Genetic determinants of micronucleus formation in vivo.

Genomic instability arising from defective responses to DNA damage1 or mitotic chromosomal imbalances2 can lead to the sequestration of DNA in aberrant extranuclear structures called micronuclei (MN). Although MN are a hallmark of ageing and diseases associated with genomic instability, the catalogue of genetic players that regulate the generation of MN remains to be determined. Here we analyse 997 mouse mutant lines, revealing 145 genes whose loss significantly increases (n = 71) or decreases (n = 74) MN formation, including many genes whose orthologues are linked to human disease. We found that mice null for Dscc1, which showed the most significant increase in MN, also displayed a range of phenotypes characteristic of patients with cohesinopathy disorders. After validating the DSCC1-associated MN instability phenotype in human cells, we used genome-wide CRISPR-Cas9 screening to define synthetic lethal and synthetic rescue interactors. We found that the loss of SIRT1 can rescue phenotypes associated with DSCC1 loss in a manner paralleling restoration of protein acetylation of SMC3. Our study reveals factors involved in maintaining genomic stability and shows how this information can be used to identify mechanisms that are relevant to human disease biology1.

SF-assemblin, the structural protein of the 2-nm filaments from striated microtubule associated fibers of algal flagellar roots, forms a segmented coiled coil.

The microtubule associated system I fibers of the basal apparatus of the flagellate green alga Spermatozopsis similis are noncontractile and display a 28-nm periodicity. Paracrystals with similar periodicities are formed in vitro by SF-assemblin, which is the major protein component of system I fibers. We have determined the amino acid sequence of SF-assemblin and show that it contains two structural domains. The NH2-terminal 31 residues form a nonhelical domain rich in proline. The rod domain of 253 residues is alpha-helical and seems to form a segmented coiled coil with a 29-residue repeat pattern based on four heptads followed by a skip residue. The distinct cluster of acidic residues at the COOH-terminal end of the motifs (periodicity about 4 nm) may be related to tubulin binding of SF-assemblin and/or its self assembly. A similar structure has been predicted from cDNA cloning of beta-giardin, a protein of the complex microtubular apparatus of the sucking disc in the protozoan flagellate Giardia lamblia. Although the rod domains of SF-assemblin and beta-giardin share only 20% sequence identity, they have exactly the same length and display 42% sequence similarity. These results predict that system I fibers and related microtubule associated structures arise from molecules able to form a special segmented coiled coil which can pack into 2-nm filaments. Such molecules seem subject to a strong evolutionary drift in sequence but not in sequence principles and length. This conservation of molecular architecture may have important implications for microtubule binding.

Major epiplasmic proteins of ciliates are articulins: cloning, recombinant expression, and structural characterization.

The cytoskeleton of certain protists comprises an extensive membrane skeleton, the epiplasm, which contributes to the cell shape and patterning of the species-specific cortical architecture. The isolated epiplasm of the ciliated protist Pseudomicrothorax dubius consists of two major groups of proteins with molecular masses of 78-80 kD and 11-13 kD, respectively. To characterize the structure of these proteins, peptide sequences of two major polypeptides (78-80 kD) as well as a cDNA representing the entire coding sequence of a minor and hitherto unidentified component (60 kD; p60) of the epiplasm have been determined. All three polypeptides share sequence similarities. They contain repeated valine- and proline-rich motifs of 12 residues with the consensus VPVP--V-V-V-. In p60 the central core domain consists of 24 tandemly repeated VPV motifs. Within the repeat motifs positively and negatively charged residues, when present, show an alternating pattern in register with the V and P positions. Recombinant p60 was purified in 8 M urea and dialyzed against buffer. Infrared spectroscopic measurements indicate 30% beta-sheet. Electron microscopy reveals short filamentous polymers with a rather homogenous diameter (approximately 15-20 nm), but variable lengths. The small polymers form thicker filaments, ribbons, and larger sheets or tubes. A core domain similar to that of P. dubius p60 is also found in the recently described epiplasmic proteins of the flagellate Euglena, the so-called articulins. Our results show that the members of this protein family are not restricted to flagellates, but are also present in the distantly related ciliates where they are major constituents of the epiplasm. Comparison of flagellate and ciliate articulins highlights common features of this novel family of cytoskeletal proteins.

Intermediate filament forming ability of desmin derivatives lacking either the amino-terminal 67 or the carboxy-terminal 27 residues.

