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Liang Y, Luan YX. The functional evolution of collembolan Ubx on the regulation of abdominal appendage formation. Dev Genes Evol 2024:10.1007/s00427-024-00718-0. [PMID: 38980376 DOI: 10.1007/s00427-024-00718-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 06/18/2024] [Indexed: 07/10/2024]
Abstract
Folsomia candida is a tiny soil-living arthropod belonging to the Collembola, which is an outgroup to Insecta. It resembles insects as having a pair of antennae and three pairs of thorax legs, while it also possesses three abdominal appendages: a ventral tube located in the first abdominal segment (A1), a retinaculum in A3, and a furca in A4. Collembolan Ubx and AbdA specify abdominal appendages, but they are unable to repress appendage marker gene Dll. The genetic basis of collembolan appendage formation and the mechanisms by which Ubx and AbdA regulate Dll transcription and appendage development remains unknown. In this study, we analysed the developmental transcriptomes of F. candida and identified candidate appendage formation genes, including Ubx (FcUbx). The expression data revealed the dominance of Dll over Ubx during the embryonic 3.5 and 4.5 days, suggesting that Ubx is deficient in suppressing Dll at early appendage formation stages. Furthermore, via electrophoretic mobility shift assays and dual luciferase assays, we found that the binding and repression capacity of FcUbx on Drosophila Dll resembles those of the longest isoform of Drosophila Ubx (DmUbx_Ib), while the regulatory mechanism of the C-terminus of FcUbx on Dll repression is similar to that of the crustacean Artemia franciscana Ubx (AfUbx), demonstrating that the function of collembolan Ubx is intermediate between that of Insecta and Crustacea. In summary, our study provides novel insights into collembolan appendage formation and sheds light on the functional evolution of Ubx. Additionally, we propose a model that collembolan Ubx regulates abdominal segments in a context-specific manner.
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Affiliation(s)
- Yan Liang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Yun-Xia Luan
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
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2
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Ertl HA, Bayala EX, Siddiq MA, Wittkopp PJ. Divergence of Grainy head affects chromatin accessibility, gene expression, and embryonic viability in Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.07.588430. [PMID: 38645200 PMCID: PMC11030446 DOI: 10.1101/2024.04.07.588430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Pioneer factors are critical for gene regulation and development because they bind chromatin and make DNA more accessible for binding by other transcription factors. The pioneer factor Grainy head (Grh) is present across metazoans and has been shown to retain a role in epithelium development in fruit flies, nematodes, and mice despite extensive divergence in both amino acid sequence and length. Here, we investigate the evolution of Grh function by comparing the effects of the fly ( Drosophila melanogaster ) and worm ( Caenorhabditis elegans ) Grh orthologs on chromatin accessibility, gene expression, embryonic development, and viability in transgenic D. melanogaster . We found that the Caenorhabditis elegans ortholog rescued cuticle development but not full embryonic viability in Drosophila melanogaster grh null mutants. At the molecular level, the C. elegans ortholog only partially rescued chromatin accessibility and gene expression. Divergence in the disordered N-terminus of the Grh protein contributes to these differences in embryonic viability and molecular phenotypes. These data show how pioneer factors can diverge in sequence and function at the molecular level while retaining conserved developmental functions at the organismal level. SUMMARY STATEMENT Despite divergence in a disordered region that affects function at both molecular and organismal levels, the Caenorhabditis elegans Grainy head (Grh) protein rescued cuticle morphology in D. melanogaster embryos.
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Lynch VJ, Wagner GP. Cooption of polyalanine tract into a repressor domain in the mammalian transcription factor HoxA11. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:486-495. [PMID: 34125492 DOI: 10.1002/jez.b.23063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
An enduring problem in biology is explaining how novel functions of genes originated and how those functions diverge between species. Despite detailed studies on the functional evolution of a few proteins, the molecular mechanisms by which protein functions have evolved are almost entirely unknown. Here, we show that a polyalanine tract in the homeodomain transcription factor HoxA11 arose in the stem-lineage of mammals and functions as an autonomous repressor module by physically interacting with the PAH domains of SIN3 proteins. These results suggest that long polyalanine tracts, which are common in transcription factors and often associated with disease, may tend to function as repressor domains and can contribute to the diversification of transcription factor functions despite the deleterious consequences of polyalanine tract expansion.
