Modularity and diversity of target selectors in Tn7 transposons

To spread, transposons must integrate into target sites without disruption of essential genes while avoiding host defense systems. Tn7-like transposons employ multiple mechanisms for target-site selection, including protein-guided targeting and, in CRISPR-associated transposons (CASTs), RNA-guided targeting. Combining phylogenomic and structural analyses, we conducted a broad survey of target selectors, revealing diverse mechanisms used by Tn7 to recognize target sites, including previously uncharacterized target-selector proteins found in newly discovered transposable elements (TEs). We experimentally characterized a CAST I-D system and a Tn6022-like transposon that uses TnsF, which contains an inactivated tyrosine recombinase domain, to target the comM gene. Additionally, we identified a non-Tn7 transposon, Tsy, encoding a homolog of TnsF with an active tyrosine recombinase domain, which we show also inserts into comM. Our findings show that Tn7 transposons employ modular architecture and co-opt target selectors from various sources to optimize target selection and drive transposon spread.

Evidence that beta-tubulin induces a conformation change in the cytosolic chaperonin which stabilizes binding: implications for the mechanism of action

The class II chaperonin CCT facilitates protein folding by a process that is not well-understood. One striking feature of this chaperonin is its apparent selectivity in vivo, folding only actin, tubulin, and several other proteins. In contrast, the class I chaperonin GroEL is thought to facilitate the folding of many proteins within Escherichia coli. It has been proposed that this apparent selectivity is associated with certain regions of a substrate protein's primary structure. Using limiting amounts of beta-tubulin, beta-tubulin mutants, and beta-tubulin/ftsZ chimeras, we assessed the contribution of select regions of beta-tubulin to CCT binding. In a complementary study, we investigated inter-ring communication in CCT where we exploited polypeptide binding sensitivity to nucleotide to quantitate nucleotide binding. beta-Tubulin bound with a high apparent affinity to CCT in the absence of nucleotide (apparent K(D) approximately 3 nM; its apparent binding free energy, DeltaG, ca. -11.8 kcal/mol). Despite this, the interactions appear to be weak and distributed throughout much of the sequence, although certain sites ("hot spots") may interact somewhat more strongly with CCT. Globally averaged over the beta-tubulin sequence, these interactions appear to contribute ca. -9 to -11 cal/mol per residue, and to account for no more than 50-60% of the total binding free energy. We propose that a conformation change or deformation induced in CCT by substrate binding provides the missing free energy which stabilizes the binary complex. We suggest that by coupling CCT deformation with polypeptide binding, CCT avoids the need for high "intrinsic" affinities for its substrates. This strategy allows for dynamic interactions between chaperonin and bound substrate, which may facilitate folding on the interior surface of CCT in the absence of nucleotide and/or productive release of bound polypeptide into the central cavity upon subsequent MgATP binding. CCT displayed negative inter-ring cooperativity like GroEL. When ring 1 of CCT bound MgATP or beta-tubulin, the affinity of ring 2 for polypeptide or nucleotide was apparently reduced approximately 100-fold.

Deletion of amino acids from the carboxy-terminal end of actin

A series of deletions was made from the C-terminal end of actin by inserting termination codons into a full length cDNA of human alpha-skeletal muscle actin. These included deletions of 2, 3, 10, 20, 30, and 40 amino acids. The cDNA clones were transcribed and the resulting mRNAs were translated in vitro using 35S-labeled methionine. The 35S-labeled actin and actin mutants were then tested for the ability to coassemble with carrier actin, bind DNAse I, bind myosin S-1, bind a 27 kDa proteolytic fragment of alpha-actinin, and incorporate into myofibrils in vitro. Removal of the C-terminal two or three amino acids did not grossly alter the properties of actin tested. Deletion of an additional 7 amino acids (10 amino acids total) significantly decreased coassembly, binding to DNAse I, and incorporation into myofibrils, but did not dramatically reduce binding to myosin S-1 or the 27 kDa fragment of alpha-actinin. Deletion of 20 or more amino acids virtually abolished all normal actin function tested. By examining the structure of actin, we propose that the effect of removing residues 356-365 is due to the important role Trp356 plays in maintaining hydrophobic bonds between three non-contiguous segments of actin. We also suggest that removal of residues 366-372 adversely affected the structure or orientation of the DNAse I binding loop and that this change can account for defects in actin binding to DNAse I, coassembly with wild type actin, and incorporation into myofibrils.

