Evolution of hard proteins in the sauropsid integument in relation to the cornification of skin derivatives in amniotes

Insights into the adaptive evolution of chromosome and essential traits through chromosome-level genome assembly of Gekko japonicus

Gekko japonicus possesses flexible climbing and detoxification abilities under insectivorous habits. Still, the evolutionary mechanisms behind these traits remain unclarified. This study presents a chromosome-level G. japonicus genome, revealing that its evolutionary breakpoint regions were enriched with specific repetitive elements and defense response genes. Gene families unique to G. japonicus and positively selected genes are mainly enriched in immune, sensory, and nervous pathways. Expansion of bitter taste receptor type 2 primarily in insectivorous species could be associated with toxin clearance. Detox cytochrome P450 in G. japonicus has undergone more birth and death processes than biosynthesis-type P450 genes. Proline, cysteine, glycine, and serine in corneous beta proteins of G. japonicus might influence flexibility and setae adhesiveness. Certain thermosensitive transient receptor potential channels under relaxed purifying selection or positive selection in G. japonicus might enhance adaptation to climate change. This genome assembly offers insights into the adaptive evolution of gekkotans.

Scales of non-avian reptiles and their derivatives contain corneous beta proteins coded from genes localized in the Epidermal Differentiation Complex

The evolution of modern reptiles from basic reptilian ancestors gave rise to scaled vertebrates. Scales are of different types, and their corneous layer can shed frequently during the year in lepidosaurians (lizards, snakes), 1-2 times per year in the tuatara and in some freshwater turtle, irregularly in different parts of the body in crocodilians, or simply wore superficially in marine and terrestrial turtles. Lepidosaurians possess tuberculate, non-overlapped or variably overlapped scales with inter-scale (hinge) regions. The latter are hidden underneath the outer scale surface or may be more exposed in specific body areas. Hinge regions allow stretching during growth and movement so that the skin remains mechanically functional. Crocodilian and turtles feature flat and shield scales (scutes) with narrow inter-scale regions for stretching and growth. The epidermis of non-avian reptilian hinge regions is much thinner than the exposed outer surface of scales and is less cornified. Despite the thickness of the epidermis, scales are mainly composed of variably amount of Corneous Beta Proteins (CBPs) that are coded in a gene cluster known as EDC (Epidermal Differentiation Complex). These are small proteins, 100-200 amino acid long of 8-25 kDa, rich in glycine and cysteine but also in serine, proline and valine that participate to the formation of beta-sheets in the internal part of the protein, the beta-region. This region determines the further polymerization of CBPs in filamentous proteins that, together a network of Intermediate Filament Keratins (IFKs) and other minor epidermal proteins from the EDC make the variable pliable or inflexible corneous material of reptilian scales, claws and of turtle beak. The acquisition of scales and skin derivatives with different mechanical and material properties, mainly due to the evolution of reptile CBPs, is essential for the life and different adaptations of these vertebrates.

General aspects on skin development in vertebrates with emphasis on sauropsids epidermis

General cellular aspects of skin development in vertebrates are presented with emphasis on the epidermis of sauropsids. Anamniote skin develops into a multilayered mucogenic and soft keratinized epidermis made of Intermediate Filament Keratins (IFKs) that is reinforced in most fish and few anurans by dermal bony and fibrous scales. In amniotes, the developing epidermis in contact with the amniotic fluid initially transits through a mucogenic phase recalling that of their anamniotes progenitors. A new gene cluster termed EDC (Epidermal Differentiation Complex) evolved in amniotes contributing to the origin of the stratum corneum. The EDC contains numerous genes coding for over 100 types of corneous proteins (CPs). In sauropsids 2-8 layers of embryonic epidermis accumulate soft keratins (IFKs) but do not form a compact corneous layer. The embryonic epidermis of reptiles and birds produces small amount of other, poorly known proteins in addition to IFKs and mucins. In the following development, a resistant corneous layer is formed underneath the embryonic epidermis that is shed before hatching. The definitive corneous epidermis of sauropsids is mainly composed of CBPs (Corneous beta proteins, formerly indicated as beta-keratins) derived from the EDC. CBPs belong to a gene sub-family of CPs unique for sauropsids, contain an inner amino acid region formed by beta-sheets, are rich in cysteine and glycine, and make most of the protein composition of scales, claws, beaks and feathers. In mammalian epidermis CPs missing the beta-sheet region are instead produced, and include loricrin, involucrin, filaggrin and various cornulins. Small amount of CPs accumulate in the 2-3 layers of mammalian embryonic epidermis and their appendages, that is replaced with the definitive corneous layers before birth. Differently from sauropsids, mammals utilize KAPs (keratin associated proteins) rich in cysteine and glycine for making the hard corneous material of hairs, claws, hooves, horns, and occasionally also scales.

Keratinization and Cornification are not equivalent processes but keratinization in fish and amphibians evolved into cornification in terrestrial vertebrates

The present account offers a generalized view of the evolution of process of terminal differentiation in keratinocytes of the epidermis in anamniotes, indicated as keratinization, into a further differentiating process of cornification in the skin and appendages of terrestrial vertebrates. Keratinization indicates the prevalent accumulation of intermediate filaments of keratins (IFKs) and is present in most fish and amphibian epidermis and inner epithelia of all vertebrates. During land adaptation, terrestrial vertebrates evolved a process of cornification and keratinocytes became dead corneocytes by the addition of numerous others proteins to the IFKs framework, represented by keratin-associated proteins (KAPs) and corneous proteins (CPs). Most of genes coding for these types of proteins are localized in chromosomal loci different and un-related from those of IFKs, and CPs originated from a gene cluster indicated as epidermal differentiation complex. During the evolution of reptiles and birds, the epidermis and corneous derivatives such as scales, claws, beaks and feathers mainly accumulate a type of CPs that overcome IFKs and containing a 34 amino acid beta-sheet core indicated as corneous beta proteins, formerly known as beta-keratins. Mammals did not evolve a beta-sheet core in their CPs and KAPs but instead produced numerous cysteine-rich IFKs in their epidermis and specialized KAPs in hairs, claws, nails, hooves and horns.