Amino acid sequence data and results from limited proteolytic digestion have been used to define the three-domain structure of intermediate filament proteins. A centrally located highly alpha-helical domain of about 310 residues well-conserved in sequence principles and length is flanked by the highly variable sequences of the non-alpha-helical headpiece and tailpiece. A direct involvement in filament formation of one or both terminal domains was previously proposed for desmin since chymotryptic removal of head and tailpiece provided a derivative unable to form filaments. In order to evaluate directly the importance of these regions we have prepared desmin derivatives lacking either the amino-terminal 67 (T-desmin) or carboxy-terminal 27 residues (L-desmin). Whereas the latter derivative is fully polymerization-competent the fragment lacking only the basic and arginine-rich headpiece cannot form filaments on its own and remains in a protofilamentous stage. These structures of T-desmin are not incorporated into filaments when mixed with protofilaments of desmin. If, however, the two proteins are mixed in 7 M-urea subsequent dialysis provides morphologically normal filaments containing T-desmin. The results suggest that at least certain hybrid protofilaments containing less than four headpieces are accepted in the filament. The removal of the 27 carboxy-terminal residues in L-desmin, although not interfering with filament formation, leads to a change in surface since filaments show lateral aggregation at 170 mM but not at 50 mM salt. The results are discussed in relation to current models of intermediate filament structure.

Antiparallel orientation of the two double-stranded coiled-coils in the tetrameric protofilament unit of intermediate filaments.

The chymotryptically excised middle domain of desmin slightly exceeds in length the structurally conserved alpha-helical middle region documented in all intermediate filament proteins by amino acid sequence data. This rod domain is a protofilament derivative with a tetrameric organization, thus indicating the presence of two double-stranded coiled-coil units. We now show by immunoelectron microscopy that Fab fragments of a desmin-specific monoclonal antibody mixed with the rod lead to dumb-bell-shaped structures. The tagging of both ends together with the length of the rod (48 nm) argues for an antiparallel orientation of the two coiled-coils without a major stagger. This information combined with the lateral 21 nm periodicity of the intermediate filament observed by us and others leads to a structural hypothesis similar to those entertained from X-ray data on wool alpha-keratins, although here an antiparallel tetrameric unit of some 60 to 66 nm is invoked, which has never been isolated. The structure that we discuss allows for the existence of both the particles, and the antibody experiment strongly supports the antiparallel orientation postulated in both approaches. The tube-like filament structure proposed for the intermediate filament agrees with recent mass per unit length measurements and allows for two minor classes of intermediate filaments with different values in this property as also found experimentally.

Assembly and architecture of invertebrate cytoplasmic intermediate filaments reconcile features of vertebrate cytoplasmic and nuclear lamin-type intermediate filaments.

The two major intermediate filament (IF) proteins from the esophagus epithelium of the snail Helix pomatia and the two major IF proteins from muscle tissue of the nematode Ascaris suum were investigated under a variety of assembly conditions. The lowest-order complexes from each of the four protostomic invertebrate (p-INV) IF proteins are parallel, unstaggered dimers involving two-stranded alpha-helical coiled coil formation of their approximately 350 amino acid residue central rod domain (i.e. long-rod). In the electron microscope these are readily recognized by their distinct approximately 56 nm long rod with two globular domains (i.e. representing the non-helical carboxy-terminal tail domain of the p-INV IF proteins) attached at one end, closely resembling vertebrate lamin dimers. The next-higher-order oligomers are tetramers, which are easily recognized by their two pairs of globular tail domains attached at either end of a approximately 72 nm long central rod portion. According to their size and shape, these tetramers are built from two dimers associated laterally in an antiparallel, approximately half-staggered fashion via the amino-terminal halves of their rod domains. This is similar to the NN-type tetramers found as the most abundant oligomer species in all types of vertebrate cytoplasmic IF proteins, which contain a approximately 310 amino acid residue central rod domain (i.e. short-rod). As a first step toward filament formation, the p-INV IF tetramers anneal longitudinally into protofilaments by antiparallel CC-type association of the carboxy-terminal halves of their dimer rods. The next step involves radial growth, occurring initially through lateral association of two four-chain protofilaments into octameric subfibrils, which then further associate into mature, full-width filaments. Head-to-tail polymers of dimers and paracrystalline fibers commonly observed with vertebrate lamins were only rarely seen with p-INV IF proteins. The globular domains residing at the carboxy-terminal end of p-INV IF dimers were studding the surface of the filaments at regular, approximately 24.5 nm intervals, thereby giving them a "beaded" appearance with an axial periodicity of about 24.5 nm, which is approximately 3 nm longer than the corresponding approximately 21.5 nm repeat pattern exhibited by short-rod vertebrate IFs.

Divide-and-conquer crystallographic approach towards an atomic structure of intermediate filaments.

Intermediate filaments (IFs) represent an essential component of the cytoskeleton in higher eukaryotic cells. The elementary building block of the IF architecture is an elongated dimer with its dominant central part being a parallel double-stranded alpha-helical coiled coil. Filament formation proceeds via a specific multi-step association of the dimers into the unit-length filaments, which subsequently anneal longitudinally and finally radially compact into mature filaments. To tackle the challenge of a crystallographic structure determination, we have produced and characterised 17 overlapping soluble fragments of human IF protein vimentin. For six fragments ranging in length between 39 and 84 amino acid residues, conditions yielding macroscopic crystals could be established and X-ray diffraction data were collected to the highest resolution limit between 1.4 and 3 A. We expect that solving the crystal structures of these and further fragments will eventually allow us to patch together a molecular model for the full-length vimentin dimer. This divide-and-conquer approach will be subsequently extended to determining the crystal structures of a number of complexes formed by appropriate vimentin fragments, and will eventually allow us to establish the three- dimensional architecture of complete filaments at atomic resolution.

