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Huang L, Ho C, Ye X, Gao Y, Guo W, Chen J, Sun J, Wen D, Liu Y, Liu Y, Zhang Y, Li Q. Mechanisms and translational applications of regeneration in limbs: From renewable animals to humans. Ann Anat 2024; 255:152288. [PMID: 38823491 DOI: 10.1016/j.aanat.2024.152288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 04/08/2024] [Accepted: 05/27/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND The regenerative capacity of organisms declines throughout evolution, and mammals lack the ability to regenerate limbs after injury. Past approaches to achieving successful restoration through pharmacological intervention, tissue engineering, and cell therapies have faced significant challenges. OBJECTIVES This review aims to provide an overview of the current understanding of the mechanisms behind animal limb regeneration and the successful translation of these mechanisms for human tissue regeneration. RESULTS Particular attention was paid to the Mexican axolotl (Ambystoma mexicanum), the only adult tetrapod capable of limb regeneration. We will explore fundamental questions surrounding limb regeneration, such as how amputation initiates regeneration, how the limb knows when to stop and which parts to regenerate, and how these findings can apply to mammalian systems. CONCLUSIONS Given the urgent need for regenerative therapies to treat conditions like diabetic foot ulcers and trauma survivors, this review provides valuable insights and ideas for researchers, clinicians, and biomedical engineers seeking to facilitate the regeneration process or elicit full regeneration from partial regeneration events.
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Affiliation(s)
- Lu Huang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China; Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA.
| | - Chiakang Ho
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Xinran Ye
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Ya Gao
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Weiming Guo
- Shanghai Key Laboratory of Stomatology, 639 Zhizaoju Road, Shanghai 200011, China; National Clinical Research Center for Oral Diseases, Shanghai 200011, China; National Center for Stomatology, Shanghai 200011, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai 200011, China; Department of Orthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Julie Chen
- Department of Ophthalmology, Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Jiaming Sun
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Dongsheng Wen
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Yangdan Liu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Yuxin Liu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Yifan Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China.
| | - Qingfeng Li
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China.
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Bose A, Schuster K, Kodali C, Sonam S, Smith-Bolton R. The pioneer transcription factor Zelda facilitates the exit from regeneration and restoration of patterning in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596672. [PMID: 38854062 PMCID: PMC11160785 DOI: 10.1101/2024.05.30.596672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
For a damaged tissue to regenerate, the injured site must repair the wound, proliferate, and restore the correct patterning and cell types. We found that Zelda, a pioneer transcription factor largely known for its role in embryonic zygotic genome activation, is dispensable for normal wing development but crucial for wing disc patterning during regeneration. Impairing Zelda function during disc regeneration resulted in adult wings with a plethora of cell fate errors, affecting the veins, margins, and posterior compartment identity. Using CUT&RUN, we identified and validated targets of Zelda including the cell fate genes cut, Delta and achaete, which failed to return to their normal expression patterns upon loss of Zelda. In addition, Zelda controls expression of factors previously established to preserve cell fate during regeneration like taranis and osa, which stabilizes engrailed expression during regeneration, thereby preserving posterior identity. Finally, Zelda ensures proper expression of the integrins encoded by multiple edematous wings and myospheroid during regeneration to prevent blisters in the resuting adult wing. Thus, Zelda is crucial for maintaining cell fate and structural architecture of the regenerating tissue.
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Affiliation(s)
- Anish Bose
- Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Keaton Schuster
- Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chandril Kodali
- Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Surabhi Sonam
- Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rachel Smith-Bolton
- Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Witzmann F, Fröbisch N. Morphology and ontogeny of carpus and tarsus in stereospondylomorph temnospondyls. PeerJ 2023; 11:e16182. [PMID: 37904842 PMCID: PMC10613440 DOI: 10.7717/peerj.16182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/05/2023] [Indexed: 11/01/2023] Open
Abstract
Skeletal development is well known in temnospondyls, the most diverse group of Paleozoic and Mesozoic amphibians. However, the elements of carpus and tarsus (i.e., the mesopodium) were always the last bones to ossify relative to the other limb bones and with regard to the rest of the skeleton, and are preserved only in rare cases. Thus, in contrast to the other parts of the limb skeleton, little is known about the ontogeny and sequence of ossification of the temnospondyl carpus and tarsus. We intended to close this gap by studying the ontogenies of a number of Permo/Carboniferous stereospondylomorphs, the only temnospondyls with preserved growth series in which the successive ossification of carpals and tarsals can be traced. Studying the degree of mesopodial ossification within the same species show that it is not necessarily correlated with body size. This indicates that individual age rather than size determined the degree of mesopodial ossification in stereospondylomorphs and that the largest individuals are not necessarily the oldest ones. In the stereospondylomorph tarsus, the distal tarsals show preaxial development in accordance with most early tetrapods and salamanders. However, the more proximal mesopodials exhibit postaxial dominance, i.e., the preaxial column (tibiale, centrale 1) consistently started to ossify after the central column (centralia 2-4, intermedium) and the postaxial column (fibulare). Likewise, we observed preaxial development of the distal carpals in the stereospondylomorph carpus, as in most early tetrapods for which a statement can be made. However, in contrast to the tarsus, the more proximal carpals were formed by preaxial development, i.e., the preaxial column (radiale, centrale 1) ossified after the central column (centralia 2-4, intermedium) and before the postaxial column (ulnare). This pattern is unique among known early tetrapods and occurs only in certain extant salamanders. Furthermore, ossification proceeded from distal to proximal in the central column of the stereospondylomorph carpus, whereas the ossification advanced from proximal to distal in the central column of the tarsus. Despite these differences, a general ossification pattern that started from proximolateral (intermedium or centrale 4) to mediodistal (distal tarsal and carpal 1) roughly in a diagonal line is common to all stereospondylomorph mesopodials investigated. This pattern might basically reflect the alignment of stress within the mesopodium during locomotion. Our observations might point to a greater variability in the development of the mesopodium in stereospondylomorphs and probably other early tetrapods than in most extant tetrapods, possibly mirroring a similar variation as seen in the early phases of skeletogenesis in salamander carpus and tarsus.
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Affiliation(s)
- Florian Witzmann
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Nadia Fröbisch
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- Department of Biology, Humboldt Universität Berlin, Berlin, Germany
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Tajer B, Savage AM, Whited JL. The salamander blastema within the broader context of metazoan regeneration. Front Cell Dev Biol 2023; 11:1206157. [PMID: 37635872 PMCID: PMC10450636 DOI: 10.3389/fcell.2023.1206157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023] Open
Abstract
Throughout the animal kingdom regenerative ability varies greatly from species to species, and even tissue to tissue within the same organism. The sheer diversity of structures and mechanisms renders a thorough comparison of molecular processes truly daunting. Are "blastemas" found in organisms as distantly related as planarians and axolotls derived from the same ancestral process, or did they arise convergently and independently? Is a mouse digit tip blastema orthologous to a salamander limb blastema? In other fields, the thorough characterization of a reference model has greatly facilitated these comparisons. For example, the amphibian Spemann-Mangold organizer has served as an amazingly useful comparative template within the field of developmental biology, allowing researchers to draw analogies between distantly related species, and developmental processes which are superficially quite different. The salamander limb blastema may serve as the best starting point for a comparative analysis of regeneration, as it has been characterized by over 200 years of research and is supported by a growing arsenal of molecular tools. The anatomical and evolutionary closeness of the salamander and human limb also add value from a translational and therapeutic standpoint. Tracing the evolutionary origins of the salamander blastema, and its relatedness to other regenerative processes throughout the animal kingdom, will both enhance our basic biological understanding of regeneration and inform our selection of regenerative model systems.
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Affiliation(s)
| | | | - Jessica L. Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
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Wu L, Lambert JD. Clade-specific genes and the evolutionary origin of novelty; new tools in the toolkit. Semin Cell Dev Biol 2023; 145:52-59. [PMID: 35659164 DOI: 10.1016/j.semcdb.2022.05.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/27/2022] [Accepted: 05/25/2022] [Indexed: 10/18/2022]
Abstract
Clade-specific (a.k.a. lineage-specific) genes are very common and found at all taxonomic levels and in all clades examined. They can arise by duplication of previously existing genes, which can involve partial truncations or combinations with other protein domains or regulatory sequences. They can also evolve de novo from non-coding sequences, leading to potentially truly novel protein domains. Finally, since clade-specific genes are generally defined by lack of sequence homology with other proteins, they can also arise by sequence evolution that is rapid enough that previous sequence homology can no longer be detected. In such cases, where the rapid evolution is followed by constraint, we consider them to be ontologically non-novel but likely novel at a functional level. In general, clade-specific genes have received less attention from biologists but there are increasing numbers of fascinating examples of their roles in important traits. Here we review some selected recent examples, and argue that attention to clade-specific genes is an important corrective to the focus on the conserved developmental regulatory toolkit that has been the habit of evo-devo as a field. Finally, we discuss questions that arise about the evolution of clade-specific genes, and how these might be addressed by future studies. We highlight the hypothesis that clade-specific genes are more likely to be involved in synapomorphies that arose in the stem group where they appeared, compared to other genes.