Deep Time Paleoproteomics: Looking Forward

The goal of paleoproteomics is to characterize proteins from specimens that have been subjected to the degrading and obscuring effects of time, thus obtaining biological information about tissues or organisms both unobservable in the present and unobtainable through morphological study. Although the description of sequences from Tyrannosaurus rex and Brachylophosaurus canadensis suggested that proteins may persist over tens of millions of years, the majority of paleoproteomic analyses have focused on historical, archeological, or relatively young paleontological samples that rarely exceed 1 million years in age. However, recent advances in methodology and analyses of diverse tissues types (e.g., fossil eggshell, dental enamel) have begun closing the large window of time that remains unexplored in the fossil history of the Cenozoic. In this perspective, we discuss the history and current state of deep time paleoproteomics (DTPp), here defined as paleoproteomic study of samples ∼1 million years (1 Ma) or more in age. We then discuss the future of DTPp research, including what we see as critical ways the field can expand, advancements in technology that can be utilized, and the types of questions DTPp can address if such a future is realized.

Introduction to the Study on Regeneration in Lizards as an Amniote Model of Organ Regeneration

Initial observations on the regeneration of the tail in lizards were recorded in brief notes by Aristotle over 2000 years ago, as reported in his book, History of Animals (cited from [...].

Vertebrate keratinization evolved into cornification mainly due to transglutaminase and sulfhydryl oxidase activities on epidermal proteins: An immunohistochemical survey

The epidermis of vertebrates forms an extended organ to protect and exchange gas, water, and organic molecules with aquatic and terrestrial environments. Herein, the processes of keratinization and cornification in aquatic and terrestrial vertebrates were compared using immunohistochemistry. Keratins with low cysteine and glycine contents form the main bulk of proteins in the anamniote epidermis, which undergoes keratinization. In contrast, specialized keratins rich in cysteine-glycine and keratin associated corneous proteins rich in cysteine, glycine, and tyrosine form the bulk of proteins of amniote soft cornification in the epidermis and hard cornification in scales, claws, beak, feathers, hairs, and horns. Transglutaminase (TGase) and sulfhydryl oxidase (SOXase) are the main enzymes involved in cornification. Their evolution was fundamental for the terrestrial adaptation of vertebrates. Immunohistochemistry results revealed that TGase and SOXase were low to absent in fish and amphibian epidermis, while they increased in the epidermis of amniotes with the evolution of the stratum corneum and skin appendages. TGase aids the formation of isopeptide bonds, while SOXase forms disulfide bonds that generate numerous cross-links between keratins and associated corneous proteins, likely increasing the mechanical resistance and durability of the amniote epidermis and its appendages. TGase is low to absent in the beta-corneous layers of sauropsids but is detected in the softer but pliable alpha-layers of sauropsids, mammalian epidermis, medulla, and inner root sheath of hairs. SOXase is present in hard and soft corneous appendages of reptiles, birds, and mammals, and determines cross-linking among corneous proteins of scales, claws, beaks, hairs, and feathers.

Evolution of an Epidermal Differentiation Complex (EDC) Gene Family in Birds

The transition of amniotes to a fully terrestrial lifestyle involved the adaptation of major molecular innovations to the epidermis, often in the form of epidermal appendages such as hair, scales and feathers. Feathers are diverse epidermal structures of birds, and their evolution has played a key role in the expansion of avian species to a wide range of lifestyles and habitats. As with other epidermal appendages, feather development is a complex process which involves many different genetic and protein elements. In mammals, many of the genetic elements involved in epidermal development are located at a specific genetic locus known as the epidermal differentiation complex (EDC). Studies have identified a homologous EDC locus in birds, which contains several genes expressed throughout epidermal and feather development. A family of avian EDC genes rich in aromatic amino acids that also contain MTF amino acid motifs (EDAAs/EDMTFs), that includes the previously reported histidine-rich or fast-protein (HRP/fp), an important marker in feather development, has expanded significantly in birds. Here, we characterize the EDAA gene family in birds and investigate the evolutionary history and possible functions of EDAA genes using phylogenetic and sequence analyses. We provide evidence that the EDAA gene family originated in an early archosaur ancestor, and has since expanded in birds, crocodiles and turtles, respectively. Furthermore, this study shows that the respective amino acid compositions of avian EDAAs are characteristic of structural functions associated with EDC genes and feather development. Finally, these results support the hypothesis that the genes of the EDC have evolved through tandem duplication and diversification, which has contributed to the evolution of the intricate avian epidermis and epidermal appendages.

Identification of epidermal differentiation genes of the tuatara provides insights into the early evolution of lepidosaurian skin

The tuatara (Sphenodon punctatus) is the phylogenetically closest relative of squamates (including lizards and snakes) from which it diverged around 250 million years ago. Together, they constitute the clade Lepidosauria. Fully terrestrial vertebrates (amniotes) form their skin barrier to the environment under the control of a gene cluster, termed the epidermal differentiation complex (EDC). Here we identified EDC genes in the genome of the tuatara and compared them to those of other amniotes. The organization of the EDC and proteins encoded by EDC genes are most similar in the tuatara and squamates. A subcluster of lepidosaurian EDC genes encodes corneous beta-proteins (CBPs) of which three different types are conserved in the tuatara. Small proline-rich proteins have undergone independent expansions in the tuatara and some, but not all subgroups of squamates. Two genes encoding S100 filaggrin-type proteins (SFTPs) are expressed during embryonic skin development of the tuatara whereas SFTP numbers vary between 1 and 3 in squamates. Our comparative analysis of the EDC in the tuatara genome suggests that many molecular features of the skin that were previously identified in squamates have evolved prior to their divergence from the lineage leading to the tuatara.

