On chemistry of γ-chitin Kaya, Murat; Mujtaba, Muhammad; Ehrlich, Hermann ...
Carbohydrate polymers,
11/2017, Letnik:
176
Journal Article
Recenzirano
•First detailed physicochemical characterization of γ-chitin was carried-out.•The isolated γ-chitin was compared with α and β forms.•Chemical structure of the chitins was expressed through Quantum ...chemical calculations.•γ-chitin was found much closer to α-chitin than β-chitin.
The biological material, chitin, is present in nature in three allomorphic forms: α, β and γ. Whereas most studies have dealt with α- and β-chitin, only few investigations have focused on γ-chitin, whose structural and physicochemical properties have not been well delineated. In this study, chitin obtained for the first time from the cocoon of the moth (Orgyia dubia) was subjected to extensive physicochemical analyses and examined, in parallel, with α-chitin from exoskeleton of a freshwater crab and β-chitin from cuttlebone of the common cuttlefish. Our results, which are supported by13C CP-MAS NMR, XRD, FT-IR, Raman spectroscopy, TGA, DSC, SEM, AFM, chitinase digestive test and elemental analysis, verify the authenticity of γ-chitin. Further, quantum chemical calculations were conducted on all three allomorphic forms, and, together with our physicochemical analyses, demonstrate that γ-chitin is distinct, yet closer in structure to α-chitin than β-chitin.
Chitin, a biopolymer of N-acetylglucosamine, is abundant in invertebrates and fungi and is an important structural molecule 1, 2. There has been a longstanding belief that vertebrates do not produce ...chitin; however, we have obtained compelling evidence to the contrary. Chitin synthase genes are present in numerous fishes and amphibians, and chitin is localized in situ to the lumen of the developing zebrafish gut, in epithelial cells of fish scales, and in at least three different cell types in larval salamander appendages. Chitin synthase gene knockdowns and various histochemical experiments in zebrafish further authenticated our results. Finally, a polysaccharide was extracted from scales of salmon that exhibited all the chemical hallmarks of chitin. Our data and analyses demonstrate the existence of endogenous chitin in vertebrates and suggest that it serves multiple roles in vertebrate biology.
•Chitin synthase gene activity was detected in zebrafish, salmon, and axolotl•Chitin per se was detected in situ in multiple fish and axolotl tissues•Knockdown of chitin synthase in zebrafish embryos resulted in reduction of chitin•Polysaccharides from fish scale epithelia exhibited spectral properties of chitin
It has been widely held that vertebrates do not produce chitin, a glyco-polymer found abundantly in nature. However, using multiple experimental approaches, Tang et al. provide strong evidence for the endogenous production of chitin in fishes and amphibians, raising questions as to its biological role within the vertebrates.
Programmed DNA rearrangements in the single-celled eukaryote Oxytricha trifallax completely rewire its germline into a somatic nucleus during development. This elaborate, RNA-mediated pathway ...eliminates noncoding DNA sequences that interrupt gene loci and reorganizes the remaining fragments by inversions and permutations to produce functional genes. Here, we report the Oxytricha germline genome and compare it to the somatic genome to present a global view of its massive scale of genome rearrangements. The remarkably encrypted genome architecture contains >3,500 scrambled genes, as well as >800 predicted germline-limited genes expressed, and some posttranslationally modified, during genome rearrangements. Gene segments for different somatic loci often interweave with each other. Single gene segments can contribute to multiple, distinct somatic loci. Terminal precursor segments from neighboring somatic loci map extremely close to each other, often overlapping. This genome assembly provides a draft of a scrambled genome and a powerful model for studies of genome rearrangement.
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•Oxytricha’s encrypted germline genome contains >3,500 scrambled genes•>225,000 DNA segments assemble, some combinatorially, to form the somatic genome•Thousands of gene segments for different somatic loci interweave with each other•Hundreds of germline-limited genes are expressed during development, then deleted
A draft assembly of the Oxytricha germline genome, including a comparison to the somatic genome, to present a global view of its massive scale of genome rearrangements.
