ssbB plays a key role in chromosome segregation during sporulation. In the ssbB mutant, ∼30% of spores lacked DNA. The two ssb genes were expressed differently; in minimal medium, gene expression was prolonged for both genes and significantly upregulated for ssbB. The ssbA gene is transcribed as part of a polycistronic mRNA from two initiation sites, 163 bp and 75 bp upstream of the rpsF translational start codon. The ssbB gene is transcribed as a monocistronic mRNA, from an unusual promoter region, 73 bp upstream of the AUG codon. Distinctive DNA-binding affinities of single-stranded DNA-binding proteins monitored by tryptophan fluorescent quenching and electrophoretic mobility shift were observed. The crystal structure of SsbB at 1.7 Å resolution revealed a common OB-fold, lack of the clamp-like structure conserved in SsbA and previously unpublished S-S bridges between the A/B and C/D subunits. This is the first report of the determination of paralogous single-stranded DNA-binding protein structures from the same organism. Phylogenetic analysis revealed frequent duplication of ssb genes in Actinobacteria, whereas their strong retention suggests that they are involved in important cellular functions.

Idiosyncratic helix-turn-helix motif in Methanosarcina barkeri seryl-tRNA synthetase has a critical architectural role

All seryl-tRNA synthetases (SerRSs) are functional homodimers with a C-terminal active site domain typical for class II aminoacyl-tRNA synthetases and an N-terminal domain involved in tRNA binding. The recently solved three-dimensional structure of Methanosarcina barkeri SerRS revealed the idiosyncratic features of methanogenic-type SerRSs; that is, an active site zinc ion, a unique tRNA binding domain, and an insertion of approximately 30 residues in the catalytic domain, which adopt a helix-turn-helix (HTH) fold. Here, we present biochemical evidence for multiple roles of the HTH motif; it is important for dimerization of the enzyme, contributes to the overall stability, and is critical for the proper positioning of the tRNA binding domain relative to the catalytic domain. The changes in intrinsic fluorescence during denaturation of the wild-type M. barkeri SerRS and of the mutated variant lacking the HTH motif combined with cross-linking and gel analysis of protein subunits during various stages of the unfolding process revealed significantly reduced stability of the mutant dimers. In vitro kinetic analysis of enzymes, mutated in one of the N-terminal helices and the HTH motif, shows impaired tRNA binding and aminoacylation and emphasizes the importance of this domain for the overall architecture of the enzyme. The role of the idiosyncratic HTH motif in dimer stabilization and association between the catalytic and tRNA binding domain has been additionally confirmed by a yeast two-hybrid approach. Furthermore, we provide experimental evidence that tRNA binds across the dimer.

The coronary subclavian steal syndrome: an uncommon sequel to internal mammary-coronary artery bypass surgery

Coronary subclavian steal syndrome is a possible sequel in patients who have undergone myocardial revascularization with an internal mammary artery. We report a case of this syndrome in a 67-years-old man. In 1990 he underwent a quadruple bypass: aorta-obtuse margin, aorta-right coronary (two sequential), internal artery mammary-descending coronary artery. Three months later he started to have angina pectoris. In April 1992 an aortic arch angiography and a coronary angiography were performed. The examination showed an occlusion of the left subclavian artery at its origin. The artery was opacified countercurrently by the left vertebral artery but the left mammary artery was not opacified. Left coronary angiography showed a very severe disease of left anterior descending coronary artery and retrograde flow through the anastomosis in the left mammary artery. The patient underwent a left common carotid-subclavian artery bypass operation using a 6 mm vascutex graft. Eighteen months later the patient is doing well without angina pectoris and with very little alteration of the perfusion in the left frontal lobe observed by SPECT neuroimaging with a lipophilic tracer (99mTc-HMPAO). We think that the coronary-subclavian steal syndrome can be treated successfully with low risk by means of common carotid-subclavian artery bypass.