Corneous beta proteins of the epidermal differentiation complex (EDC) form large part of the corneous material of claws and rhamphothecae in turtles

The presence of specific protein types in claws and beaks of turtles is poorly known. The present immunological study describes the localization of some of the main corneous beta proteins (CBPs) coded in the epidermal differentiation complex of turtles. Three antibodies here utilized revealed that glycine-, cysteine-, tyrosine-, and valine-rich CBPs are present in differentiating keratinocytes of the beak and of the dorsal (unguis) and ventral (sub-unguis) sides of the claw in different species, semi-aquatic and terrestrial. These proteins provide mechanical resilience to the horny material of claws and beaks through the formation of numerous -S-S- bonds and also hydrophobicity that contributes to preserve wearing of the horny material. The thicker corneous layer of the unguis is made of elongated and partially merged corneocytes, and no or few cells desquamate superficially. Unknown junctional proteins may contribute to maintain corneocytes connected one to another. In contrast, corneocytes of the sub-unguis show an elongated but lenticular shape and form a looser corneous layer whose cells remain separate and desquamate superficially. This suggests that other specific corneous proteins are present in the unguis in comparison with the sub-unguis to determine this different compaction. The wearing process present in the sub-unguis creates a loss of tissue that may favor the slow by continuous apical migration of corneocytes from the unguis into the initial part of the sub-unguis. Beak corneocytes form a compact corneous layer like the unguis but numerous superficial cells desquamate on both outer (epidermal) and inner (oral) sides.

Immunolocalization of corneous proteins including a serine-tyrosine-rich beta-protein in the adhesive pads in the tokay gecko

Adhesive pads of geckos contain many thousands of nanoscale spatulae for the adhesion and movement along vertical or inverted surfaces. Setae are composed of interlaced corneous bundles made of small cysteine-glycine-rich corneous beta proteins (CBPs, formerly indicated as beta-keratins), embedded in a matrix material composed of cytoskeletal proteins and lipids. Negatively charged intermediate filament keratins (IFKs) and positively charged CBPs likely interact within setae, aside disulphide bonds, giving rise to a flexible and resistant corneous material. Using differernt antibodies against CBPs and IFKs an updated model of the composition of setae and spatulae is presented. Immunofluorescence and ultrastructural immunogold labeling reveal that one type of neutral serine-tyrosine-rich CBP is weakly localized in the setae while it is absent from the spatula. This uncharged protein is mainly present in the thin Oberhautchen layer sustaining the setae, although with a much lower intensity with respect to the cysteine-rich CBPs. These proteins in the spatula likely originate a positively charged or neutral contact surface with the substrate but the influence of lipids and cytoskeletal proteins present in setae on the mechanism of adhesion is not known. In the spatula, protein-lipid complexes may impart the pliability for the attachment and adapt to irregular surfaces. The presence of cysteine-glycine medium rich CBPs and softer IFKs in alpha-layers sustaining the setae forms a flexible base for compliance of the setae to substrate and improved adhesion.

Immunolocalization of corneous beta proteins of the Epidermal Differentiation Complex in the developing claw of the alligator

Knowledge on the sharpness, mechanical and hydration resistance of the corneous material of claws requires information on its constituent proteins. The present immunohistochemical study has localized some of the main corneous beta proteins (CBPs, formerly termed beta-keratins) indicated to be present in alligator claws only by genomic data. Using specific antibodies we show the immunolocalization of representative claws CBPs of the Epidermal Differentiation Complex (Beta A1 group) during late stages of claw development in alligator. Intense but asymmetric proliferation, revealed by 5BrdU-immunolabeling, determines the formation of a curved dorsal part (unguis) and a linear ventral part (sub-unguis). The large beta-cells generated in the unguis and their packing into a solid corneous layer occur before thinner beta-cells appear in the sub-unguis. In the latter, CBPs are also immune-detected but with less intensity compared to the unguis, and corneocytes remain separated and desquamate. It is suggested that at the tip of the developing claw beta-corneocytes move downward into the initial part of the sub-unguis. This circular movement contributes to sharpen the claw as these cells fully cornify and are desquamated from the sub-unguis. Corneocytes of the unguis contain 10-16 kDa proline-serine-rich proteins that also possess high percentages of glycine, cysteine, tyrosine, valine and leucine. Cysteines likely give rise to numerous SS bonds in the constituent hard horny material, tyrosine contribute to packing proteins into a dense horny material while glycine, valine and leucine increase the hydrophobic property of claws in these water-adapted predators.

Disulfide-bond-mediated cross-linking of corneous beta-proteins in lepidosaurian epidermis

Corneous beta-proteins (CBPs), formerly referred to as beta-keratins, are major protein components of the epidermis in lepidosaurian reptiles and are largely responsible for their material properties. These proteins have been suggested to form filaments of 3.4nm in thickness and to interact with themselves or with other proteins, including intermediate filament (IF) keratins. Here, we performed immunocytochemical labeling of CBPs in the epidermis of different lizards and snakes and investigated by immunoblotting analysis whether the reduction of disulfide bonds or protein oxidation affects the solubility and mobility of these CBPs. Immunogold labeling suggested that CBPs are partly co-localized with IF-keratins in differentiating and mature beta-cells. The chemical reduction of epidermal proteins from lizard and snake epidermis increased the abundance of CBP-immunoreactive bands in the size range of CBP monomers on Western blots. Conversely, in vitro oxidation of epidermal proteins reduced the abundance of putative CBP monomers. Some modifications in the IF-keratin range were also noted. These results strongly indicate that CBPs associate with IF-keratins and other proteins via disulfide bonds in the epidermis of lizards and snakes, which likely contributes to the resilience of the cornified beta- and alpha-layers of the lepidosaurian epidermis in live animals and after shedding.