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Affiliation(s)
- Vincent J Lynch
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | - Gunter P Wagner
- Department of Ecology and Evolutionary Biology and Yale Systems Biology Institute, Yale University, New Haven, Connecticut, USA
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4
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Mier P, Andrade-Navarro MA. The nucleotide landscape of polyXY regions. Comput Struct Biotechnol J 2023; 21:5408-5412. [PMID: 38022702 PMCID: PMC10652141 DOI: 10.1016/j.csbj.2023.10.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023] Open
Abstract
PolyXY regions are compositionally biased regions composed of two different amino acids. They are classified according to the arrangement of the two amino acid types 'X' and 'Y' into direpeats (composed of alternating amino acids, e.g. 'XYXYXY'), joined (composed of two consecutive stretches of each amino acid, e.g. 'XXXYYY') and shuffled (other arrangements, e.g., 'XYXXYY'). They have been characterized at the amino acid level in all domains of life, and are described as often found within intrinsically disordered regions. Since DNA replication slippage has been proposed as a driver of repeat variation, and given that some polyXY have a repetitive nature, we hypothesized that characterizing the nucleotide coding of various types of polyXY could give hints about their origin and evolution. To test this, we obtained all polyXY regions in the human transcriptome, categorized them, and studied their coding nucleotide sequences. We observed that polyXY exacerbates the codon biases, and that the similarity between the X and Y codons is higher than in the background proteome. Our results support a general mechanism of emergence and evolution of polyXY from single-codon polyX. PolyXY are revealed as hotspots for replication slippage, particularly those composed of repeats: joined and direpeat polyXY. Inter-conversion to shuffled polyXY disrupts nucleotide repeats and restricts further evolution by replication slippage, a mechanism that we previously observed in polyX. Our results shed light on polyXY composition and should simplify the determination of their functions.
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Affiliation(s)
- Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Miguel A. Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
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5
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Vaglietti S, Villeri V, Dell’Oca M, Marchetti C, Cesano F, Rizzo F, Miller D, LaPierre L, Pelassa I, Monje FJ, Colnaghi L, Ghirardi M, Fiumara F. PolyQ length-based molecular encoding of vocalization frequency in FOXP2. iScience 2023; 26:108036. [PMID: 37860754 PMCID: PMC10582585 DOI: 10.1016/j.isci.2023.108036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/18/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
The transcription factor FOXP2, a regulator of vocalization- and speech/language-related phenotypes, contains two long polyQ repeats (Q1 and Q2) displaying marked, still enigmatic length variation across mammals. We found that the Q1/Q2 length ratio quantitatively encodes vocalization frequency ranges, from the infrasonic to the ultrasonic, displaying striking convergent evolution patterns. Thus, species emitting ultrasonic vocalizations converge with bats in having a low ratio, whereas species vocalizing in the low-frequency/infrasonic range converge with elephants and whales, which have higher ratios. Similar, taxon-specific patterns were observed for the FOXP2-related protein FOXP1. At the molecular level, we observed that the FOXP2 polyQ tracts form coiled coils, assembling into condensates and fibrils, and drive liquid-liquid phase separation (LLPS). By integrating evolutionary and molecular analyses, we found that polyQ length variation related to vocalization frequency impacts FOXP2 structure, LLPS, and transcriptional activity, thus defining a novel form of polyQ length-based molecular encoding of vocalization frequency.