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Affiliation(s)
- Longjun Wu
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - J David Lambert
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.
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6
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Zhao Y, Huang S, Zhang Y, Tan C, Feng H. Role of Brassica orphan gene BrLFM on leafy head formation in Chinese cabbage (Brassica rapa). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:170. [PMID: 37420138 DOI: 10.1007/s00122-023-04411-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/22/2023] [Indexed: 07/09/2023]
Abstract
Brassica orphan gene BrFLM, identified by two allelic mutants, was involved in leafy head formation in Chinese cabbage. Leafy head formation is a unique agronomic trait of Chinese cabbage that determines its yield and quality. In our previous study, an EMS mutagenesis Chinese cabbage mutant library was constructed using the heading Chinese cabbage double haploid (DH) line FT as the wild-type. Here, we screened two extremely similar leafy head deficiency mutants lfm-1 and lfm-2 with geotropic growth leaves from the library to investigate the gene(s) related to leafy head formation. Reciprocal crossing results showed that these two mutants were allelic. We utilized lfm-1 to identify the mutant gene(s). Genetic analysis showed that the mutated trait was controlled by a single nuclear gene Brlfm. Mutmap analysis showed that Brlfm was located on chromosome A05, and BraA05g012440.3C or BraA05g021450.3C were the candidate gene. Kompetitive allele-specific PCR analysis eliminated BraA05g012440.3C from the candidates. Sanger sequencing identified an SNP from G to A at the 271st nucleotide on BraA05g021450.3C. The sequencing of lfm-2 detected another non-synonymous SNP (G to A) located at the 266st nucleotide on BraA05g021450.3C, which verified its function on leafy head formation. We blasted BraA05g021450.3C on database and found that it belongs to a Brassica orphan gene encoding an unknown 13.74 kDa protein, named BrLFM. Subcellular localization showed that BrLFM was located in the nucleus. These findings reveal that BrLFM is involved in leafy head formation in Chinese cabbage.
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Affiliation(s)
- Yonghui Zhao
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Shengnan Huang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Yun Zhang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Chong Tan
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China.
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7
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Fakhar AZ, Liu J, Pajerowska-Mukhtar KM, Mukhtar MS. The Lost and Found: Unraveling the Functions of Orphan Genes. J Dev Biol 2023; 11:27. [PMID: 37367481 PMCID: PMC10299390 DOI: 10.3390/jdb11020027] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/19/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023] Open
Abstract
Orphan Genes (OGs) are a mysterious class of genes that have recently gained significant attention. Despite lacking a clear evolutionary history, they are found in nearly all living organisms, from bacteria to humans, and they play important roles in diverse biological processes. The discovery of OGs was first made through comparative genomics followed by the identification of unique genes across different species. OGs tend to be more prevalent in species with larger genomes, such as plants and animals, and their evolutionary origins remain unclear but potentially arise from gene duplication, horizontal gene transfer (HGT), or de novo origination. Although their precise function is not well understood, OGs have been implicated in crucial biological processes such as development, metabolism, and stress responses. To better understand their significance, researchers are using a variety of approaches, including transcriptomics, functional genomics, and molecular biology. This review offers a comprehensive overview of the current knowledge of OGs in all domains of life, highlighting the possible role of dark transcriptomics in their evolution. More research is needed to fully comprehend the role of OGs in biology and their impact on various biological processes.
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Affiliation(s)
| | | | | | - M. Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL 35294, USA
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Takeda T, Shirai K, Kim YW, Higuchi-Takeuchi M, Shimizu M, Kondo T, Ushijima T, Matsushita T, Shinozaki K, Hanada K. A de novo gene originating from the mitochondria controls floral transition in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2023; 111:189-203. [PMID: 36306001 DOI: 10.1007/s11103-022-01320-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
De novo genes created in the plant mitochondrial genome have frequently been transferred into the nuclear genome via intergenomic gene transfer events. Therefore, plant mitochondria might be a source of de novo genes in the nuclear genome. However, the functions of de novo genes originating from mitochondria and the evolutionary fate remain unclear. Here, we revealed that an Arabidopsis thaliana specific small coding gene derived from the mitochondrial genome regulates floral transition. We previously identified 49 candidate de novo genes that induce abnormal morphological changes on overexpression. We focused on a candidate gene derived from the mitochondrial genome (sORF2146) that encodes 66 amino acids. Comparative genomic analyses indicated that the mitochondrial sORF2146 emerged in the Brassica lineage as a de novo gene. The nuclear sORF2146 emerged following an intergenomic gene transfer event in the A. thaliana after the divergence between Arabidopsis and Capsella. Although the nuclear and mitochondrial sORF2146 sequences are the same in A. thaliana, only the nuclear sORF2146 is transcribed. The nuclear sORF2146 product is localized in mitochondria, which may be associated with the pseudogenization of the mitochondrial sORF2146. To functionally characterize the nuclear sORF2146, we performed a transcriptomic analysis of transgenic plants overexpressing the nuclear sORF2146. Flowering transition-related genes were highly regulated in the transgenic plants. Subsequent phenotypic analyses demonstrated that the overexpression and knockdown of sORF2146 in transgenic plants resulted in delayed and early flowering, respectively. These findings suggest that a lineage-specific de novo gene derived from mitochondria has an important regulatory effect on floral transition.
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Affiliation(s)
- Tomoyuki Takeda
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-Shi, Fukuoka, 820-8502, Japan
| | - Kazumasa Shirai
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-Shi, Fukuoka, 820-8502, Japan
| | - You-Wang Kim
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-Shi, Fukuoka, 820-8502, Japan
| | | | - Minami Shimizu
- RIKEN Center for Sustainable Resource Science, Yokohama-Shi, Kanagawa, 230-0045, Japan
| | - Takayuki Kondo
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-Shi, Fukuoka, 820-8502, Japan
| | - Tomokazu Ushijima
- Department of Agricultural Science and Technology, Faculty of Agriculture, Setsunan University, Osaka, Japan
| | - Tomonao Matsushita
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science, Yokohama-Shi, Kanagawa, 230-0045, Japan
| | - Kousuke Hanada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-Shi, Fukuoka, 820-8502, Japan.
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Carbonell-M B, Zapata Cardona J, Delgado JP. Post-amputation reactive oxygen species production is necessary for axolotls limb regeneration. Front Cell Dev Biol 2022; 10:921520. [PMID: 36092695 PMCID: PMC9458980 DOI: 10.3389/fcell.2022.921520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/28/2022] [Indexed: 11/26/2022] Open
Abstract
Introduction: Reactive oxygen species (ROS) represent molecules of great interest in the field of regenerative biology since several animal models require their production to promote and favor tissue, organ, and appendage regeneration. Recently, it has been shown that the production of ROS such as hydrogen peroxide (H2O2) is required for tail regeneration in Ambystoma mexicanum. However, to date, it is unknown whether ROS production is necessary for limb regeneration in this animal model. Methods: forelimbs of juvenile animals were amputated proximally and the dynamics of ROS production was determined using 2′7- dichlorofluorescein diacetate (DCFDA) during the regeneration process. Inhibition of ROS production was performed using the NADPH oxidase inhibitor apocynin. Subsequently, a rescue assay was performed using exogenous hydrogen peroxide (H2O2). The effect of these treatments on the size and skeletal structures of the regenerated limb was evaluated by staining with alcian blue and alizarin red, as well as the effect on blastema formation, cell proliferation, immune cell recruitment, and expression of genes related to proximal-distal identity. Results: our results show that inhibition of post-amputation limb ROS production in the A. mexicanum salamander model results in the regeneration of a miniature limb with a significant reduction in the size of skeletal elements such as the ulna, radius, and overall autopod. Additionally, other effects such as decrease in the number of carpals, defective joint morphology, and failure of integrity between the regenerated structure and the remaining tissue were identified. In addition, this treatment affected blastema formation and induced a reduction in the levels of cell proliferation in this structure, as well as a reduction in the number of CD45+ and CD11b + immune system cells. On the other hand, blocking ROS production affected the expression of proximo-distal identity genes such as Aldha1a1, Rarβ, Prod1, Meis1, Hoxa13, and other genes such as Agr2 and Yap1 in early/mid blastema. Of great interest, the failure in blastema formation, skeletal alterations, as well as the expression of the genes evaluated were rescued by the application of exogenous H2O2, suggesting that ROS/H2O2 production is necessary from the early stages for proper regeneration and patterning of the limb.