Exceptional preservation and the fossil record of tetrapod integument

The fossil record of exceptionally preserved soft tissues in Konservat-Lagerstätten provides rare yet significant insight into past behaviours and ecologies. Such deposits are known to occur in bursts rather than evenly through time, but reasons for this pattern and implications for the origins of novel structures remain unclear. Previous assessments of these records focused on marine environments preserving chemically heterogeneous tissues from across animals. Here, we investigate the preservation of skin and keratinous integumentary structures in land-dwelling vertebrates (tetrapods) through time, and in distinct terrestrial and marine depositional environments. We also evaluate previously proposed biotic and abiotic controls on the distribution of 143 tetrapod Konservat-Lagerstätten from the Permian to the Pleistocene in a multivariate framework. Gap analyses taking into account sampling intensity and distribution indicate that feathers probably evolved close to their first appearance in the fossil record. By contrast, hair and archosaur filaments are weakly sampled (five times less common than feathers), and their origins may significantly pre-date earliest known occurrences in the fossil record. This work suggests that among-integument variation in preservation can bias the reconstructed first origins of integumentary novelties and has implications for predicting where, and in what depositional environments, to expect further discoveries of exquisitely preserved tetrapod integument.

Relating form to function in the hummingbird feeding apparatus

A complete understanding of the feeding structures is fundamental in order to study how animals survive. Some birds use long and protrusible tongues as the main tool to collect their central caloric source (e.g., woodpeckers and nectarivores). Hummingbirds are the oldest and most diverse clade of nectarivorous vertebrates, being a perfect subject to study tongue specializations. Their tongue functions to intraorally transport arthropods through their long bills and enables them to exploit the nectarivorous niche by collecting small amounts of liquid, therefore it is of vital importance to study its anatomy and structure at various scales. I focused on the portions of the hummingbird tongue that have been shown to be key for understanding their feeding mechanisms. I used histology, transmission and scanning electron microscopy, microCT, and ex-vivo experiments in order to advance the comprehension of the morphology and functioning of the hummingbird feeding apparatus. I found that hummingbird tongues are composed mainly of thin cornified epithelium, lack papillae, and completely fill the internal cast of the rostral oropharyngeal cavity. Understanding this puzzle-piece match between bill and tongue will be essential for the study of intraoral transport of nectar. Likewise, I found that the structural composition and tissue architecture of the tongue groove walls provide the rostral portion of the tongue with elastic properties that are central to the study of tongue-nectar interactions during the feeding process. Detailed studies on hummingbirds set the basis for comparisons with other nectar-feeding birds and contribute to comprehend the natural solutions to collecting liquids in the most efficient way possible.

Statistical investigation of extraction parameters of keratin from chicken feather using Design-Expert

Uncontrolled disposal of feathers from the poultry industry and slaughterhouses is environmentally undesirable. The feathers are composed of approximately 90% of keratin which is an important ingredient of cosmetics, shampoos and hair treatment creams. This study aimed to determine the optimum conditions for the extraction of keratin from chicken feathers. The extraction of keratin using various reducing agents was studied using statistical experimental design. In the extraction process, pH, temperature, ratio of reducing agents, mass of chicken feathers and incubation time were analyzed. The keratin in the total extracted protein was purified by size exclusion chromatography, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and further characterized using amino acids profile analysis. The surface morphology and chemical composition were studied by scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR) analysis. Sodium sulfide (Na₂S) yielded 84.5% of keratin as compared to sodium hydroxide (43.8), urea mixture (50.6), mixture of sodium dodecyl sulfate (SDS) and sodium bisulfite (18.3) and a mixture of Na₂S and sodium hydroxide (41.5%) under optimized conditions. The optimum yield of keratin was achieved at 80.9 °C in 9.5 h with 0.05 M sodium sulfide using response surface methodology (RSM). Among the five parameters screened, pH was found not to be significant because the p value was greater than 0.05.

Review: cornification, morphogenesis and evolution of feathers

Feathers are corneous microramifications of variable complexity derived from the morphogenesis of barb ridges. Histological and ultrastructural analyses on developing and regenerating feathers clarify the three-dimensional organization of cells in barb ridges. Feather cells derive from folds of the embryonic epithelium of feather germs from which barb/barbule cells and supportive cells organize in a branching structure. The following degeneration of supportive cells allows the separation of barbule cells which are made of corneous beta-proteins and of lower amounts of intermediate filament (IF)(alpha) keratins, histidine-rich proteins, and corneous proteins of the epidermal differentiation complex. The specific protein association gives rise to a corneous material with specific biomechanic properties in barbules, rami, rachis, or calamus. During the evolution of different feather types, a large expansion of the genome coding for corneous feather beta-proteins occurred and formed 3-4-nm-thick filaments through a different mechanism from that of 8-10 nm IF keratins. In the chick, over 130 genes mainly localized in chromosomes 27 and 25 encode feather corneous beta-proteins of 10-12 kDa containing 97-105 amino acids. About 35 genes localized in chromosome 25 code for scale proteins (14-16 kDa made of 122-146 amino acids), claws and beak proteins (14-17 kDa proteins of 134-164 amino acids). Feather morphogenesis is periodically re-activated to produce replacement feathers, and multiple feather types can result from the interactions of epidermal and dermal tissues. The review shows schematic models explaining the translation of the morphogenesis of barb ridges present in the follicle into the three-dimensional shape of the main types of branched or un-branched feathers such as plumulaceous, pennaceous, filoplumes, and bristles. The temporal pattern of formation of barb ridges in different feather types and the molecular control from the dermal papilla through signaling molecules are poorly known. The evolution and diversification of the process of morphogenesis of barb ridges and patterns of their formation within feathers follicle allowed the origin and diversification of numerous types of feathers, including the asymmetric planar feathers for flight.