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Affiliation(s)
- Serena Vaglietti
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Veronica Villeri
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Marco Dell’Oca
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Chiara Marchetti
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Federico Cesano
- Department of Chemistry, University of Turin, 10125 Turin, Italy
| | - Francesca Rizzo
- Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR 518057, China
| | - Dave Miller
- Cascades Pika Watch, Oregon Zoo, Portland, OR 97221, USA
| | - Louis LaPierre
- Deptartment of Natural Science, Lower Columbia College, Longview, WA 98632, USA
| | - Ilaria Pelassa
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Francisco J. Monje
- Department of Neurophysiology and Neuropharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Luca Colnaghi
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Mirella Ghirardi
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Ferdinando Fiumara
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
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Luo X, Xu YQ, Jin DC, Guo JJ, Yi TC. Role of the Hox Genes, Sex combs reduced, Fushi tarazu and Antennapedia, in Leg Development of the Spider Mite Tetranychus urticae. Int J Mol Sci 2023; 24:10391. [PMID: 37373537 DOI: 10.3390/ijms241210391] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/17/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023] Open
Abstract
Mites, the second largest arthropod group, exhibit rich phenotypic diversity in the development of appendages (legs). For example, the fourth pair of legs (L4) does not form until the second postembryonic developmental stage, namely the protonymph stage. These leg developmental diversities drive body plan diversity in mites. However, little is known about the mechanisms of leg development in mites. Hox genes, homeotic genes, can regulate the development of appendages in arthropods. Three Hox genes, Sex combs reduced (Scr), Fushi tarazu (Ftz) and Antennapedia (Antp), have previously been shown to be expressed in the leg segments of mites. Here, the quantitative real-time reverse transcription PCR shows that three Hox genes are significantly increased in the first molt stage. RNA interference results in a set of abnormalities, including L3 curl and L4 loss. These results suggest that these Hox genes are required for normal leg development. Furthermore, the loss of single Hox genes results in downregulating the expression of the appendage marker Distal-less (Dll), suggesting that the three Hox genes can work together with Dll to maintain leg development in Tetranychus urticae. This study will be essential to understanding the diversity of leg development in mites and changes in Hox gene function.
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Affiliation(s)
- Xiang Luo
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang 550025, China
- Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang 550025, China
| | - Yu-Qi Xu
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang 550025, China
- Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang 550025, China
| | - Dao-Chao Jin
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang 550025, China
- Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang 550025, China
| | - Jian-Jun Guo
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang 550025, China
- Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang 550025, China
| | - Tian-Ci Yi
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang 550025, China
- Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang 550025, China
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7
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Gonzalez CJ, Hildebrandt TR, O'Donnell B. Characterizing Hox genes in mayflies (Ephemeroptera), with Hexagenia limbata as a new mayfly model. EvoDevo 2022; 13:15. [PMID: 35897030 PMCID: PMC9331126 DOI: 10.1186/s13227-022-00200-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 06/28/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hox genes are key regulators of appendage development in the insect body plan. The body plan of mayfly (Ephemeroptera) nymphs differs due to the presence of abdominal appendages called gills. Despite mayflies' phylogenetic position in Paleoptera and novel morphology amongst insects, little is known of their developmental genetics, such as the appendage-regulating Hox genes. To address this issue we present an annotated, early instar transcriptome and embryonic expression profiles for Antennapedia, Ultrabithorax, and Abdominal A proteins in the mayfly Hexagenia limbata, identify putative Hox protein sequences in the mayflies H. limbata, Cloeon dipterum, and Ephemera danica, and describe the genomic organization of the Hox gene cluster in E. danica. RESULTS Transcriptomic sequencing of early instar H. limbata nymphs yielded a high-quality assembly of 83,795 contigs, of which 22,975 were annotated against Folsomia candida, Nilaparvata lugens, Zootermopsis nevadensis and UniRef90 protein databases. Homeodomain protein phylogeny and peptide annotations identified coding sequences for eight of the ten canonical Hox genes (excluding zerknüllt/Hox3 and fushi tarazu) in H. limbata and C. dipterum, and all ten in E. danica. Mayfly Hox protein sequences and embryonic expression patterns of Antp, Ubx, and Abd-A appear highly conserved with those seen in other non-holometabolan insects. Similarly, the genomic organization of the Hox cluster in E. danica resembles that seen in most insects. CONCLUSIONS We present evidence that mayfly Hox peptide sequences and the embryonic expression patterns for Antp, Ubx, and Abd-A are extensively conserved with other insects, as is organization of the mayfly Hox gene cluster. The protein data suggest mayfly Antp, Ubx, and Abd-A play appendage promoting and repressing roles during embryogenesis in the thorax and abdomen, respectively, as in other insects. The identified expression of eight Hox genes, including Ubx and abd-A, in early instar nymphs further indicates a post-embryonic role, possibly in gill development. These data provide a basis for H. limbata as a complementary Ephemeridae model to the growing repertoire of mayfly model species and molecular techniques.