The lamprey (Petromyzon marinus) undergoes developmentally programmed genome rearrangements that mediate deletion of∼20% of germline DNA from somatic cells during early embryogenesis. This genomic ...differentiation of germline and soma is intriguing, because the germline plays a unique biological role wherein it must possess the ability to undergo meiotic recombination and the capacity to differentiate into every cell type. These evolutionarily indispensable functions set the germline at odds with somatic tissues, because factors that promote recombination and pluripotency can potentially disrupt genome integrity or specification of cell fate when misexpressed in somatic cell lineages (e.g., in oncogenesis). Here, we describe the development of new genomic and transcriptomic resources for lamprey and use these to identify hundreds of genes that are targeted for programmed deletion from somatic cell lineages. Transcriptome sequencing and targeted validation studies further confirm that somatically deleted genes function both in adult (meiotic) germline and in the development of primordial germ cells during embryogenesis. Inferred functional information from deleted regions indicates that developmentally programmed rearrangement serves as a (perhaps ancient) biological strategy to ensure segregation of pluripotency functions to the germline, effectively eliminating the potential for somatic misexpression.
► The lamprey (Petromyzon marinus) undergoes developmentally programmed gene deletions ► Analysis of lamprey germline shotgun sequence identifies germline-specific genes ► Deleted genes are specifically enriched in pluripotency-related functions ► Deleted genes function in meiotic germline and in developing primordial germ cells
The neural crest (NC) is an embryonic cell population that contributes to key vertebrate-specific features including the craniofacial skeleton and peripheral nervous system. Here we examine the ...transcriptional and epigenomic profiles of NC cells in the sea lamprey, in order to gain insight into the ancestral state of the NC gene regulatory network (GRN). Transcriptome analyses identify clusters of co-regulated genes during NC specification and migration that show high conservation across vertebrates but also identify transcription factors (TFs) and cell-adhesion molecules not previously implicated in NC migration. ATAC-seq analysis uncovers an ensemble of cis-regulatory elements, including enhancers of Tfap2B, SoxE1 and Hox-α2 validated in the embryo. Cross-species deployment of lamprey elements identifies the deep conservation of lamprey SoxE1 enhancer activity, mediating homologous expression in jawed vertebrates. Our data provide insight into the core GRN elements conserved to the base of the vertebrates and expose others that are unique to lampreys.
One of the most remarkable innovations of the vertebrate adaptive immune system is the progressive organization of the lymphoid tissues that leads to increased efficiency of immune surveillance and ...cell interactions. The mucosal immune system of endotherms has evolved organized secondary mucosal lymphoid tissues (O-MALT) such as Peyer’s patches, tonsils, and adenoids. Primitive semi-organized lymphoid nodules or aggregates (LAs) were found in the mucosa of anuran amphibians 1, suggesting that O-MALT evolved from amphibian LAs ∼250 million years ago 1–4. This study shows for the first time the presence of O-MALT in the mucosa of the African lungfish, an extant representative of the closest ancestral lineage to all tetrapods. Lungfish LAs are lymphocyte-rich structures associated with a modified covering epithelium and express all IGH genes except for IGHW2L. In response to infection, nasal LAs doubled their size and increased the expression of CD3 and IGH transcripts. Additionally, de novo organogenesis of inducible LAs resembling mammalian tertiary lymphoid structures was observed. Using deep-sequencing transcriptomes, we identified several members of the tumor necrosis factor (TNF) superfamily, and subsequent phylogenetic analyses revealed its extraordinary diversification within sarcopterygian fish. Attempts to find AICDA in lungfish transcriptomes or by RT-PCR failed, indicating the possible absence of somatic hypermutation in lungfish LAs. These findings collectively suggest that the origin of O-MALT predates the emergence of tetrapods and that TNF family members play a conserved role in the organization of vertebrate mucosal lymphoid organs.
•African lungfish possess O-MALT in their nasal and intestinal mucosa•Lungfish O-MALT is rich in lymphocytes but lacks segregation of B and T cells•O-MALT changes its architecture in response to bacterial infection•TNF superfamily members such as lymphotoxins diversified in lungfish
Organized MALT is thought to be an innovation of endotherms, whereas ectothermic amphibians have primitive O-MALT in the form of lymphoid aggregates. Tacchi et al. show that primitive O-MALT first appeared in sarcopterygian fish like the African lungfish, and therefore its origins predate the transition of vertebrates from water to land.
The sea lamprey (Petromyzon marinus) serves as a comparative model for reconstructing vertebrate evolution. To enable more informed analyses, we developed a new assembly of the lamprey germline ...genome that integrates several complementary data sets. Analysis of this highly contiguous (chromosome-scale) assembly shows that both chromosomal and whole-genome duplications have played significant roles in the evolution of ancestral vertebrate and lamprey genomes, including chromosomes that carry the six lamprey HOX clusters. The assembly also contains several hundred genes that are reproducibly eliminated from somatic cells during early development in lamprey. Comparative analyses show that gnathostome (mouse) homologs of these genes are frequently marked by polycomb repressive complexes (PRCs) in embryonic stem cells, suggesting overlaps in the regulatory logic of somatic DNA elimination and bivalent states that are regulated by early embryonic PRCs. This new assembly will enhance diverse studies that are informed by lampreys' unique biology and evolutionary/comparative perspective.
