Gene silencing in chick embryos with a vector-based small interfering RNA system

In this paper, the use of vector-based RNA interference (RNAi) to specifically interfere with gene expression in chick embryos is reported. In ovo electroporation was carried out to transfer a small interfering RNA (siRNA) expression vector into chick embryos. En2 was chosen for the target gene because the family gene, En1, is expressed in a similar pattern. Four sets of 19-mer sequences were designed with the En2 open reading frame region connected to a sequence of short hairpin RNA (shRNA), which exerts siRNA effects after being transcribed, and inserted into pSilencer U6-1.0 vector. En2 and En1 expression were suppressed by the siRNA whose sequence completely matched En2 and En1. Suppression occurred when the siRNA sequence differed by up to two nucleotides from the target sequence. The sequence that differed by four nucleotides from the target gene did not show siRNA effects. One set that completely matched the En2 target did not show siRNA effects, which may be due to location of the siRNA in the target gene. Thus, multiple sets of shRNA must be prepared if we are to consider. This system will greatly contribute to the analysis of function of genes of interest, because the target gene can be silenced in a locally and temporally desired manner.     

Dioxane contributes to the altered conformation and oligomerization state of a designed engrailed homeodomain variant

Our goal was to compute a stable, full-sequence design of the Drosophila melanogaster engrailed homeodomain. Thermal and chemical denaturation data indicated the design was significantly more stable than was the wild-type protein. The data were also nearly identical to those for a similar, later full-sequence design, which was shown by NMR to adopt the homeodomain fold: a three-helix, globular monomer. However, a 1.65 A crystal structure of the design described here turned out to be of a completely different fold: a four-helix, rodlike tetramer. The crystallization conditions included approximately 25% dioxane, and subsequent experiments by circular dichroism and sedimentation velocity analytical ultracentrifugation indicated that dioxane increases the helicity and oligomerization state of the designed protein. We attribute at least part of the discrepancy between the target fold and the crystal structure to the presence of a high concentration of dioxane.     

Possible role of Hes5 for the rostrocaudal polarity formation of the tectum

The alar plate of the mesencephalon differentiates into the optic tectum. Retinal fibers project to the tectum topographically in a retinotopic manner. Engrailed (En) is responsible for the tectum polarity formation and regionalization. Former study indicated the presence of the molecule whose expression is repressed by En and that represses the isthmus-related gene expression. To isolate such molecules, we constructed a subtracted library between cDNA population of the normal rostral mesencephalon and of the rostral mesencephalon that misexpresses En2. From the library, we isolated cHes5, a chicken homolog of Drosophila hairy/Enhancer of split. cHes5 begins to be expressed in the rostral part of the E2 mesencephalon, and spreads to caudal mesencephalon by E3. To our expectation, cHes5 expression was repressed by En2. Furthermore, misexpression of cHes5 in the mesencephalon inhibited expression of ephrinA2, a marker of caudal mesencephalon. An active repressor form of Hes5, which is a chimeric molecule of Hes5 and repressor domain of En2, showed a similar but more severe phenotype. The results indicate that Hes5 is regulated by En and is responsible for rostral identity of mesencephalon by repressing ephrinA2.     

Evolution of the cephalopod head complex by assembly of multiple molluscan body parts: Evidence from Nautilus embryonic development

Cephalopod head parts are among the most complex occurring in all invertebrates. Hypotheses for the evolutionary process require a drastic body-plan transition in relation to the life-style changes from benthos to active nekton. Determining these transitions, however, has been elusive because of scarcity of fossil records of soft tissues and lack of some of the early developmental stages of the basal species. Here we report the first embryological evidence in the nautiloid cephalopod Nautilus pompilius for the morphological development of the head complex by a unique assembly of multiple archetypical molluscan body parts. Using a specialized aquarium system, we successfully obtained a series of developmental stages that enabled us to test previous controversial scenarios. Our results demonstrate that the embryonic organs exhibit body plans that are primarily bilateral and antero-posteriorly elongated at stereotyped positions. The distinct cephalic compartment, foot, brain cords, mantle, and shell resemble the body plans of monoplacophorans and basal gastropods. The numerous digital tentacles of Nautilus develop from simple serial and spatially-patterned bud-like anlagen along the anterior-posterior axis, indicating that origins of digital tentacles or arms of all other cephalopods develop not from the head but from the foot. In middle and late embryos, the primary body plans largely change to those of juveniles or adults, and finally form a "head" complex assembled by anlagen of the foot, cephalic hood, collar, hyponome (funnel), and the foot-derived epidermal covers. We suggest that extensions of the collar-funnel compartment and free epidermal folds derived from multiple topological foot regions may play an important role in forming the head complex, which is thought to be an important feature during the body plan transition.     