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Affiliation(s)
- Belfran Carbonell-M
- Grupo de Genética, Regeneración y Cáncer, Universidad de Antioquia, Sede de Investigación Universitaria, Medellín, Colombia
- Departamento de Estudios Básicos Integrados, Facultad de Odontología, Universidad de Antioquia, Medellín, Colombia
- *Correspondence: Belfran Carbonell-M, ; Jean Paul Delgado,
| | - Juliana Zapata Cardona
- Grupo de Investigación en Patobiología Quiron, Escuela de MedicinaVeterinaria, Universidad de Antioquia, Medellín, Colombia
| | - Jean Paul Delgado
- Grupo de Genética, Regeneración y Cáncer, Universidad de Antioquia, Sede de Investigación Universitaria, Medellín, Colombia
- *Correspondence: Belfran Carbonell-M, ; Jean Paul Delgado,
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Yu ZY, Shiga S, Casco-Robles MM, Takeshima K, Maruo F, Chiba C. The latent dedifferentiation capacity of newt limb muscles is unleashed by a combination of metamorphosis and body growth. Sci Rep 2022; 12:11653. [PMID: 35915110 PMCID: PMC9343386 DOI: 10.1038/s41598-022-15879-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 06/30/2022] [Indexed: 11/25/2022] Open
Abstract
Newts can regenerate their limbs throughout their life-span. Focusing on muscle, certain species of newts such as Cynops pyrrhogaster dedifferentiate muscle fibers in the limb stump and mobilize them for muscle creation in the regenerating limb, as they grow beyond metamorphosis. However, which developmental process is essential for muscle dedifferentiation, metamorphosis or body growth, is unknown. To address this issue, we tracked muscle fibers during limb regeneration under conditions in which metamorphosis and body growth were experimentally shifted along the axis of development. Our results indicate that a combination of metamorphosis and body growth is necessary for muscle dedifferentiation. On the other hand, ex vivo tracking of larval muscle fibers revealed that newt muscle fibers have the ability to dedifferentiate independently of metamorphosis and body growth. These results suggest that newt muscle fibers have an intrinsic ability to dedifferentiate, but that metamorphosis and body growth are necessary for them to exhibit this hidden ability. Presumably, changes in the extracellular environment (niche) during developmental processes allow muscle fibers to contribute to limb regeneration through dedifferentiation. This study can stimulate research on niches as well as gene regulation for dedifferentiation, contributing to a further understanding of regeneration and future medical applications.
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Affiliation(s)
- Zhan Yang Yu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8572, Japan
| | - Shota Shiga
- Graduate School of Science and Technology, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8572, Japan
| | - Martin Miguel Casco-Robles
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8572, Japan
| | - Kazuhito Takeshima
- Radioisotope Research Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Fumiaki Maruo
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8572, Japan
| | - Chikafumi Chiba
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8572, Japan.
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Jiang M, Li X, Dong X, Zu Y, Zhan Z, Piao Z, Lang H. Research Advances and Prospects of Orphan Genes in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:947129. [PMID: 35874010 PMCID: PMC9305701 DOI: 10.3389/fpls.2022.947129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Orphan genes (OGs) are defined as genes having no sequence similarity with genes present in other lineages. OGs have been regarded to play a key role in the development of lineage-specific adaptations and can also serve as a constant source of evolutionary novelty. These genes have often been found related to various stress responses, species-specific traits, special expression regulation, and also participate in primary substance metabolism. The advancement in sequencing tools and genome analysis methods has made the identification and characterization of OGs comparatively easier. In the study of OG functions in plants, significant progress has been made. We review recent advances in the fast evolving characteristics, expression modulation, and functional analysis of OGs with a focus on their role in plant biology. We also emphasize current challenges, adoptable strategies and discuss possible future directions of functional study of OGs.
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Affiliation(s)
- Mingliang Jiang
- School of Agriculture, Jilin Agricultural Science and Technology College, Jilin, China
| | - Xiaonan Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Xiangshu Dong
- School of Agriculture, Yunnan University, Kunming, China
| | - Ye Zu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zongxiang Zhan
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zhongyun Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hong Lang
- School of Agriculture, Jilin Agricultural Science and Technology College, Jilin, China
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12
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Otsuki L, Tanaka EM. Positional Memory in Vertebrate Regeneration: A Century's Insights from the Salamander Limb. Cold Spring Harb Perspect Biol 2022; 14:a040899. [PMID: 34607829 PMCID: PMC9248832 DOI: 10.1101/cshperspect.a040899] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Salamanders, such as axolotls and newts, can regenerate complex tissues including entire limbs. But what mechanisms ensure that an amputated limb regenerates a limb, and not a tail or unpatterned tissue? An important concept in regeneration is positional memory-the notion that adult cells "remember" spatial identities assigned to them during embryogenesis (e.g., "head" or "hand") and use this information to restore the correct body parts after injury. Although positional memory is well documented at a phenomenological level, the underlying cellular and molecular bases are just beginning to be decoded. Herein, we review how major principles in positional memory were established in the salamander limb model, enabling the discovery of positional memory-encoding molecules, and advancing insights into their pattern-forming logic during regeneration. We explore findings in other amphibians, fish, reptiles, and mammals and speculate on conserved aspects of positional memory. We consider the possibility that manipulating positional memory in human cells could represent one route toward improved tissue repair or engineering of patterned tissues for therapeutic purposes.
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Affiliation(s)
- Leo Otsuki
- Research Institute of Molecular Pathology, 1030 Vienna, Austria
| | - Elly M Tanaka
- Research Institute of Molecular Pathology, 1030 Vienna, Austria
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13
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Royle SR, Young JJ. Developmental biology: A 5'Hoxd-Gli3 balance in tetrapod axial polarity. Curr Biol 2021; 31:R1487-R1490. [PMID: 34813756 DOI: 10.1016/j.cub.2021.10.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Almost all living tetrapods exhibit postaxial dominance in digit formation, apart from urodele amphibians, which show preaxial dominance. Recent work shines light on the genetic differences between the two modes of limb development, suggesting that differences in 5'Hoxd expression, mediated by Gli3, may explain the switch in axial polarity.
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Affiliation(s)
- Samantha R Royle
- Department of Genetics, Balvatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - John J Young
- Biology Department, Simmons University, Boston, MA 02115, USA.
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14
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Reviewing the Effects of Skin Manipulations on Adult Newt Limb Regeneration: Implications for the Subcutaneous Origin of Axial Pattern Formation. Biomedicines 2021; 9:biomedicines9101426. [PMID: 34680543 PMCID: PMC8533417 DOI: 10.3390/biomedicines9101426] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022] Open
Abstract
Newts are unique salamanders that can regenerate their limbs as postmetamorphic adults. In order to regenerate human limbs as newts do, it is necessary to determine whether the cells homologous to those contributing to the limb regeneration of adult newts also exist in humans. Previous skin manipulation studies in larval amphibians have suggested that stump skin plays a pivotal role in the axial patterning of regenerating limbs. However, in adult newts such studies are limited, though they are informative. Therefore, in this article we have conducted skin manipulation experiments such as rotating the skin 180° around the proximodistal axis of the limb and replacing half of the skin with that of another location on the limb or body. We found that, contrary to our expectations, adult newts robustly regenerated limbs with a normal axial pattern regardless of skin manipulation, and that the appearance of abnormalities was stochastic. Our results suggest that the tissue under the skin, rather than the skin itself, in the intact limb is of primary importance in ensuring the normal axial pattern formation in adult newt limb regeneration. We propose that the important tissues are located in small areas underlying the ventral anterior and ventral posterior skin.