Review: mapping epidermal beta-protein distribution in the lizard Anolis carolinensis shows a specific localization for the formation of scales, pads, and claws

The epidermis of lizards is made of multiple alpha- and beta-layers with different characteristics comprising alpha-keratins and corneous beta-proteins (formerly beta-keratins). Three main modifications of body scales are present in the lizard Anolis carolinensis: gular scales, adhesive pad lamellae, and claws. The 40 corneous beta-proteins present in this specie comprise glycine-rich and glycine-cysteine-rich subfamilies, while the 41 alpha-keratins comprise cysteine-poor and cysteine-rich subfamilies, the latter showing homology to hair keratins. Other genes for corneous proteins are present in the epidermal differentiation complex, the locus where corneous protein genes are located. The review summarizes the main sites of immunolocalization of beta-proteins in different scales and their derivatives producing a unique map of body distribution for these structural proteins. Small glycine-rich beta-proteins participate in the formation of the mechanically resistant beta-layer of most scales. Small glycine-cysteine beta-proteins have a more varied localization in different scales and are also present in the pliable alpha-layer. In claws, cysteine-rich alpha-keratins prevail over cysteine-poor alpha-keratins and mix to glycine-cysteine-rich beta-proteins. The larger beta-proteins with a molecular mass similar to that of alpha-keratins participate in the formation of the fibrous meshwork present in differentiating beta-cells and likely interact with alpha-keratins. The diverse localization of alpha-keratins, beta-proteins, and other proteins of the epidermal differentiation complex gives rise to variably pliable, elastic, or hard corneous layers in different body scales. The corneous layers formed in the softer or harder scales, in the elastic pad lamellae, or in the resistant claws possess peculiar properties depending on the ratio of specific corneous proteins.

Evidence of a molecular boundary lubricant at snakeskin surfaces

During slithering locomotion the ventral scales at a snake's belly are in direct mechanical interaction with the environment, while the dorsal scales provide optical camouflage and thermoregulation. Recent work has demonstrated that compared to dorsal scales, ventral scales provide improved lubrication and wear protection. While biomechanic adaption of snake motion is of growing interest in the fields of material science and robotics, the mechanism for how ventral scales influence the friction between the snake and substrate, at the molecular level, is unknown. In this study, we characterize the outermost surface of snake scales using sum frequency generation (SFG) spectra and near-edge X-ray absorption fine structure (NEXAFS) images collected from recently shed California kingsnake (Lampropeltis californiae) epidermis. SFG's nonlinear optical selection rules provide information about the outermost surface of materials; NEXAFS takes advantage of the shallow escape depth of the electrons to probe the molecular structure of surfaces. Our analysis of the data revealed the existence of a previously unknown lipid coating on both the ventral and dorsal scales. Additionally, the molecular structure of this lipid coating closely aligns to the biological function: lipids on ventral scales form a highly ordered layer which provides both lubrication and wear protection at the snake's ventral surface.

The anatomical placode in reptile scale morphogenesis indicates shared ancestry among skin appendages in amniotes

Most mammals, birds, and reptiles are readily recognized by their hairs, feathers, and scales, respectively. However, the lack of fossil intermediate forms between scales and hairs and substantial differences in their morphogenesis and protein composition have fueled the controversy pertaining to their potential common ancestry for decades. Central to this debate is the apparent lack of an "anatomical placode" (that is, a local epidermal thickening characteristic of feathers' and hairs' early morphogenesis) in reptile scale development. Hence, scenarios have been proposed for the independent development of the anatomical placode in birds and mammals and parallel co-option of similar signaling pathways for their morphogenesis. Using histological and molecular techniques on developmental series of crocodiles and snakes, as well as of unique wild-type and EDA (ectodysplasin A)-deficient scaleless mutant lizards, we show for the first time that reptiles, including crocodiles and squamates, develop all the characteristics of an anatomical placode: columnar cells with reduced proliferation rate, as well as canonical spatial expression of placode and underlying dermal molecular markers. These results reveal a new evolutionary scenario where hairs, feathers, and scales of extant species are homologous structures inherited, with modification, from their shared reptilian ancestor's skin appendages already characterized by an anatomical placode and associated signaling molecules.

Histology of the Skin of Three Limbless Squamates Dwelling in Mesic and Arid Environments

The skin of limbless squamates has an increased contact with the substrate compared with limbed counterparts. Comparatively, the contact with the substrate is intensified in fossorial species, where the whole circumference of the body interacts with the soil during underground locomotion. Although fossoriality in Squamata, specifically lizards and snakes, has been studied ecologically and morphologically (e.g., osteological changes), not enough detail is yet available regarding changes in organs critical for underground lifestyle such as the skin. Here we used histological and microscopical techniques (scanning electron microscopy and transmission electron microscopy) to uncover the structural detail of the epidermis and dermis in three limbless reptiles, the amphisbaenian Diplometopon zarudnyi, and two snakes, Indotyphlops braminus (Typhlopidae) and Cerastes cerastes (Viperidae). The skin of these taxa shows pronounced morphological diversity, which is likely associated to different environmental and functional demands upon these reptiles. Anat Rec, 299:979-989, 2016. © 2016 Wiley Periodicals, Inc.