Balance between DNA‐binding affinity and specificity enables selective recognition of longer target sequences in vivo

Although genome‐editing enzymes such as TALEN and CRISPR/Cas9 are being widely used, they have an essential limitation in that their relatively high‐molecular weight makes them difficult to be delivered to cells. To develop a novel genome‐editing enzyme with a smaller molecular weight, we focused on the engrailed homeodomain (EHD). We designed and constructed proteins composed of two EHDs connected by a linker to increase sequence specificity. In bacterial one‐hybrid assays and electrophoresis mobility shift assay analyses, the created proteins exhibited good affinity for DNA sequences consisting of two tandemly aligned EHD target sequences. However, they also bound to individual EHD targets. To avoid binding to single target sites, we introduced amino acid mutations to reduce the protein–DNA affinity of each EHD monomer and successfully created a small protein with high specificity for tandem EHD target sequences.     

The expression of two engrailed-related genes in an apterygote insect and a phylogenetic analysis of insect engrailed-related genes

 Homologues of the Drosophila segment polarity gene engrailed have been cloned from many insect species, as well as other arthropods and non-arthropods. We have cloned partial cDNAs of two engrailed homologues, which we call engrailed-related genes, from the phylogenetically basal insect, Thermobia domestica (Order Thysanura) and possibly as many as four engrailed-related genes from the phylogenetically intermediate insect, Oncopeltus fasciatus (Order Hemiptera). Previous to our findings, only single engrailed-related homologues had been found in phylogenetically intermediate insect species (Tribolium and Schistocerca) and in the crustacean Artemia, while two engrailed-related homologues have been found in more derived orders (Hymenoptera and the engrailed and invected genes of lepidopterans and dipterans). Consequently, we performed a phylogenetic analysis of insect engrailed-related genes to determine whether insects ancestrally had one or two engrailed-related genes. We have found evidence of concerted evolution among engrailed-related paralogues, however, that masks the true phylogenetic history of these genes; the phylogeny may only be decipherable, therefore, by examining the presence or absence of engrailed-specific and invected-specific motifs, which will require cloning the full length cDNAs from more species. In addition, we examined the embryonic expression pattern of the two Thermobia engrailed-related genes; like Drosophila engrailed and invected, they are expressed in very similar patterns, but show one temporal difference in pregnathal segments that correlates with the tentative phylogenetic placement of the genes. Thermobia engrailed-related expression also confirms that the dorsal ridge is an ancient structure in insects. Received: 4 May 1998 / Accepted: 2 August 1998     

Evolution of distinct expression patterns for engrailed paralogues in higher crustaceans (Malacostraca)

The segment-polarity gene engrailed of Drosophila melanogaster and its homologues in other arthropods possess a highly conserved expression domain in the posterior portion of each segment. We report here that the two pan-specific antibodies, Mab4D9 and Mab4F11, reveal strikingly different accumulation patterns in both of the malacostracan crustaceans Porcellio scaber (Isopoda) and Procambarus clarkii (Decapoda), compared with insects. The signal detected with Mab4D9 resides in the posterior part of each segment, including the appendages, the ventral and lateral sides of the trunk and the CNS. However, Mab4F11 reveals a signal only in small groups of neurons in the CNS and PNS, primarily localized in the pereon. We observe similar Mab4D9 and Mab4F11 patterns in the crayfish P. clarkii, except that no Mab4F11 signal is detected in the pleon. To address the possibility of multiple engrailed paralogues, we cloned partial cDNAs of two engrailed genes, Ps-en1 and Ps-en2, from P. scaber, and studied their expression patterns using whole-mount in situ hybridization. Although the Ps-en1 and Ps-en2 patterns are comparable in early development, they become distinct in late embryogenesis. Ps-en1 is expressed in the CNS, where Mab4F11 stains, but also accumulates in the epidermis. In contrast, Ps-en2 is expressed in the lateral aspect and limbs of all segments. Phylogenetic analysis of en sequences from crustaceans and insects suggests that the two en genes from the apterygote insect Thermobia domestica (Thysanura) may be related to en1 and en2 of higher crustaceans. Received: 14 February 2000 / Accepted: 1 June 2000     

The high-resolution NMR structure of the early folding intermediate of the Thermus thermophilus ribonuclease H

Elucidation of the high-resolution structures of folding intermediates is a necessary but difficult step toward the ultimate understanding of the mechanism of protein folding. Here, using hydrogen-exchange-directed protein engineering, we populated the folding intermediate of the Thermus thermophilus ribonuclease H, which forms before the rate-limiting transition state, by removing the unfolded regions of the intermediate, including an α-helix and two β-strands (51 folded residues). Using multidimensional NMR, we solved the structure of this intermediate mimic to an atomic resolution (backbone rmsd, 0.51 Å). It has a native-like backbone topology and shows some local deviations from the native structure, revealing that the structure of the folded region of an early folding intermediate can be as well defined as the native structure. The topological parameters calculated from the structures of the intermediate mimic and the native state predict that the intermediate should fold on a millisecond time scale or less and form much faster than the native state. Other factors that may lead to the slow folding of the native state and the accumulation of the intermediate before the rate-limiting transition state are also discussed.