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15
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Bonett RM, Ledbetter NM, Hess AJ, Herrboldt MA, Denoël M. Repeated ecological and life cycle transitions make salamanders an ideal model for evolution and development. Dev Dyn 2021; 251:957-972. [PMID: 33991029 DOI: 10.1002/dvdy.373] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/16/2021] [Accepted: 05/10/2021] [Indexed: 11/11/2022] Open
Abstract
Observations on the ontogeny and diversity of salamanders provided some of the earliest evidence that shifts in developmental trajectories have made a substantial contribution to the evolution of animal forms. Since the dawn of evo-devo there have been major advances in understanding developmental mechanisms, phylogenetic relationships, evolutionary models, and an appreciation for the impact of ecology on patterns of development (eco-evo-devo). Molecular phylogenetic analyses have converged on strong support for the majority of branches in the Salamander Tree of Life, which includes 764 described species. Ancestral reconstructions reveal repeated transitions between life cycle modes and ecologies. The salamander fossil record is scant, but key Mesozoic species support the antiquity of life cycle transitions in some families. Colonization of diverse habitats has promoted phenotypic diversification and sometimes convergence when similar environments have been independently invaded. However, unrelated lineages may follow different developmental pathways to arrive at convergent phenotypes. This article summarizes ecological and endocrine-based causes of life cycle transitions in salamanders, as well as consequences to body size, genome size, and skeletal structure. Salamanders offer a rich source of comparisons for understanding how the evolution of developmental patterns has led to phenotypic diversification following shifts to new adaptive zones.
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Affiliation(s)
- Ronald M Bonett
- Department of Biological Science, The University of Tulsa, Tulsa, Oklahoma, USA
| | | | - Alexander J Hess
- Department of Biological Science, The University of Tulsa, Tulsa, Oklahoma, USA
| | - Madison A Herrboldt
- Department of Biological Science, The University of Tulsa, Tulsa, Oklahoma, USA
| | - Mathieu Denoël
- Laboratory of Ecology and Conservation of Amphibians (LECA), Freshwater and Oceanic science Unit of reSearch (FOCUS), University of Liège, Liège, Belgium
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16
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Salnikov L, Baramiya MG. From Autonomy to Integration, From Integration to Dynamically Balanced Integrated Co-existence: Non-aging as the Third Stage of Development. FRONTIERS IN AGING 2021; 2:655315. [PMID: 35822034 PMCID: PMC9261420 DOI: 10.3389/fragi.2021.655315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/02/2021] [Indexed: 01/03/2023]
Abstract
Reversible senescence at the cellular level emerged together with tissue specialization in Metazoans. However, this reversibility (ability to permanently rejuvenate) through recapitulation of early stages of development, was originally a part of ontogenesis, since the pressure of integrativeness was not dominant. The complication of specialization in phylogenesis narrowed this “freedom of maneuver”, gradually “truncating” remorphogenesis to local epimorphosis and further up to the complete disappearance of remorphogenesis from the ontogenesis repertoire. This evolutionary trend transformed cellular senescence into organismal aging and any recapitulation of autonomy into carcinogenesis. The crown of specialization, Homo sapiens, completed this post-unicellular stage of development, while in the genome all the potential for the next stage of development, which can be called the stage of balanced coexistence of autonomous and integrative dominants within a single whole. Here, completing the substantiation of the new section of developmental biology, we propose to call it Developmental Biogerontology.
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Affiliation(s)
- Lev Salnikov
- SibEnzyme US LLC, West Roxbury, MA, United States
- *Correspondence: Lev Salnikov,
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17
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Dwaraka VB, Voss SR. Towards comparative analyses of salamander limb regeneration. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 336:129-144. [PMID: 31584252 PMCID: PMC8908358 DOI: 10.1002/jez.b.22902] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/13/2019] [Accepted: 08/31/2019] [Indexed: 08/29/2023]
Abstract
Among tetrapods, only salamanders can regenerate their limbs and tails throughout life. This amazing regenerative ability has attracted the attention of scientists for hundreds of years. Now that large, salamander genomes are beginning to be sequenced for the first time, omics tools and approaches can be used to integrate new perspectives into the study of tissue regeneration. Here we argue the need to move beyond the primary salamander models to investigate regeneration in other species. Salamanders at first glance come across as a phylogenetically conservative group that has not diverged greatly from their ancestors. While salamanders do present ancestral characteristics of basal tetrapods, including the ability to regenerate limbs, data from fossils and data from studies that have tested for species differences suggest there may be considerable variation in how salamanders develop and regenerate their limbs. We review the case for expanded studies of salamander tissue regeneration and identify questions and approaches that are most likely to reveal commonalities and differences in regeneration among species. We also address challenges that confront such an initiative, some of which are regulatory and not scientific. The time is right to gain evolutionary perspective about mechanisms of tissue regeneration from comparative studies of salamander species.
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Affiliation(s)
- Varun B. Dwaraka
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, Kentucky
- Department of Biology, University of Kentucky, Lexington, Kentucky
| | - S. Randal Voss
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, Kentucky
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18
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Ponssa ML, Abdala V. Sesamoids in Caudata and Gymnophiona (Lissamphibia): absences and evidence. PeerJ 2021; 8:e10595. [PMID: 33384907 PMCID: PMC7751427 DOI: 10.7717/peerj.10595] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/26/2020] [Indexed: 11/30/2022] Open
Abstract
An integrative definition of sesamoid bones has been recently proposed, highlighting their relationship with tendons and ligaments, their genetic origin, the influence of epigenetic stimuli on their development, and their variable tissue composition. Sesamoid bones occur mainly associated with a large number of mobile joints in vertebrates, most commonly in the postcranium. Here, we present a survey of the distribution pattern of sesamoids in 256 taxa of Caudata and Gymnophiona and 24 taxa of temnospondyls and lepospondyls, based on dissections, high-resolution X-ray computed tomography from digital databases and literature data. These groups have a pivotal role in the interpretation of the evolution of sesamoids in Lissamphibia and tetrapods in general. Our main goals were: (1) to contribute to the knowledge of the comparative anatomy of sesamoids in Lissamphibia; (2) to assess the evolutionary history of selected sesamoids. We formally studied the evolution of the observed sesamoids by optimizing them in the most accepted phylogeny of the group. We identified only three bony or cartilaginous sesamoids in Caudata: the mandibular sesamoid, which is adjacent to the jaw articulation; one located on the mandibular symphysis; and one located in the posterior end of the maxilla. We did not observe any cartilaginous or osseous sesamoid in Gymnophiona. Mapping analyses of the sesamoid dataset of urodeles onto the phylogeny revealed that the very conspicuous sesamoid in the mandibular symphysis of Necturus beyeri and Amphiuma tridactylum is an independent acquisition of these taxa. On the contrary, the sesamoid located between the maxilla and the lower jaw is a new synapomorphy that supports the node of Hydromantes platycephalus and Karsenia coreana. The absence of a mandibular sesamoid is plesiomorphic to Caudata, whereas it is convergent in seven different families. The absence of postcranial sesamoids in salamanders might reveal a paedomorphic pattern that would be visible in their limb joints.
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Affiliation(s)
- María Laura Ponssa
- Área Herpetología, Unidad Ejecutora Lillo (UEL), CONICET-Fundación Miguel Lillo, San Miguel de Tucumán, Tucumán, Argentina
| | - Virginia Abdala
- Instituto de Biodiversidad Neotropical (IBN), UNT-CONICET. Cátedra de Biología General, Facultad de Ciencias Naturales e IML, UNT, Yerba Buena, Tucuman, Argentina
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19
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O’Conner S, Li L. Mitochondrial Fostering: The Mitochondrial Genome May Play a Role in Plant Orphan Gene Evolution. FRONTIERS IN PLANT SCIENCE 2020; 11:600117. [PMID: 33424897 PMCID: PMC7793901 DOI: 10.3389/fpls.2020.600117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/02/2020] [Indexed: 05/12/2023]
Abstract
Plant mitochondrial genomes exhibit unique evolutionary patterns. They have a high rearrangement but low mutation rate, and a large size. Based on massive mitochondrial DNA transfers to the nucleus as well as the mitochondrial unique evolutionary traits, we propose a "Mitochondrial Fostering" theory where the organelle genome plays an integral role in the arrival and development of orphan genes (genes with no homologs in other lineages). Two approaches were used to test this theory: (1) bioinformatic analysis of nuclear mitochondrial DNA (Numts: mitochondrial originating DNA that migrated to the nucleus) at the genome level, and (2) bioinformatic analysis of particular orphan sequences present in both the mitochondrial genome and the nuclear genome of Arabidopsis thaliana. One study example is given about one orphan sequence that codes for two unique orphan genes: one in the mitochondrial genome and another one in the nuclear genome. DNA alignments show regions of this A. thaliana orphan sequence exist scattered throughout other land plant mitochondrial genomes. This is consistent with the high recombination rates of mitochondrial genomes in land plants. This may also enable the creation of novel coding sequences within the orphan loci, which can then be transferred to the nuclear genome and become exposed to new evolutionary pressures. Our study also reveals a high correlation between the amount of mitochondrial DNA transferred to the nuclear genome and the number of orphan genes in land plants. All the data suggests the mitochondrial genome may play a role in nuclear orphan gene evolution in land plants.