Comparative Genomics Identifies Epidermal Proteins Associated with the Evolution of the Turtle Shell

The evolution of reptiles, birds, and mammals was associated with the origin of unique integumentary structures. Studies on lizards, chicken, and humans have suggested that the evolution of major structural proteins of the outermost, cornified layers of the epidermis was driven by the diversification of a gene cluster called Epidermal Differentiation Complex (EDC). Turtles have evolved unique defense mechanisms that depend on mechanically resilient modifications of the epidermis. To investigate whether the evolution of the integument in these reptiles was associated with specific adaptations of the sequences and expression patterns of EDC-related genes, we utilized newly available genome sequences to determine the epidermal differentiation gene complement of turtles. The EDC of the western painted turtle (Chrysemys picta bellii) comprises more than 100 genes, including at least 48 genes that encode proteins referred to as beta-keratins or corneous beta-proteins. Several EDC proteins have evolved cysteine/proline contents beyond 50% of total amino acid residues. Comparative genomics suggests that distinct subfamilies of EDC genes have been expanded and partly translocated to loci outside of the EDC in turtles. Gene expression analysis in the European pond turtle (Emys orbicularis) showed that EDC genes are differentially expressed in the skin of the various body sites and that a subset of beta-keratin genes within the EDC as well as those located outside of the EDC are expressed predominantly in the shell. Our findings give strong support to the hypothesis that the evolutionary innovation of the turtle shell involved specific molecular adaptations of epidermal differentiation.

Topographical mapping of α- and β-keratins on developing chicken skin integuments: Functional interaction and evolutionary perspectives

Avian integumentary organs include feathers, scales, claws, and beaks. They cover the body surface and play various functions to help adapt birds to diverse environments. These keratinized structures are mainly composed of corneous materials made of α-keratins, which exist in all vertebrates, and β-keratins, which only exist in birds and reptiles. Here, members of the keratin gene families were used to study how gene family evolution contributes to novelty and adaptation, focusing on tissue morphogenesis. Using chicken as a model, we applied RNA-seq and in situ hybridization to map α- and β-keratin genes in various skin appendages at embryonic developmental stages. The data demonstrate that temporal and spatial α- and β-keratin expression is involved in establishing the diversity of skin appendage phenotypes. Embryonic feathers express a higher proportion of β-keratin genes than other skin regions. In feather filament morphogenesis, β-keratins show intricate complexity in diverse substructures of feather branches. To explore functional interactions, we used a retrovirus transgenic system to ectopically express mutant α- or antisense β-keratin forms. α- and β-keratins show mutual dependence and mutations in either keratin type results in disrupted keratin networks and failure to form proper feather branches. Our data suggest that combinations of α- and β-keratin genes contribute to the morphological and structural diversity of different avian skin appendages, with feather-β-keratins conferring more possible composites in building intrafeather architecture complexity, setting up a platform of morphological evolution of functional forms in feathers.

Immunolocalization of sulfhydryl oxidase in reptilian epidermis indicates that the enzyme participates mainly to the hardening process of the beta-corneous layer

Reptilian skin is tough and scaled representing an evolutionary adaptation to the terrestrial environment. The presence of sulfhydryl oxidase during the process of hardening of the corneous layer in reptilian epidermis has been analyzed by immunocytochemistry and immunoblotting. Sulfhydryl oxidase-like immunoreactivity of proteins in the 50-65 kDa range of molecular weight is mainly observed in the transitional and pre-corneous layers of crocodilians, chelonian, and in the forming beta-layer of lepidosaurians. The ultrastructural localization of the enzyme by immunogold in lizard epidermis during renewal and resting stages shows that the labeling is mainly distributed in the cytoplasm and along the accumulating beta-packets of differentiating beta-cells while it appears very low to undetectable in differentiating alpha-cells of the lacunar, clear, mesos, and alpha-layers. The labeling however becomes absent or undetectable also in the fully mature beta-layer. The study shows that an oxidative enzyme is likely responsible of the cross-linking of the numerous cysteines present in the main proteins accumulated in corneocytes of reptilian epidermis, known as corneous beta-proteins (beta-keratins). This process of disulphide bond formation is probably largely responsible for the formation of hard beta-corneous layers in reptilian scales, a difference with alpha-corneous layers where substrate proteins of transglutaminase appear predominant.

Immunolocalization of loricrin in the maturing α-layer of normal and regenerating epidermis of the lizard Anolis carolinensis

Numerous corneous proteins are produced during the differentiation of the complex lizard epidermis, comprising hard β-layers and softer α-layers. In the present ultrastructural and immunocytochemical study, we have localized a homolog of the mammalian skin barrier protein loricrin in the skin of the green anole lizard (Anolis carolinensis). We used an antibody specific to the carboxyterminus of loricrin 1, a gene of the epidermal differentiation complex (EDC) of A. carolinensis. Lizard loricrin is present in the maturing α-layer (lacunar cells) of normal scale epidermis and in the accumulating corneocytes of the wound epidermis (lacunar cells) of the regenerating epidermis. The protein appears as a component of the α-layer but not of the β-layer. Lizard loricrin is diffused in the cytoplasm of pre-corneous α-keratinocytes but eventually concentrates in the packing corneous material of the maturing corneocytes of the α-layer (lacunar) in normal epidermis or in the wound epidermis of regenerating epidermis. The protein likely contributes to the composition and pliability of the corneous material but is not specifically accumulated on the corneous cell envelope (marginal layer) that is scarcely differentiated in these cells. The study contributes to the knowledge on the distribution of specific corneous proteins that give rise to the different material properties of α-layers versus β-layers in lizard epidermis.