Chemical crosslinking with disuccinimidyl tartrate defines the relative positions of the two antiparallel coiled coils of the desmin protofilament unit.

Filaments formed by desmin, the myogenic intermediate filament protein, were crosslinked with the lysine specific crosslinker DST (disuccinimidyl tartrate; 0.64 nm span) and three DST crosslinked peptides were characterized. Two correspond to crosslinks previously obtained with the longer crosslinker EGS (ethylene glycol bis(succinimidylsuccinate), 1.61 nm span) which defined the antiparallel on-stagger relationship of neighbouring coiled coils. The two DST crosslinks now provide the relative positions of the coiled coils within a limit of about 9 alpha-helical residues. The third DST crosslink most likely connecting two helices of a single coiled coil gives a direct measure of the distance spanned in DST crosslinks.

Proteolysis of the neurofilament 68 kDa protein explains several previously described brain proteins of unique composition and high acidity.

Neurofilaments follow the structural principles of non-neuronal intermediate filaments but contain additional sequences which are carboxyterminally located and increase in length between triplet proteins (68 kDa, 160 kDa and 200 kDa). The tailpiece domain has been sequenced in the case of the porcine 68 kDa protein. It has a unique amino acid composition. Within 106 residues there are only 12 different amino acid types, and glutamic acid accounts for 46% of the sequence. Examination of the literature on highly acidic brain proteins leads us to the proposal that microglutamic acid-rich protein, Glu-50, macroglutamic protein, as well as some unusual components of the S100 class, are most likely proteolytic degradation products of the neurofilament 68 kDa protein.

Location and sequence characterization of the major phosphorylation sites of the high molecular mass neurofilament proteins M and H.

Diagonal fingerprinting allows the specific purification of those tryptic peptides which change electrophoretic mobility due to a dephosphorylation step introduced after the first dimension. Nine tryptic peptides from the tail domain of porcine neurofilament M protein identify a minimum of 6 phosphorylated serines. Unexpectedly, four of the nine peptides characterize a region of degenerate repetitive sequences. Results on neurofilament H tail, although less complete, yield longer sequences of degenerate repetitive character. Here, all serines present appear to be contained in a lysine-serine-proline unit. This motif also occurs in some but not all M peptides. We suggest that degenerate repetitive sequences in neurofilament M and H tails have a high species-specific drift.

Amino acid sequence characterization of mammalian vimentin, the mesenchymal intermediate filament protein.

The amino-terminal 98 residues of porcine vimentin have been determined by amino acid sequence studies. Extensive overlap is seen with the corresponding region of the carboxyterminal 448 residues of hamster vimentin predicted from DNA sequence studies, which left the very amino-terminal region unknown. The combined data show that contrary to gel electrophoretic results, mammalian vimentin contains only about 467 residues, and that species-specific drift occurs mainly in the amino-terminal non-alpha-helical array. The results are discussed parallel to emerging concepts on intermediate filament protein diversity.

SDS-PAGE strongly overestimates the molecular masses of the neurofilament proteins.

Direct molecular mass determination of the three porcine neurofilament proteins (H, M and L) was performed in 6 M guanidine-HCl using analytical gel filtration and sedimentation equilibrium centrifugation. The results show that SDS-PAGE strongly overestimates the values of the 'higher molecular mass' components H and M. This discrepancy stems from the carboxyterminal extensions known to have unusual amino acid composition.

The complete amino acid sequence of the major mammalian neurofilament protein (NF-L).

The first complete amino acid sequence of a neurofilament protein has been established. Porcine NF-L contains 548 residues corresponding to a molecular mass of approximately 62 kDa. This value is noticeably smaller than the 68-72 kDa estimates from gel electrophoresis. Sequence comparison among the 6 non-epithelial intermediate filament (IF) proteins of warm-blooded vertebrates shows that the three NF proteins are the most remote members. Additionally and unexpectedly they reveal among each other lower sequence identity than the three non-neuronal IF proteins GFAP, desmin, and vimentin where the last two are particularly closely related. Certain schemes of IF protein evolution are discussed.

Identification of the nicking tyrosine of geminivirus Rep protein.

The replication initiator (Rep) proteins of geminiviruses perform a DNA cleavage and strand transfer reaction at the viral origin of replication. As a reaction intermediate, Rep proteins become covalently linked to the 5' end of the cleaved DNA. We have used tomato yellow leaf curl virus Rep protein for in vivo and in vitro analyses. Isolating a covalent peptide-nucleotide complex, we have identified the amino acid of Rep which mediates cleavage and links the protein to DNA. We show that tyrosine-103, located in a conserved sequence motif, initiates DNA cleavage and is the physical link between geminivirus Rep protein and its origin DNA.