The current paradigm of gut evolution assumes that non-bilaterian metazoan lineages either lack a gut (Porifera and Placozoa) or have a sac-like gut (Ctenophora and Cnidaria) and that a through-gut ...originated within Bilateria 1–8. An important group for understanding early metazoan evolution is Ctenophora (comb jellies), which diverged very early from the animal stem lineage 9–13. The perception that ctenophores possess a sac-like blind gut with only one major opening remains a commonly held misconception 4, 5, 7, 14, 15. Despite descriptions of the ctenophore digestive system dating to Agassiz 16 that identify two openings of the digestive system opposite of the mouth—called “excretory pores” by Chun 17, referred to as an “anus” by Main 18, and coined “anal pores” by Hyman 19—contradictory reports, particularly prominent in recent literature, posit that waste products are primarily expelled via the mouth 4, 5, 7, 14, 19–23. Here we demonstrate that ctenophores possess a unidirectional, functionally tripartite through-gut and provide an updated interpretation for the evolution of the metazoan through-gut. Our results resolve lingering questions regarding the functional anatomy of the ctenophore gut and long-standing misconceptions about waste removal in ctenophores. Moreover, our results present an intriguing evolutionary quandary that stands in stark contrast to the current paradigm of gut evolution: either (1) the through-gut has its origins very early in the metazoan stem lineage or (2) the ctenophore lineage has converged on an arrangement of organs functionally similar to the bilaterian through-gut.
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•The Ctenophora, a non-bilaterian animal lineage, possess a functional though-gut•Evacuation of waste material via anal pores is controlled by actin-rich sphincters•We describe gut cell types involved with nutrient absorption and distribution•Homology of the ctenophore through-gut to the bilaterian through-gut remains unclear
Ctenophores have historically been described as having a blind, sac-like gut. Using live imaging of ctenophore digestion in their report, Presnell et al. demonstrate that ctenophores possess a functionally tripartite through-gut, challenging the current paradigm that assumes that the through-gut originated within Bilateria.
Biological materials such as chiton tooth, squid beak, and byssal threads of bivalves have inspired the development of new technologies. To this end, we have characterized the acellular components in ...the buccal mass of the terrestrial slug Ariolimax californicus (banana slug). These components are the radula, the jaw, and the odontophore. In the radula, calcium-rich denticles are tightly interlocked one to the other on top of a nanofibrous chitin membrane. The jaw has a nanostructured morphology made of chitin to achieve compression resistance and is directly linked to the foregut cuticle, which has a protective nanofibrous structure. Finally, in the odontophore, we observed a structurally elastic microstructure that interfaces soft tissues with a highly stressed radula membrane. Based on those observations, we discuss the interaction between these components and highlight how the materials in these task-specific components have evolved. This structure-properties-function study of the A. californicus' buccal mass may aid in the design and fabrication of novel bioinspired materials.
Activation-induced cytidine deaminase (AID) is a genome-mutating enzyme that initiates class switch recombination and somatic hypermutation of antibodies in jawed vertebrates. We previously described ...the biochemical properties of human AID and found that it is an unusual enzyme in that it exhibits binding affinities for its substrate DNA and catalytic rates several orders of magnitude higher and lower, respectively, than a typical enzyme. Recently, we solved the functional structure of AID and demonstrated that these properties are due to nonspecific DNA binding on its surface, along with a catalytic pocket that predominantly assumes a closed conformation. Here we investigated the biochemical properties of AID from a sea lamprey, nurse shark, tetraodon, and coelacanth: representative species chosen because their lineages diverged at the earliest critical junctures in evolution of adaptive immunity. We found that these earliest-diverged AID orthologs are active cytidine deaminases that exhibit unique substrate specificities and thermosensitivities. Significant amino acid sequence divergence among these AID orthologs is predicted to manifest as notable structural differences. However, despite major differences in sequence specificities, thermosensitivities, and structural features, all orthologs share the unusually high DNA binding affinities and low catalytic rates. This absolute conservation is evidence for biological significance of these unique biochemical properties.
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