Probing actin incorporation into myofibrils using Asp11 and His73 actin mutants

We used a cell free system Bouché et al.: J. Cell Biol. 107:587-596, 1988] to study the incorporation of actin into myofibrils. We used alpha-skeletal muscle actin and actins with substitutions of either His73 [Solomon and Rubenstein: J. Biol.Chem. 262:11382, 1987], or Asp11 [Solomon et al.: J. Biol. Chem. 263:19662, 1988]. Actins were translated in reticulocyte lysate and incubated with myofibrils. The incorporated wild type actin could be cross-linked into dimers using N,N'-1,4-phenylenebismaleimide (PBM), indicating that the incorporated actin is actually inserted into the thin filaments of the myofibril. The His73 mutants incorporated to the same extent as wild type actin and was also cross-linked with PBM. Although some of the Asp11 mutants co-assembled with carrier actin, only 1-3% of the Asp11 mutant actins incorporated after 2 min and did not increase after 2 hr. Roughly 17% of wild type actin incorporated after 2 min and 31% after 2 hr. ATP increased the release of wild type actin from myofibrils, but did not increase the release of Asp11 mutants. We suggest that (1) the incorporation of wild type and His73 mutant actins was due to a physiological process whereas association of Asp11 mutants with myofibrils was non-specific, (2) the incorporation of wild type actin involved a rapid initial phase, followed by a slower phase, and (3) since some of the Asp11 mutants can co-assemble with wild type actin, the ability to self-assemble was not sufficient for incorporation into myofibrils. Thus, incorporation probably includes interaction between actin and a thin filament associated protein. We also showed that incorporation occurred at actin concentrations which would cause disassembly of F-actin. Since the myofibrils did not show large scale disassembly but incorporated actin, filament stability and monomer incorporation are likely to be mediated by actin associated proteins of the myofibril.

Actin filament structure probed with monoclonal antibodies

The interaction of two monoclonal antibodies (mAbs) with actin has been characterized to map the epitopes defined by these mAbs and to determine the accessibility of these sites in the actin filament (F-actin). Both mAbs react specifically with actin in radioimmunoassays and Western blot assays, and by immunoprecipitation. The location of the epitopes within the primary structure of actin has been determined using limited proteolysis of actin and Western blots, or using immunoprecipitation of truncated actin fragments synthesized in a cell free translation assay. Both mAbs bind to the C-terminal fragment of actin (residues 68-375) produced by chymotrypsin cleavage. One epitope is further localized to a 9.9 kD peptide corresponding to residues 5-93. Therefore, the epitope defined by this mAb (2G11.4) lies between residues Lys68 and Glu93 of actin. The location of the other epitope was determined by immunoprecipitation of actin fragments synthesized in vitro. Removal of residues 356-365 from the C-terminus of actin completely abolished the binding of mAb 4E3.adl. Therefore, this mAb defines an epitope that involves residues between Trp356 and Ala365. The accessibility of these epitopes in native F-actin was determined with solution binding assays and characterized by immunoelectron microscopy. Monoclonal antibody 4E3.adl binds strongly to filaments, resulting in bundling or decoration of F-actin depending on the valency of the mAb, and indicating that the epitope is readily accessible in F-actin. In contrast, mAb 2G11.4 disrupts F-actin structure, resulting in the formation of an amorphous immunoprecipitate. These results place constraints on models of actin filament structure.

Post-translational incorporation of actin into myofibrils in vitro: evidence for isoform specificity

The incorporation of actin into myofibrils has been examined in a cell-free system [Bouché et al.: Journal of Cell Biology 107:587-596, 1988; Goldfine et al.: Cellular and Molecular Biology of Muscle Development, 1989]. Actin was translated in a reticulocyte lysate in the presence of 35S-methionine (35S-actin) or purified from muscle and labeled with fluorescein-5-isothiocyanate (FITC-actin). Myofibrils were incubated with either 35S-actin or FITC-actin and then analyzed by gel electrophoresis or fluorescence microscopy. When myofibrils were incubated with FITC-actin monomer in the reticulocyte lysate buffer, strong fluorescent labeling was observed in Z-band regions and less so in I-bands. No fluorescence was detected in non-overlap regions of A-bands. Confocal microscopic analysis of these myofibrils indicated that FITC-actin was distributed evenly across the diameter of the myofibrils. These observations suggest that actin incorporation in the reticulocyte lysate buffer occurred at sites in the sarcomere which contain actin. In contrast, FITC-actin showed a variety of non-physiological incorporation patterns when incubated with myofibrils in the presence of an isotonic buffer (I-buffer). However, when ATP was added to I-buffer, FITC-actin showed a pattern of incorporation into myofibrils similar to that seen in the reticulocyte lysate buffer. Immunoblots indicated that actin of native size was released from myofibrils during incubation in the reticulocyte lysate buffer. No actin release was detected when the myofibrils were incubated in I-buffer lacking ATP. We used this system to compare the incorporation of actin isoforms into myofibrils. Both alpha- and beta-actins exhibited incorporation into the myofibrils but there was a three-fold greater incorporation of the alpha isoform. We propose that the differential affinities of actin isoforms for myofibrils and other cytoskeletal structures could provide a mechanism for actin isoform targeting within the cytoplasm.