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Affiliation(s)
| | - Tobias R Hildebrandt
- Computational and Applied Mathematic Science, Plymouth State University, Plymouth, NH, USA
| | - Brigid O'Donnell
- Biological Sciences, Plymouth State University, Plymouth, NH, USA
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8
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Expression of Abdominal-B in the brine shrimp, Artemia franciscana, expands our evolutionary understanding of the crustacean abdomen. Dev Biol 2022; 489:178-184. [PMID: 35732224 DOI: 10.1016/j.ydbio.2022.06.011] [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: 10/04/2021] [Revised: 04/19/2022] [Accepted: 06/16/2022] [Indexed: 11/03/2022]
Abstract
The brine shrimp, Artemia franciscana, has a body plan composed of 11 thoracic segments, followed by 2 genital segments, and then 6 additional abdominal segments. Previous studies of Artemia reported that expression of the posterior-most Hox gene, Abdominal-B (Abd-B), is restricted to the genital segments and is not observed posteriorly in the abdomen at any developmental stage. This report was remarkable because it suggested that the Artemia abdomen posterior to the genital segments was a novel body region of 6 segments that bore no homology to any region in other crustaceans and was unique amongst arthropods in being a Hox-free segmented domain outside of the head. In this study, we used RT-PCR, antibody staining, and in situ hybridization on various stages of Artemia nauplii to show that Abd-B mRNA and protein are in fact expressed throughout the abdominal segments during Artemia development, but this expression later retracts to the two genital segments (G1, G2) and the T11 appendages. This suggests that Abd-B does play a role in specifying abdominal segment identity in all crustaceans that have been examined and suggests a common evolutionary origin for the crustacean abdomen.
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9
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Singh NP, Krumlauf R. Diversification and Functional Evolution of HOX Proteins. Front Cell Dev Biol 2022; 10:798812. [PMID: 35646905 PMCID: PMC9136108 DOI: 10.3389/fcell.2022.798812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/08/2022] [Indexed: 01/07/2023] Open
Abstract
Gene duplication and divergence is a major contributor to the generation of morphological diversity and the emergence of novel features in vertebrates during evolution. The availability of sequenced genomes has facilitated our understanding of the evolution of genes and regulatory elements. However, progress in understanding conservation and divergence in the function of proteins has been slow and mainly assessed by comparing protein sequences in combination with in vitro analyses. These approaches help to classify proteins into different families and sub-families, such as distinct types of transcription factors, but how protein function varies within a gene family is less well understood. Some studies have explored the functional evolution of closely related proteins and important insights have begun to emerge. In this review, we will provide a general overview of gene duplication and functional divergence and then focus on the functional evolution of HOX proteins to illustrate evolutionary changes underlying diversification and their role in animal evolution.
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Affiliation(s)
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, United States
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, United States
- *Correspondence: Robb Krumlauf,
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10
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Auradkar A, Bulger EA, Devkota S, McGinnis W, Bier E. Dissecting the evolutionary role of the Hox gene proboscipedia in Drosophila mouthpart diversification by full locus replacement. SCIENCE ADVANCES 2021; 7:eabk1003. [PMID: 34757777 PMCID: PMC8580299 DOI: 10.1126/sciadv.abk1003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Hox genes determine positional codes along the head-to-tail axis. Here, we replaced the entire Drosophila melanogaster proboscipedia (pb) Hox locus, which controls the development of the proboscis and maxillary palps, with that from Drosophila mimica, a related species with highly modified mouthparts. The D. mimica replacement rescues most aspects of adult proboscis morphology; however, the shape and orientation of maxillary palps were modified, resembling D. mimica and closely related species. Expressing the D. mimica Pb protein in the D. melanogaster pattern fully rescued D. melanogaster morphology. However, the expression pattern directed by D. mimica pb cis-regulatory sequences differed from that of D. melanogaster pb in cells that produce altered maxillary structures, indicating that pb regulatory sequences can evolve in related species to alter morphology.