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Affiliation(s)
| | - Ling Li
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
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20
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Khan PA, Crawford MJ. Regeneration and development. An amphibian call to arms. Dev Dyn 2020; 250:896-901. [DOI: 10.1002/dvdy.272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 01/22/2023] Open
Affiliation(s)
- Paul A. Khan
- Department of Biomedical Sciences University of Windsor Windsor Ontario Canada
| | - Michael J. Crawford
- Department of Biomedical Sciences University of Windsor Windsor Ontario Canada
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21
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Jiang M, Zhan Z, Li H, Dong X, Cheng F, Piao Z. Brassica rapa orphan genes largely affect soluble sugar metabolism. HORTICULTURE RESEARCH 2020; 7:181. [PMID: 33328469 PMCID: PMC7603504 DOI: 10.1038/s41438-020-00403-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/31/2020] [Accepted: 09/01/2020] [Indexed: 05/04/2023]
Abstract
Orphan genes (OGs), which are genes unique to a specific taxon, play a vital role in primary metabolism. However, little is known about the functional significance of Brassica rapa OGs (BrOGs) that were identified in our previous study. To study their biological functions, we developed a BrOG overexpression (BrOGOE) mutant library of 43 genes in Arabidopsis thaliana and assessed the phenotypic variation of the plants. We found that 19 of the 43 BrOGOE mutants displayed a mutant phenotype and 42 showed a variable soluble sugar content. One mutant, BrOG1OE, with significantly elevated fructose, glucose, and total sugar contents but a reduced sucrose content, was selected for in-depth analysis. BrOG1OE showed reduced expression and activity of the Arabidopsis sucrose synthase gene (AtSUS); however, the activity of invertase was unchanged. In contrast, silencing of two copies of BrOG1 in B. rapa, BraA08002322 (BrOG1A) and BraSca000221 (BrOG1B), by the use of an efficient CRISPR/Cas9 system of Chinese cabbage (B. rapa ssp. campestris) resulted in decreased fructose, glucose, and total soluble sugar contents because of the upregulation of BrSUS1b, BrSUS3, and, specifically, the BrSUS5 gene in the edited BrOG1 transgenic line. In addition, we observed increased sucrose content and SUS activity in the BrOG1 mutants, with the activity of invertase remaining unchanged. Thus, BrOG1 probably affected soluble sugar metabolism in a SUS-dependent manner. This is the first report investigating the function of BrOGs with respect to soluble sugar metabolism and reinforced the idea that OGs are a valuable resource for nutrient metabolism.
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Affiliation(s)
- Mingliang Jiang
- Molecular Biology of Vegetable Laboratory, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zongxiang Zhan
- Molecular Biology of Vegetable Laboratory, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Haiyan Li
- Molecular Biology of Vegetable Laboratory, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiangshu Dong
- School of Agriculture, Yunnan University, Kunming, 650504, China
| | - Feng Cheng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhongyun Piao
- Molecular Biology of Vegetable Laboratory, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.
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22
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Evolution of novel genes in three-spined stickleback populations. Heredity (Edinb) 2020; 125:50-59. [PMID: 32499660 PMCID: PMC7413265 DOI: 10.1038/s41437-020-0319-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 04/27/2020] [Accepted: 04/30/2020] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic genomes frequently acquire new protein-coding genes which may significantly impact an organism’s fitness. Novel genes can be created, for example, by duplication of large genomic regions or de novo, from previously non-coding DNA. Either way, creation of a novel transcript is an essential early step during novel gene emergence. Most studies on the gain-and-loss dynamics of novel genes so far have compared genomes between species, constraining analyses to genes that have remained fixed over long time scales. However, the importance of novel genes for rapid adaptation among populations has recently been shown. Therefore, since little is known about the evolutionary dynamics of transcripts across natural populations, we here study transcriptomes from several tissues and nine geographically distinct populations of an ecological model species, the three-spined stickleback. Our findings suggest that novel genes typically start out as transcripts with low expression and high tissue specificity. Early expression regulation appears to be mediated by gene-body methylation. Although most new and narrowly expressed genes are rapidly lost, those that survive and subsequently spread through populations tend to gain broader and higher expression levels. The properties of the encoded proteins, such as disorder and aggregation propensity, hardly change. Correspondingly, young novel genes are not preferentially under positive selection but older novel genes more often overlap with FST outlier regions. Taken together, expression of the surviving novel genes is rapidly regulated, probably via epigenetic mechanisms, while structural properties of encoded proteins are non-debilitating and might only change much later.
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23
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Suzuki N, Ochi H. Regeneration enhancers: A clue to reactivation of developmental genes. Dev Growth Differ 2020; 62:343-354. [PMID: 32096563 PMCID: PMC7383998 DOI: 10.1111/dgd.12654] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 12/18/2022]
Abstract
During tissue and organ regeneration, cells initially detect damage and then alter nuclear transcription in favor of tissue/organ reconstruction. Until recently, studies of tissue regeneration have focused on the identification of relevant genes. These studies show that many developmental genes are reused during regeneration. Concurrently, comparative genomics studies have shown that the total number of genes does not vastly differ among vertebrate taxa. Moreover, functional analyses of developmental genes using various knockout/knockdown techniques demonstrated that the functions of these genes are conserved among vertebrates. Despite these data, the ability to regenerate damaged body parts varies widely between animals. Thus, it is important to determine how regenerative transcriptional programs are triggered and why animals with low regenerative potential fail to express developmental genes after injury. Recently, we discovered relevant enhancers and named them regeneration signal-response enhancers (RSREs) after identifying their activation mechanisms in a Xenopus laevis transgenic system. In this review, we summarize recent studies of injury/regeneration-associated enhancers and then discuss their mechanisms of activation.
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Affiliation(s)
- Nanoka Suzuki
- Amphibian Research CenterHiroshima UniversityHigashi‐HiroshimaJapan
| | - Haruki Ochi
- Institute for Promotion of Medical Science ResearchFaculty of MedicineYamagata UniversityYamagataJapan
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24
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Bothe V, Mahlow K, Fröbisch NB. A histological study of normal and pathological limb regeneration in the Mexican axolotl Ambystoma mexicanum. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 336:116-128. [PMID: 32394624 DOI: 10.1002/jez.b.22950] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 03/30/2020] [Accepted: 04/08/2020] [Indexed: 01/13/2023]
Abstract
Salamanders show unparalleled capacities of tissue regeneration amongst tetrapods (four-legged vertebrates), being able to repair and renew lost or damage body parts, such as tails, jaws, and limbs in a seemingly perfect fashion. Despite countless studies on axolotl (Ambystoma mexicanum) regeneration, only a few studies have thus far compared gross morphological and histological features of the original and regenerated limb skeleton. Therein, most studies have focused on nerves or muscles, while even fewer have provided detailed information about bones and cartilage. This study compares skeletal tissue structures of original and regenerated limbs with respect to tissue level histology. Histological serial sections of 55 axolotl larvae were generated, including 29 limbs that were severed by conspecifics, and 26 that were subject to targeted amputations. Amputations were executed in several larval stages (48, 52, and 53) and at different limb positions (humeral midshaft, above the mesopod). In addition, 3D reconstructions were prepared based on X-ray microtomography scans. The results demonstrate that regenerated forelimbs show a diversity of limb and digit abnormalities as a result of imperfect regeneration. Furthermore, abnormalities were more severe and more frequent in regenerated forelimbs caused by natural bites as compared with regenerated forelimbs after amputation. The results indicate that abnormalities occur frequently after regeneration in larval axolotls contradicting the notion of regeneration generally resulting in perfect limbs.