Chylothorax after pleuro-pulmonary surgery: a rare but unavoidable complication

The incidence of chylothorax after pleuro-pulmonary operations as well as its treatment is reported. Of 1744 operations performed postoperative chylothorax developed in 13 (0.74%). It resulted in two cases from the transection of the thoracic duct, in six from the transection of the so-called minor lymph channels, which drain lymph from mediastinal nodes straight into the thoracic duct or drain lung segments into the thoracic duct via the pulmonary ligament; the transection of these channels occurred during mediastinal lymphadenectomy or during the section of the pulmonary ligament. In 5 patients the site of leakage was not determined as reoperation was not required. Conservative treatment with low-fat diet and medium-chain triglycerides and/or total parenteral nutrition was attempted in all but one patient but was successful only in 5 cases whose mean losses were 292 ml/day. Seven patients were reoperated after a mean of 11 days; their mean losses were 930 ml/day. One patient was reoperated on the third postoperative day without attempting conservative treatment; his mean loss was 850 ml/day. Lymphadenectomy seems to be an important risk factor for postoperative chylothorax. Chyle leakage around 500 ml/day or higher that tends to decrease below 500 ml/day after a few days of dietary manipulation usually stops within 10-20 days, while leakage over 500 ml/day that does not tend to decrease below 500 ml/day seldom if ever stops without surgery, so that a more aggressive attitude is justified.

Lung resections concomitant to coronary artery bypass grafting

From 1980 through 1993 ten patients underwent concomitant coronary artery bypass grafting and lung resection via median sternotomy. In eight patients a lung malignancy was resected, of which one was a small cell lung cancer. The lung resection was carried out before cardiopulmonary bypass in eight patients and during cardiopulmonary bypass in two. Coronary artery bypass grafting was performed using saphenous vein in eight patients; internal mammary artery was used as arterial conduit in two patients. There was one postoperative death while postoperative complications during hospital stay occurred in two patients. Pulmonary bleeding did not occur in any patient in whom lung resection was performed either before or during cardiopulmonary bypass. Both the patients who had internal mammary artery grafting experienced complications related to an associated lobectomy. A staged procedure is advisable if internal mammary artery has to be used and a lobectomy is required. The long-term survival in the patients with lung cancer was less than expected but the number of patients is too small to draw definite conclusions.

[The aneurysmal degeneration of aortocoronary bypasses. A case report]

A 67-year-old man presenting with oppressive atypical chest pain 13 years after aorto-coronary saphenous vein bypass surgery, was found to have a large left anterior mediastinal mass on chest x-rays. Computerized tomography and digital subtraction angiography showed conflicting evidence on the vascular nature of the structure: the suspect diagnosis was of aortic pseudoaneurysm originating in the area of previous aortic cannulation. Selective coronary and bypass angiography showed extreme irregularity and dilatation of the grafts, and revealed the mediastinal mass to be represented by aneurysmal dilatation of the saphenous vein graft to the obtuse marginal coronary artery, partially filled with thrombus. At operation, another smaller aneurysm was found on the right coronary artery graft. Aneurysmal degeneration of vein grafts in the coronary circulation is exceedingly rare, and in only 6 reported cases has such an aneurysm presented as a mediastinal mass. To our knowledge, this is the first case in which an aneurysmal dilatation involved two saphenous vein coronary grafts.

[Lipoma of the interventricular septum: its diagnosis and treatment]

We describe a case of left ventricular intramyocardial lipoma in a patient symptomatic for chest pain and syncope. The two-dimensional echocardiographic investigation showed a hyperechogenic mass inside the interventricular septum; presence of the mass was confirmed by CT scan and nuclear magnetic resonance imaging. In our experience only the CT scan was useful to clearly identify the histologic characteristics of tissue. The patient underwent successful surgical removal of the mass and the histologic examination revealed normal fat tissue.

[Two-dimensional echocardiographic diagnosis of a thromboembolic mass in the right atrium]

We describe the case of a patient with massive pulmonary embolism, in which two-dimensional echocardiography demonstrated the presence of a free-floating mass in the right atrial cavity. The patient was urgently and successfully operated on. We describe the echocardiographic findings and emphasize the value of two dimensional echocardiography in detecting right-sided intracavitary thromboemboli, a condition in which immediate surgical treatment is mandatory.