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Affiliation(s)
- Ankush Auradkar
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
- Tata Institute for Genetics and Society-UCSD, La Jolla, CA 92093-0335, USA
| | - Emily A. Bulger
- Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, and Gladstone Institutes, San Francisco, CA 94158, USA
| | - Sushil Devkota
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - William McGinnis
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
- Tata Institute for Genetics and Society-UCSD, La Jolla, CA 92093-0335, USA
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11
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Onal P, Gunasinghe HI, Umezawa KY, Zheng M, Ling J, Azeez L, Dalmeus A, Tazin T, Small S. Suboptimal Intermediates Underlie Evolution of the Bicoid Homeodomain. Mol Biol Evol 2021; 38:2179-2190. [PMID: 33599280 PMCID: PMC8136501 DOI: 10.1093/molbev/msab051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Changes in regulatory networks generate materials for evolution to create phenotypic diversity. For transcription networks, multiple studies have shown that alterations in binding sites of cis-regulatory elements correlate well with the gain or loss of specific features of the body plan. Less is known about alterations in the amino acid sequences of the transcription factors (TFs) that bind these elements. Here we study the evolution of Bicoid (Bcd), a homeodomain (HD) protein that is critical for anterior embryo patterning in Drosophila. The ancestor of Bcd (AncBcd) emerged after a duplication of a Zerknullt (Zen)-like ancestral protein (AncZB) in a suborder of flies. AncBcd diverged from AncZB, gaining novel transcriptional and translational activities. We focus on the evolution of the HD of AncBcd, which binds to DNA and RNA, and is comprised of four subdomains: an N-terminal arm (NT) and three helices; H1, H2, and Recognition Helix (RH). Using chimeras of subdomains and gene rescue assays in Drosophila, we show that robust patterning activity of the Bcd HD (high frequency rescue to adulthood) is achieved only when amino acid substitutions in three separate subdomains (NT, H1, and RH) are combined. Other combinations of subdomains also yield full rescue, but with lower penetrance, suggesting alternative suboptimal activities. Our results suggest a multistep pathway for the evolution of the Bcd HD that involved intermediate HD sequences with suboptimal activities, which constrained and enabled further evolutionary changes. They also demonstrate critical epistatic forces that contribute to the robust function of a DNA-binding domain.
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Affiliation(s)
- Pinar Onal
- Department of Biology, New York University, New York, NY, USA
| | | | | | - Michael Zheng
- Department of Biology, New York University, New York, NY, USA
| | - Jia Ling
- Department of Biology, New York University, New York, NY, USA
| | - Leen Azeez
- Department of Biology, New York University, New York, NY, USA
| | - Anecine Dalmeus
- Department of Biology, New York University, New York, NY, USA
| | - Tasmima Tazin
- Department of Biology, New York University, New York, NY, USA
| | - Stephen Small
- Department of Biology, New York University, New York, NY, USA
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12
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Giraud G, Paul R, Duffraisse M, Khan S, Shashidhara LS, Merabet S. Developmental Robustness: The Haltere Case in Drosophila. Front Cell Dev Biol 2021; 9:713282. [PMID: 34368162 PMCID: PMC8343187 DOI: 10.3389/fcell.2021.713282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/30/2021] [Indexed: 11/24/2022] Open
Abstract
Developmental processes have to be robust but also flexible enough to respond to genetic and environmental variations. Different mechanisms have been described to explain the apparent antagonistic nature of developmental robustness and plasticity. Here, we present a “self-sufficient” molecular model to explain the development of a particular flight organ that is under the control of the Hox gene Ultrabithorax (Ubx) in the fruit fly Drosophila melanogaster. Our model is based on a candidate RNAi screen and additional genetic analyses that all converge to an autonomous and cofactor-independent mode of action for Ubx. We postulate that this self-sufficient molecular mechanism is possible due to an unusually high expression level of the Hox protein. We propose that high dosage could constitute a so far poorly investigated molecular strategy for allowing Hox proteins to both innovate and stabilize new forms during evolution.