Evolutionary origin and diversification of epidermal barrier proteins in amniotes

The evolution of amniotes has involved major molecular innovations in the epidermis. In particular, distinct structural proteins that undergo covalent cross-linking during cornification of keratinocytes facilitate the formation of mechanically resilient superficial cell layers and help to limit water loss to the environment. Special modes of cornification generate amniote-specific skin appendages such as claws, feathers, and hair. In mammals, many protein substrates of cornification are encoded by a cluster of genes, termed the epidermal differentiation complex (EDC). To provide a basis for hypotheses about the evolution of cornification proteins, we screened for homologs of the EDC in non-mammalian vertebrates. By comparative genomics, de novo gene prediction and gene expression analyses, we show that, in contrast to fish and amphibians, the chicken and the green anole lizard have EDC homologs comprising genes that are specifically expressed in the epidermis and in skin appendages. Our data suggest that an important component of the cornified protein envelope of mammalian keratinocytes, that is, loricrin, has originated in a common ancestor of modern amniotes, perhaps during the acquisition of a fully terrestrial lifestyle. Moreover, we provide evidence that the sauropsid-specific beta-keratins have evolved as a subclass of EDC genes. Based on the comprehensive characterization of the arrangement, exon-intron structures and conserved sequence elements of EDC genes, we propose new scenarios for the evolutionary origin of epidermal barrier proteins via fusion of neighboring S100A and peptidoglycan recognition protein genes, subsequent loss of exons and highly divergent sequence evolution.

Feather development genes and associated regulatory innovation predate the origin of Dinosauria

The evolution of avian feathers has recently been illuminated by fossils and the identification of genes involved in feather patterning and morphogenesis. However, molecular studies have focused mainly on protein-coding genes. Using comparative genomics and more than 600,000 conserved regulatory elements, we show that patterns of genome evolution in the vicinity of feather genes are consistent with a major role for regulatory innovation in the evolution of feathers. Rates of innovation at feather regulatory elements exhibit an extended period of innovation with peaks in the ancestors of amniotes and archosaurs. We estimate that 86% of such regulatory elements and 100% of the nonkeratin feather gene set were present prior to the origin of Dinosauria. On the branch leading to modern birds, we detect a strong signal of regulatory innovation near insulin-like growth factor binding protein (IGFBP) 2 and IGFBP5, which have roles in body size reduction, and may represent a genomic signature for the miniaturization of dinosaurian body size preceding the origin of flight.

Presence of a glycine-cysteine-rich beta-protein in the oberhautchen layer of snake epidermis marks the formation of the shedding layer

The complex differentiation of snake epidermis largely depends on the variation in the production of glycine-cysteine-rich versus glycine-rich beta-proteins (beta-keratins) that are deposited on a framework of alpha-keratins. The knowledge of the amino acid sequences of beta-proteins in the snake Pantherophis guttatus has allowed the localization of a glycine-cysteine-rich beta-protein in the spinulated oberhautchen layer of the differentiating shedding complex before molting takes place. This protein decreases in the beta-layer and disappears in mesos and alpha-layers. Conversely, while the mRNA for a glycine-rich beta-protein is highly expressed in differentiating beta-cells, the immunolocalization for this protein is low in these cells. This discrepancy between expression and localization suggests that the epitope in glycine-rich beta-proteins is cleaved or modified by posttranslational processes that take place during the differentiation and maturation of the beta-layer. The present study suggests that among the numerous beta-proteins coded in the snake genome to produce epidermal layers with different textures, the glycine-cysteine-rich beta-protein marks the shedding complex formed between alpha- and beta-layers that allows for molting while its disappearance between the beta- and alpha-layers (mesos region for scale growth) is connected to the formation of the alpha-layers.

Mammalian keratin associated proteins (KRTAPs) subgenomes: disentangling hair diversity and adaptation to terrestrial and aquatic environments

Background

Adaptation of mammals to terrestrial life was facilitated by the unique vertebrate trait of body hair, which occurs in a range of morphological patterns. Keratin associated proteins (KRTAPs), the major structural hair shaft proteins, are largely responsible for hair variation.

Results

We exhaustively characterized the KRTAP gene family in 22 mammalian genomes, confirming the existence of 30 KRTAP subfamilies evolving at different rates with varying degrees of diversification and homogenization. Within the two major classes of KRTAPs, the high cysteine (HS) subfamily experienced strong concerted evolution, high rates of gene conversion/recombination and high GC content. In contrast, high glycine-tyrosine (HGT) KRTAPs showed evidence of positive selection and low rates of gene conversion/recombination. Species with more hair and of higher complexity tended to have more KRATP genes (gene expansion). The sloth, with long and coarse hair, had the most KRTAP genes (175 with 141 being intact). By contrast, the “hairless” dolphin had 35 KRTAPs and the highest pseudogenization rate (74% relative to the 19% mammalian average). Unique hair-related phenotypes, such as scales (armadillo) and spines (hedgehog), were correlated with changes in KRTAPs. Gene expression variation probably also influences hair diversification patterns, for example human have an identical KRTAP repertoire as apes, but much less hair.

Conclusions

We hypothesize that differences in KRTAP gene repertoire and gene expression, together with distinct rates of gene conversion/recombination, pseudogenization and positive selection, are likely responsible for micro and macro-phenotypic hair diversification among mammals in response to adaptations to ecological pressures.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-779) contains supplementary material, which is available to authorized users.

Evolutionary origin and diversification of epidermal barrier proteins in amniotes

The evolution of amniotes has involved major molecular innovations in the epidermis. In particular, distinct structural proteins that undergo covalent cross-linking during cornification of keratinocytes facilitate the formation of mechanically resilient superficial cell layers and help to limit water loss to the environment. Special modes of cornification generate amniote-specific skin appendages such as claws, feathers, and hair. In mammals, many protein substrates of cornification are encoded by a cluster of genes, termed the epidermal differentiation complex (EDC). To provide a basis for hypotheses about the evolution of cornification proteins, we screened for homologs of the EDC in non-mammalian vertebrates. By comparative genomics, de novo gene prediction and gene expression analyses, we show that, in contrast to fish and amphibians, the chicken and the green anole lizard have EDC homologs comprising genes that are specifically expressed in the epidermis and in skin appendages. Our data suggest that an important component of the cornified protein envelope of mammalian keratinocytes, that is, loricrin, has originated in a common ancestor of modern amniotes, perhaps during the acquisition of a fully terrestrial lifestyle. Moreover, we provide evidence that the sauropsid-specific beta-keratins have evolved as a subclass of EDC genes. Based on the comprehensive characterization of the arrangement, exon-intron structures and conserved sequence elements of EDC genes, we propose new scenarios for the evolutionary origin of epidermal barrier proteins via fusion of neighboring S100A and peptidoglycan recognition protein genes, subsequent loss of exons and highly divergent sequence evolution.