Polarized release of enveloped viruses in the embryonic chick heart: demonstration of epithelial polarity in the presumptive myocardium

The presumptive myocardium of the embryonic vertebrate heart is composed of cells which exhibit the morphology of a cuboidal epithelium. To examine the functional polarity of these developing myocytes, embryonic chick hearts (Hamburger-Hamilton stages 10-13) were infected with either influenza virus (FLU) or vesicular stomatitis virus (VSV). These viruses have been shown to sort vectorially to either apical (FLU) or basolateral (VSV) membrane surfaces in monolayers of polarized kidney (MDCK) cells. Our results demonstrate that these viruses bud with comparable polarity from differentiating myocytes. However, there appear to be stage-dependent differences in the polarized budding of the two viruses: restricted basolateral release of VSV is present before or shortly after the formation of the heart tube, whereas polarized budding of FLU is established later in development. These results are discussed in terms of plasma membrane organization during the early stages of cardiac development.

Biochemical and immunological analyses of cytoskeletal domains of neurons

We have used cultured sympathetic neurons to identify microtubule proteins (tubulin and microtubule-associated proteins [MAPs]) and neurofilament (NF) proteins in pure preparations of axons and also to examine the distribution of these proteins between axons and cell bodies + dendrites. Pieces of sympathetic ganglia containing thousands of neurons were plated onto culture dishes and allowed to extend neurites. Dendrites remained confined to the ganglionic explant or cell body mass (CBM), while axons extended away from the CBM for several millimeters. Axons were separated from cell bodies and dendrites by dissecting the CBM away from cultures, and the resulting axonal and CBM preparations were analyzed using biochemical, immunoblotting, and immunoprecipitation methods. Cultures were used after 17 d in vitro, when 40-60% of total protein was in the axons. The 68,000-mol-wt NF subunit is present in both axons and CBM in roughly equal amounts. The 145,000- and 200,000-mol-wt NF subunits each consist of several variants which differ in phosphorylation state; poorly and nonphosphorylated species are present only in the CBM, whereas more heavily phosphorylated forms are present in axons and, to a lesser extent, the CBM. One 145,000-mol-wt NF variant was axon specific. Tubulin is roughly equally distributed between CBM and axon-like neurites of explant cultures. MAP-1a, MAP-1b, MAP-3, and the 60,000-mol-wt MAP are also present in the CBM and axon-like neurites and show distribution patterns similar to that of tubulin. In contrast, MAP-2 was detected only in the CBM, while tau and the 210,000-mol-wt MAP were greatly enriched in axons compared to the CBM. In immunostaining analyses, MAP-2 localized to cell bodies and dendrite-like neurites, but not to axon-like neurites, whereas antibodies to tubulin and MAP-1b localized to all regions of the neurons. The regional differences in composition of the neuronal cytoskeleton presumably generate corresponding differences in its structure, which may, in turn, contribute to the morphological differences between axons and dendrites.

Cultured neurons contain a variety of microtubule-associated proteins

The non-tubulin proteins associated with microtubules (MAPs) in cultures of pure sympathetic neurons have been identified using a variety of biochemical and immunochemical methods. MAPs of cultured sympathetic neurons include proteins corresponding to brain MAP-1 (consisting of MAP-1a and MAP-1b species), MAP-2, MAP-3, tau, 4 proteins that range in molecular weight from 60,000 to 76,000, and proteins with molecular weights of 210,000, 130,000 and 32,000. Many of the MAPs are phosphorylated in situ. MAP-2 and tau of cultured sympathetic neurons differ from their counterparts of brain in electrophoretic mobility. The observed variety of MAPs in sympathetic neurons together with the differences in MAPs of brain and sympathetic neurons are discussed in terms of microtubule heterogeneity in the nervous system.

The complete nucleotide sequence of the chick a-actin gene and its evolutionary relationship to the actin gene family

The nucleotide sequence of the chick a-actin gene reveals that the gene is comprised of 7 exons separated by six very short intervening sequences (IVS). The first IVS interrupts the 73 nucleotide 5' untranslated segment between nucleotides 61 and 62. The remaining IVS interrupt the translated region at codons 41/42, 150, 204, 267, and 327/328. The 272 nucleotide 3' untranslated segment is not interrupted by IVS. The amino acid sequence derived from the nucleotide sequence is identical to the published sequence for chick a-actin except for the presence of a met-cys dipeptide at the amino-terminus. The IVS positions in the chick a-actin gene are identical to those of the rat a-actin gene. While there is partial coincidence of the IVS in the a-actin genes with the vertebrate b-actin genes and 2 sea urchin actin genes, there is no coincidence with actin genes from any other source except soybean where one IVS position is shared. This discordance in IVS positions makes the actin gene family unique among the eucaryotic genes analyzed to date.