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Affiliation(s)
- Vivien Bothe
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Kristin Mahlow
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Nadia B Fröbisch
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.,Humboldt-Universität zu Berlin, Berlin, Germany
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25
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Flowers GP, Crews CM. Remembering where we are: Positional information in salamander limb regeneration. Dev Dyn 2020; 249:465-482. [PMID: 32124513 DOI: 10.1002/dvdy.167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 12/26/2022] Open
Abstract
Fifty years ago, Lewis Wolpert defined an important question in developmental biology: how are cell fates determined by the positions of cells within a system? He proposed that cells retain positional values as if they lie within a coordinate system and that the interpretation of these values produces patterns in development. He referred to this concept as positional information. Though initially controversial, this concept of positional information has proven to be profoundly influential in developmental biology. One area in which the influence of Wolpert's theoretical work can be clearly demonstrated is the study of limb regeneration in salamanders. Here, we review the work in limb regeneration leading up to Wolpert defining the concept of positional information and how his theory has guided regeneration research over the subsequent 50 years.
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Affiliation(s)
- Grant Parker Flowers
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Craig M Crews
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.,Department of Chemistry, Yale University, New Haven, Connecticut, USA.,Department of Pharmacology, Yale University, New Haven, Connecticut, USA
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26
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Perochon A, Kahla A, Vranić M, Jia J, Malla KB, Craze M, Wallington E, Doohan FM. A wheat NAC interacts with an orphan protein and enhances resistance to Fusarium head blight disease. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1892-1904. [PMID: 30821405 PMCID: PMC6737021 DOI: 10.1111/pbi.13105] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 02/19/2019] [Accepted: 02/21/2019] [Indexed: 05/05/2023]
Abstract
Taxonomically-restricted orphan genes play an important role in environmental adaptation, as recently demonstrated by the fact that the Pooideae-specific orphan TaFROG (Triticum aestivum Fusarium Resistance Orphan Gene) enhanced wheat resistance to the economically devastating Fusarium head blight (FHB) disease. Like most orphan genes, little is known about the cellular function of the encoded protein TaFROG, other than it interacts with the central stress regulator TaSnRK1α. Here, we functionally characterized a wheat (T. aestivum) NAC-like transcription factor TaNACL-D1 that interacts with TaFROG and investigated its' role in FHB using studies to assess motif analyses, yeast transactivation, protein-protein interaction, gene expression and the disease response of wheat lines overexpressing TaNACL-D1. TaNACL-D1 is a Poaceae-divergent NAC transcription factor that encodes a Triticeae-specific protein C-terminal region with transcriptional activity and a nuclear localisation signal. The TaNACL-D1/TaFROG interaction was detected in yeast and confirmed in planta, within the nucleus. Analysis of multi-protein interactions indicated that TaFROG could form simultaneously distinct protein complexes with TaNACL-D1 and TaSnRK1α in planta. TaNACL-D1 and TaFROG are co-expressed as an early response to both the causal fungal agent of FHB, Fusarium graminearum and its virulence factor deoxynivalenol (DON). Wheat lines overexpressing TaNACL-D1 were more resistant to FHB disease than wild type plants. Thus, we conclude that the orphan protein TaFROG interacts with TaNACL-D1, a NAC transcription factor that forms part of the disease response evolved within the Triticeae.
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Affiliation(s)
- Alexandre Perochon
- UCD School of Biology and Environmental Science and Earth InstituteCollege of ScienceUniversity College DublinBelfield, Dublin 4Ireland
| | - Amal Kahla
- UCD School of Biology and Environmental Science and Earth InstituteCollege of ScienceUniversity College DublinBelfield, Dublin 4Ireland
| | - Monika Vranić
- UCD School of Biology and Environmental Science and Earth InstituteCollege of ScienceUniversity College DublinBelfield, Dublin 4Ireland
| | - Jianguang Jia
- UCD School of Biology and Environmental Science and Earth InstituteCollege of ScienceUniversity College DublinBelfield, Dublin 4Ireland
| | - Keshav B. Malla
- UCD School of Biology and Environmental Science and Earth InstituteCollege of ScienceUniversity College DublinBelfield, Dublin 4Ireland
| | | | | | - Fiona M. Doohan
- UCD School of Biology and Environmental Science and Earth InstituteCollege of ScienceUniversity College DublinBelfield, Dublin 4Ireland
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27
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Bichirs employ similar genetic pathways for limb regeneration as are used in lungfish and salamanders. Gene 2019; 690:68-74. [DOI: 10.1016/j.gene.2018.12.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/29/2018] [Accepted: 12/12/2018] [Indexed: 11/22/2022]
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28
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Yang K, Kang J. Tissue Regeneration Enhancer Elements: A Way to Unlock Endogenous Healing Power. Dev Dyn 2018; 248:34-42. [PMID: 30291668 DOI: 10.1002/dvdy.24676] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 09/27/2018] [Accepted: 10/02/2018] [Indexed: 01/15/2023] Open
Abstract
Regenerative capacity is widespread throughout almost all animal phyla. However, the distribution pattern remains incompletely understood. Various examples show that very closely related species display different regenerative capacities. Why and how have diverse regenerative capacities evolved across species? One prevailing thought in the field of regeneration is that most regeneration-associated factors are evolutionarily conserved, suggesting the existence of an innate tissue regeneration ability in all species. However, its regulation is differentially controlled in distinct species, resulting in heterogeneous regenerative capabilities. In this review, we discuss regeneration-associated enhancers, the key cis-regulatory elements controlling gene expression, their underlying molecular mechanisms, and their influence on regenerative capacity. Understanding the regulatory mechanisms of regeneration enhancers can provide fundamental insights into tissue regeneration and further help us develop therapeutic strategies to unlock latent healing powers in humans. Developmental Dynamics 248:34-42, 2019. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- KaHoua Yang
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin
| | - Junsu Kang
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin
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29
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Tesařová M, Mancini L, Simon A, Adameyko I, Kaucká M, Elewa A, Lanzafame G, Zhang Y, Kalasová D, Szarowská B, Zikmund T, Novotná M, Kaiser J. A quantitative analysis of 3D-cell distribution in regenerating muscle-skeletal system with synchrotron X-ray computed microtomography. Sci Rep 2018; 8:14145. [PMID: 30237460 PMCID: PMC6148031 DOI: 10.1038/s41598-018-32459-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 09/10/2018] [Indexed: 02/07/2023] Open
Abstract
One of the greatest enigmas of modern biology is how the geometry of muscular and skeletal structures are created and how their development is controlled during growth and regeneration. Scaling and shaping of vertebrate muscles and skeletal elements has always been enigmatic and required an advanced technical level in order to analyse the cell distribution in 3D. In this work, synchrotron X-ray computed microtomography (µCT) and chemical contrasting has been exploited for a quantitative analysis of the 3D-cell distribution in tissues of a developing salamander (Pleurodeles waltl) limb – a key model organism for vertebrate regeneration studies. We mapped the limb muscles, their size and shape as well as the number and density of cells within the extracellular matrix of the developing cartilage. By using tomographic approach, we explored the polarity of the cells in 3D, in relation to the structure of developing joints. We found that the polarity of chondrocytes correlates with the planes in joint surfaces and also changes along the length of the cartilaginous elements. Our approach generates data for the precise computer simulations of muscle-skeletal regeneration using cell dynamics models, which is necessary for the understanding how anisotropic growth results in the precise shapes of skeletal structures.
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Affiliation(s)
- Markéta Tesařová
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Lucia Mancini
- Elettra-Sincrotrone Trieste S.C.p.A., Basovizza, Trieste, Italy
| | - Andras Simon
- Department of Cellular and Molecular Biology, Karolinska Institutet, Solna, 171777, Stockholm, Sweden
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, 171777, Stockholm, Sweden.,Department of Molecular Neurosciences, Medical University Vienna, Vienna, Austria
| | - Markéta Kaucká
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, 171777, Stockholm, Sweden.,Department of Molecular Neurosciences, Medical University Vienna, Vienna, Austria
| | - Ahmed Elewa
- Department of Cellular and Molecular Biology, Karolinska Institutet, Solna, 171777, Stockholm, Sweden
| | | | - Yi Zhang
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, 171777, Stockholm, Sweden.,Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Dominika Kalasová
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Bára Szarowská
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, 171777, Stockholm, Sweden
| | - Tomáš Zikmund
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Marie Novotná
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Jozef Kaiser
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic.