Genomic organization, transcriptomic analysis, and functional characterization of avian α- and β-keratins in diverse feather forms

Feathers are hallmark avian integument appendages, although they were also present on theropods. They are composed of flexible corneous materials made of α- and β-keratins, but their genomic organization and their functional roles in feathers have not been well studied. First, we made an exhaustive search of α- and β-keratin genes in the new chicken genome assembly (Galgal4). Then, using transcriptomic analysis, we studied α- and β-keratin gene expression patterns in five types of feather epidermis. The expression patterns of β-keratin genes were different in different feather types, whereas those of α-keratin genes were less variable. In addition, we obtained extensive α- and β-keratin mRNA in situ hybridization data, showing that α-keratins and β-keratins are preferentially expressed in different parts of the feather components. Together, our data suggest that feather morphological and structural diversity can largely be attributed to differential combinations of α- and β-keratin genes in different intrafeather regions and/or feather types from different body parts. The expression profiles provide new insights into the evolutionary origin and diversification of feathers. Finally, functional analysis using mutant chicken keratin forms based on those found in the human α-keratin mutation database led to abnormal phenotypes. This demonstrates that the chicken can be a convenient model for studying the molecular biology of human keratin-based diseases.

Immunolocalization of alpha-keratins and associated beta-proteins in lizard epidermis shows that acidic keratins mix with basic keratin-associated beta-proteins

The differentiation of the corneous layers of lizard epidermis has been analyzed by ultrastructural immunocytochemistry using specific antibodies against alpha-keratins and keratin associated beta-proteins (KAbetaPs, formerly indicated as beta-keratins). Both beta-cells and alpha-cells of the corneous layer derive from the same germinal layer. An acidic type I alpha-keratin is present in basal and suprabasal layers, early differentiating clear, oberhautchen, and beta-cells. Type I keratin apparently disappears in differentiated beta- and alpha-layers of the mature corneous layers. Conversely, a basic type II alpha-keratin rich in glycine is absent or very scarce in basal and suprabasal layers and this keratin likely does not pair with type I keratin to form intermediate filaments but is weakly detected in the pre-corneous and corneous alpha-layer. Single and double labeling experiments show that in differentiating beta-cells, basic KAbetaPs are added and replace type-I keratin to form the hard beta-layer. Epidermal alpha-keratins contain scarce cysteine (0.2-1.4 %) that instead represents 4-19 % of amino acids present in KAbetaPs. Possible chemical bonds formed between alpha-keratins and KAbetaPs may derive from electrostatic interactions in addition to cross-linking through disulphide bonds. Both the high content in glycine of keratins and KAbetaPs may also contribute to increase the hydrophobicy of the beta- and alpha-layers and the resistance of the corneous layer. The increase of gly-rich KAbetaPs amount and the bonds to the framework of alpha-keratins give rise to the inflexible beta-layer while the cys-rich KAbetaPs produce a pliable alpha-layer.

β-Keratin composition of the specialized spectacle scale of snakes and geckos

The eyes of snakes and most geckos are shielded beneath a layer of transparent skin (the “spectacle”), of which the outermost layer consists of an optically transparent scale. The characteristics of the spectacle scale that contribute to its transparency are not well understood but may conceivably be related to its biochemical composition. The composition of the spectacle scales of numerous snakes and two geckos was analyzed with particular focus on β-keratins, the hard proteins that form the outermost layer of squamate scales, to determine whether spectacle scales differ biochemically from other scales and whether they differ between species. Results indicate that the spectacle scale of snakes differs in the types of β-keratins it contains and that diversity in spectacle β-keratins occurs between species and bears a relationship with taxonomy, suggesting that optical transparency is not restricted to a few isoforms. Other findings include a greater β-keratin to α-keratin ratio in the embryonic spectacle of pythons compared with those from after hatch and a complete absence of β-keratin in gecko spectacle scales, an unusual characteristic for squamate integument. Expression of β-keratins in the spectacle has clearly evolved for needs specific to this specialized region of the integument.

Rapid evolution of Beta-keratin genes contribute to phenotypic differences that distinguish turtles and birds from other reptiles

Sequencing of vertebrate genomes permits changes in distinct protein families, including gene gains and losses, to be ascribed to lineage-specific phenotypes. A prominent example of this is the large-scale duplication of beta-keratin genes in the ancestors of birds, which was crucial to the subsequent evolution of their beaks, claws, and feathers. Evidence suggests that the shell of Pseudomys nelsoni contains at least 16 beta-keratins proteins, but it is unknown whether this is a complete set and whether their corresponding genes are orthologous to avian beak, claw, or feather beta-keratin genes. To address these issues and to better understand the evolution of the turtle shell at a molecular level, we surveyed the diversity of beta-keratin genes from the genome assemblies of three turtles, Chrysemys picta, Pelodiscus sinensis, and Chelonia mydas, which together represent over 160 Myr of chelonian evolution. For these three turtles, we found 200 beta-keratins, which indicate that, as for birds, a large expansion of beta-keratin genes in turtles occurred concomitantly with the evolution of a unique phenotype, namely, their plastron and carapace. Phylogenetic reconstruction of beta-keratin gene evolution suggests that separate waves of gene duplication within a single genomic location gave rise to scales, claws, and feathers in birds, and independently the scutes of the shell in turtles.