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Dwaraka VB, Smith JJ, Woodcock MR, Voss SR. Comparative transcriptomics of limb regeneration: Identification of conserved expression changes among three species of Ambystoma. Genomics 2018; 111:1216-1225. [PMID: 30092345 DOI: 10.1016/j.ygeno.2018.07.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 07/23/2018] [Accepted: 07/31/2018] [Indexed: 12/14/2022]
Abstract
Transcriptome studies are revealing the complex gene expression basis of limb regeneration in the primary salamander model - Ambystoma mexicanum (axolotl). To better understand this complexity, there is need to extend analyses to additional salamander species. Using microarray and RNA-Seq, we performed a comparative transcriptomic study using A. mexicanum and two other ambystomatid salamanders: A. andersoni, and A. maculatum. Salamanders were administered forelimb amputations and RNA was isolated and analyzed to identify 405 non-redundant genes that were commonly, differentially expressed 24 h post amputation. Many of the upregulated genes are predicted to function in wound healing and developmental processes, while many of the downregulated genes are typically expressed in muscle. The conserved transcriptional changes identified in this study provide a high-confidence dataset for identifying factors that simultaneous orchestrate wound healing and regeneration processes in response to injury, and more generally for identifying genes that are essential for salamander limb regeneration.
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Affiliation(s)
- Varun B Dwaraka
- Department of Biology, University of Kentucky, Lexington, KY 40506, United States; Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY 40536, United States.
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY 40506, United States
| | - M Ryan Woodcock
- Department of Biology, Keene State College, Keene, NH 03431, United States
| | - S Randal Voss
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY 40536, United States; Department of Neuroscience, University of Kentucky, Lexington, KY 40536, United States; Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY 40536, United States
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31
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Vasilyeva NA, Loktyushov EV, Bychkov ML, Shenkarev ZO, Lyukmanova EN. Three-Finger Proteins from the Ly6/uPAR Family: Functional Diversity within One Structural Motif. BIOCHEMISTRY (MOSCOW) 2018. [PMID: 29523067 DOI: 10.1134/s0006297917130090] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The discovery in higher animals of proteins from the Ly6/uPAR family, which have structural homology with snake "three-finger" neurotoxins, has generated great interest in these molecules and their role in the functioning of the organism. These proteins have been found in the nervous, immune, endocrine, and reproductive systems of mammals. There are two types of the Ly6/uPAR proteins: those associated with the cell membrane by GPI-anchor and secreted ones. For some of them (Lynx1, SLURP-1, SLURP-2, Lypd6), as well as for snake α-neurotoxins, the target of action is nicotinic acetylcholine receptors, which are widely represented in the central and peripheral nervous systems, and in many other tissues, including epithelial cells and the immune system. However, the targets of most proteins from the Ly6/uPAR family and the mechanism of their action remain unknown. This review presents data on the structural and functional properties of the Ly6/uPAR proteins, which reveal a variety of functions within a single structural motif.
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Affiliation(s)
- N A Vasilyeva
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia.
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32
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Kerney RR, Hanken J, Blackburn DC. Early limb patterning in the direct-developing salamander Plethodon cinereus revealed by sox9 and col2a1. Evol Dev 2018. [PMID: 29527799 DOI: 10.1111/ede.12250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Direct-developing amphibians form limbs during early embryonic stages, as opposed to the later, often postembryonic limb formation of metamorphosing species. Limb patterning is dramatically altered in direct-developing frogs, but little attention has been given to direct-developing salamanders. We use expression patterns of two genes, sox9 and col2a1, to assess skeletal patterning during embryonic limb development in the direct-developing salamander Plethodon cinereus. Limb patterning in P. cinereus partially resembles that described in other urodele species, with early formation of digit II and a generally anterior-to-posterior formation of preaxial digits. Unlike other salamanders described to date, differentiation of preaxial zeugopodial cartilages (radius/tibia) is not accelerated in relation to the postaxial cartilages, and there is no early differentiation of autopodial elements in relation to more proximal cartilages. Instead, digit II forms in continuity with the ulnar/fibular arch. This amniote-like connectivity to the first digit that forms may be a consequence of the embryonic formation of limbs in this direct-developing species. Additionally, and contrary to recent models of amphibian digit identity, there is no evidence of vestigial digits. This is the first account of gene expression in a plethodontid salamander and only the second published account of embryonic limb patterning in a direct-developing salamander species.
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Affiliation(s)
- Ryan R Kerney
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania
| | - James Hanken
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts
| | - David C Blackburn
- Florida Museum of Natural History, University of Florida, Gainesville, Florida
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33
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The axolotl genome and the evolution of key tissue formation regulators. Nature 2018; 554:50-55. [PMID: 29364872 DOI: 10.1038/nature25458] [Citation(s) in RCA: 312] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 12/13/2017] [Indexed: 02/08/2023]
Abstract
Salamanders serve as important tetrapod models for developmental, regeneration and evolutionary studies. An extensive molecular toolkit makes the Mexican axolotl (Ambystoma mexicanum) a key representative salamander for molecular investigations. Here we report the sequencing and assembly of the 32-gigabase-pair axolotl genome using an approach that combined long-read sequencing, optical mapping and development of a new genome assembler (MARVEL). We observed a size expansion of introns and intergenic regions, largely attributable to multiplication of long terminal repeat retroelements. We provide evidence that intron size in developmental genes is under constraint and that species-restricted genes may contribute to limb regeneration. The axolotl genome assembly does not contain the essential developmental gene Pax3. However, mutation of the axolotl Pax3 paralogue Pax7 resulted in an axolotl phenotype that was similar to those seen in Pax3-/- and Pax7-/- mutant mice. The axolotl genome provides a rich biological resource for developmental and evolutionary studies.
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34
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van der Vos W, Witzmann F, Fröbisch NB. Tail regeneration in the Paleozoic tetrapodMicrobrachis pelikaniand comparison with extant salamanders and squamates. J Zool (1987) 2017. [DOI: 10.1111/jzo.12516] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- W. van der Vos
- Museum für Naturkunde; Leibniz Institut für Evolutions- und Biodiversitätsforschung; Berlin Germany
| | - F. Witzmann
- Museum für Naturkunde; Leibniz Institut für Evolutions- und Biodiversitätsforschung; Berlin Germany
| | - N. B. Fröbisch
- Museum für Naturkunde; Leibniz Institut für Evolutions- und Biodiversitätsforschung; Berlin Germany
- Institut für Biologie; Humboldt Universität zu Berlin; Berlin Germany
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35
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Thümecke S, Beermann A, Klingler M, Schröder R. The flipflop orphan genes are required for limb bud eversion in the Tribolium embryo. Front Zool 2017; 14:48. [PMID: 29075305 PMCID: PMC5649079 DOI: 10.1186/s12983-017-0234-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/03/2017] [Indexed: 12/20/2022] Open
Abstract
Background Unlike Drosophila but similar to other arthropod and vertebrate embryos, the flour beetle Tribolium castaneum develops everted limb buds during embryogenesis. However, the molecular processes directing the evagination of epithelia are only poorly understood. Results Here we show that the newly discovered genes Tc-flipflop1 and Tc-flipflop2 are involved in regulating the directional budding of appendages. RNAi-knockdown of Tc-flipflop results in a variety of phenotypic traits. Most prominently, embryonic limb buds frequently grow inwards rather than out, leading to the development of inverted appendages inside the larval body. Moreover, affected embryos display dorsal closure defects. The Tc-flipflop genes are evolutionarily non-conserved, and their molecular function is not evident. We further found that Tc-RhoGEF2, a highly-conserved gene known to be involved in actomyosin-dependent cell movement and cell shape changes, shows a Tc-flipflop-like RNAi-phenotype. Conclusions The similarity of the inverted appendage phenotype in both the flipflop- and the RhoGEF2 RNAi gene knockdown led us to conclude that the Tc-flipflop orphan genes act in a Rho-dependent pathway that is essential for the early morphogenesis of polarised epithelial movements. Our work describes one of the few examples of an orphan gene playing a crucial role in an important developmental process. Electronic supplementary material The online version of this article (10.1186/s12983-017-0234-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Susanne Thümecke
- Institut für Biowissenschaften, Universität Rostock, Albert-Einsteinstr 3, D-18059 Rostock, Germany
| | - Anke Beermann
- Universität Tübingen, Auf der Morgenstelle 15, D-72076 Tübingen, Germany
| | - Martin Klingler
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Department Biologie Abt. Entwicklungsbiologie, Staudtstr. 5, D-91058 Erlangen, Germany
| | - Reinhard Schröder
- Universität Tübingen, Auf der Morgenstelle 15, D-72076 Tübingen, Germany
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36
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Boilly B, Faulkner S, Jobling P, Hondermarck H. Nerve Dependence: From Regeneration to Cancer. Cancer Cell 2017; 31:342-354. [PMID: 28292437 DOI: 10.1016/j.ccell.2017.02.005] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 12/07/2016] [Accepted: 02/08/2017] [Indexed: 02/06/2023]
Abstract
Nerve dependence has long been described in animal regeneration, where the outgrowth of axons is necessary to the reconstitution of lost body parts and tissue remodeling in various species. Recent discoveries have demonstrated that denervation can suppress tumor growth and metastasis, pointing to nerve dependence in cancer. Regeneration and cancer share similarities in regard to the stimulatory role of nerves, and there are indications that the stem cell compartment is a preferred target of innervation. Thus, the neurobiology of cancer is an emerging discipline that opens new perspectives in oncology.
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Affiliation(s)
- Benoni Boilly
- UFR de Biologie, Université de Lille, 59655 Villeneuve d'Ascq, France
| | - Sam Faulkner
- School of Biomedical Sciences and Pharmacy, Hunter Medical Research Institute, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Phillip Jobling
- School of Biomedical Sciences and Pharmacy, Hunter Medical Research Institute, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Hubert Hondermarck
- School of Biomedical Sciences and Pharmacy, Hunter Medical Research Institute, University of Newcastle, Callaghan, NSW 2308, Australia.
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37
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Nguyen M, Singhal P, Piet JW, Shefelbine SJ, Maden M, Voss SR, Monaghan JR. Retinoic acid receptor regulation of epimorphic and homeostatic regeneration in the axolotl. Development 2017; 144:601-611. [PMID: 28087637 DOI: 10.1242/dev.139873] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 12/30/2016] [Indexed: 12/16/2023]
Abstract
Salamanders are capable of regenerating amputated limbs by generating a mass of lineage-restricted cells called a blastema. Blastemas only generate structures distal to their origin unless treated with retinoic acid (RA), which results in proximodistal (PD) limb duplications. Little is known about the transcriptional network that regulates PD duplication. In this study, we target specific retinoic acid receptors (RARs) to either PD duplicate (RA treatment or RARγ agonist) or truncate (RARβ antagonist) regenerating limbs. RARE-EGFP reporter axolotls showed divergent reporter activity in limbs undergoing PD duplication versus truncation, suggesting differences in patterning and skeletal regeneration. Transcriptomics identified expression patterns that explain PD duplication, including upregulation of proximal homeobox gene expression and silencing of distal-associated genes, whereas limb truncation was associated with disrupted skeletal differentiation. RARβ antagonism in uninjured limbs induced a loss of skeletal integrity leading to long bone regression and loss of skeletal turnover. Overall, mechanisms were identified that regulate the multifaceted roles of RARs in the salamander limb including regulation of skeletal patterning during epimorphic regeneration, skeletal tissue differentiation during regeneration, and homeostatic regeneration of intact limbs.
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Affiliation(s)
- Matthew Nguyen
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Pankhuri Singhal
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Judith W Piet
- Mechanical and Industrial Engineering, Northeastern University, Boston, MA 02115, USA
| | - Sandra J Shefelbine
- Mechanical and Industrial Engineering, Northeastern University, Boston, MA 02115, USA
| | - Malcolm Maden
- Department of Biology and UF Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - S Randal Voss
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
- Spinal Cord and Brain Injury Research Center, University of Kentucky, College of Medicine, Lexington, KY 40506, USA
| | - James R Monaghan
- Department of Biology, Northeastern University, Boston, MA 02115, USA
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38
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Tanaka EM. The Molecular and Cellular Choreography of Appendage Regeneration. Cell 2017; 165:1598-1608. [PMID: 27315477 DOI: 10.1016/j.cell.2016.05.038] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/02/2016] [Accepted: 05/09/2016] [Indexed: 10/21/2022]
Abstract
Recent advances in limb regeneration are revealing the molecular events that integrate growth control, cell fate programming, and positional information to yield the exquisite replacement of the amputated limb. Parallel progress in several invertebrate and vertebrate models has provided a broader context for understanding the mechanisms and the evolution of regeneration. Together, these discoveries provide a foundation for describing the principles underlying regeneration of complex, multi-tissue structures. As such these findings should provide a wealth of ideas for engineers seeking to reconstitute regeneration from constituent parts or to elicit full regeneration from partial regeneration events.
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Affiliation(s)
- Elly M Tanaka
- DFG Research Center for Regenerative Therapies, Technische Universität Dresden Fetscherstrasse 105, 01307 Dresden, GERMANY.
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39
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Nogueira AF, Costa CM, Lorena J, Moreira RN, Frota-Lima GN, Furtado C, Robinson M, Amemiya CT, Darnet S, Schneider I. Tetrapod limb and sarcopterygian fin regeneration share a core genetic programme. Nat Commun 2016; 7:13364. [PMID: 27804976 PMCID: PMC5097137 DOI: 10.1038/ncomms13364] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/27/2016] [Indexed: 02/07/2023] Open
Abstract
Salamanders are the only living tetrapods capable of fully regenerating limbs. The discovery of salamander lineage-specific genes (LSGs) expressed during limb regeneration suggests that this capacity is a salamander novelty. Conversely, recent paleontological evidence supports a deeper evolutionary origin, before the occurrence of salamanders in the fossil record. Here we show that lungfishes, the sister group of tetrapods, regenerate their fins through morphological steps equivalent to those seen in salamanders. Lungfish de novo transcriptome assembly and differential gene expression analysis reveal notable parallels between lungfish and salamander appendage regeneration, including strong downregulation of muscle proteins and upregulation of oncogenes, developmental genes and lungfish LSGs. MARCKS-like protein (MLP), recently discovered as a regeneration-initiating molecule in salamander, is likewise upregulated during early stages of lungfish fin regeneration. Taken together, our results lend strong support for the hypothesis that tetrapods inherited a bona fide limb regeneration programme concomitant with the fin-to-limb transition.
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Affiliation(s)
- Acacio F Nogueira
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Correa, 01, Belém 66075-110, Brazil
| | - Carinne M Costa
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Correa, 01, Belém 66075-110, Brazil
| | - Jamily Lorena
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Correa, 01, Belém 66075-110, Brazil
| | - Rodrigo N Moreira
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Correa, 01, Belém 66075-110, Brazil
| | - Gabriela N Frota-Lima
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Correa, 01, Belém 66075-110, Brazil
| | - Carolina Furtado
- Unidade Genômica, Programa de Genética, Instituto Nacional do Câncer, Rio de Janeiro 20230-240, Brazil
| | - Mark Robinson
- Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, Washington 98101, USA
| | - Chris T Amemiya
- Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, Washington 98101, USA.,Department of Biology, University of Washington 106 Kincaid, Seattle, Washington 98195, USA
| | - Sylvain Darnet
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Correa, 01, Belém 66075-110, Brazil
| | - Igor Schneider
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Correa, 01, Belém 66075-110, Brazil
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40
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Tanaka HV, Ng NCY, Yang Yu Z, Casco-Robles MM, Maruo F, Tsonis PA, Chiba C. A developmentally regulated switch from stem cells to dedifferentiation for limb muscle regeneration in newts. Nat Commun 2016; 7:11069. [PMID: 27026263 PMCID: PMC4820895 DOI: 10.1038/ncomms11069] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 02/18/2016] [Indexed: 11/30/2022] Open
Abstract
The newt, a urodele amphibian, is able to repeatedly regenerate its limbs throughout its lifespan, whereas other amphibians deteriorate or lose their ability to regenerate limbs after metamorphosis. It remains to be determined whether such an exceptional ability of the newt is either attributed to a strategy, which controls regeneration in larvae, or on a novel one invented by the newt after metamorphosis. Here we report that the newt switches the cellular mechanism for limb regeneration from a stem/progenitor-based mechanism (larval mode) to a dedifferentiation-based one (adult mode) as it transits beyond metamorphosis. We demonstrate that larval newts use stem/progenitor cells such as satellite cells for new muscle in a regenerated limb, whereas metamorphosed newts recruit muscle fibre cells in the stump for the same purpose. We conclude that the newt has evolved novel strategies to secure its regenerative ability of the limbs after metamorphosis.
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Affiliation(s)
- Hibiki Vincent Tanaka
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan
| | | | - Zhan Yang Yu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan
| | - Martin Miguel Casco-Robles
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan
| | - Fumiaki Maruo
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan
| | | | - Chikafumi Chiba
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan
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