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Affiliation(s)
| | | | | | - Soumen Khan
- Indian Institute of Science Education and Research (IISER), Pune, India
| | - L S Shashidhara
- Indian Institute of Science Education and Research (IISER), Pune, India.,Ashoka University, Sonipat, India
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13
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The Hox protein conundrum: The "specifics" of DNA binding for Hox proteins and their partners. Dev Biol 2021; 477:284-292. [PMID: 34102167 PMCID: PMC8846413 DOI: 10.1016/j.ydbio.2021.06.002] [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: 12/01/2020] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/25/2022]
Abstract
Homeotic genes (Hox genes) are homeodomain-transcription factors involved in conferring segmental identity along the anterior-posterior body axis. Molecular characterization of HOX protein function raises some interesting questions regarding the source of the binding specificity of the HOX proteins. How do HOX proteins regulate common and unique target specificity across space and time? This review attempts to summarize and interpret findings in this area, largely focused on results from in vitro and in vivo studies in Drosophila and mouse systems. Recent studies related to HOX protein binding specificity compel us to reconsider some of our current models for transcription factor-DNA interactions. It is crucial to study transcription factor binding by incorporating components of more complex, multi-protein interactions in concert with small changes in binding motifs that can significantly impact DNA binding specificity and subsequent alterations in gene expression. To incorporate the multiple elements that can determine HOX protein binding specificity, we propose a more integrative Cooperative Binding model.
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14
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Molecular and evolutionary processes generating variation in gene expression. Nat Rev Genet 2020; 22:203-215. [PMID: 33268840 DOI: 10.1038/s41576-020-00304-w] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2020] [Indexed: 12/18/2022]
Abstract
Heritable variation in gene expression is common within and between species. This variation arises from mutations that alter the form or function of molecular gene regulatory networks that are then filtered by natural selection. High-throughput methods for introducing mutations and characterizing their cis- and trans-regulatory effects on gene expression (particularly, transcription) are revealing how different molecular mechanisms generate regulatory variation, and studies comparing these mutational effects with variation seen in the wild are teasing apart the role of neutral and non-neutral evolutionary processes. This integration of molecular and evolutionary biology allows us to understand how the variation in gene expression we see today came to be and to predict how it is most likely to evolve in the future.
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15
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Farris SM. The rise to dominance of genetic model organisms and the decline of curiosity-driven organismal research. PLoS One 2020; 15:e0243088. [PMID: 33259560 PMCID: PMC7707607 DOI: 10.1371/journal.pone.0243088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/13/2020] [Indexed: 12/24/2022] Open
Abstract
Curiosity-driven, basic biological research "…performed without thought of practical ends…" establishes fundamental conceptual frameworks for future technological and medical breakthroughs. Traditionally, curiosity-driven research in biological sciences has utilized experimental organisms chosen for their tractability and suitability for studying the question of interest. This approach leverages the diversity of life to uncover working solutions (adaptations) to problems encountered by living things, and evolutionary context as to the extent to which these solutions may be generalized to other species. Despite the well-documented success of this approach, funding portfolios of United States granting agencies are increasingly filled with studies on a few species for which cutting-edge molecular tools are available (genetic model organisms). While this narrow focus may be justified for biomedically-focused funding bodies such as the National Institutes of Health, it is critical that robust federal support for curiosity-driven research using diverse experimental organisms be maintained by agencies such as the National Science Foundation. Using the disciplines of neurobiology and behavioral research as an example, this study finds that NSF grant awards have declined in association with a decrease in the proportion of grants funded for experimental, rather than genetic model organism research. The decline in use of experimental organisms in the literature mirrors but predates the shift grant funding. Today's dominance of genetic model organisms was thus initiated by researchers themselves and/or by publication peer review and editorial preferences, and was further reinforced by pressure from granting agencies, academic employers, and the scientific community.
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Affiliation(s)
- Sarah M. Farris
- Department of Biology, West Virginia University, Morgantown, West Virginia, United States of America
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16
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Chavali S, Singh AK, Santhanam B, Babu MM. Amino acid homorepeats in proteins. Nat Rev Chem 2020; 4:420-434. [PMID: 37127972 DOI: 10.1038/s41570-020-0204-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2020] [Indexed: 12/16/2022]
Abstract
Amino acid homorepeats, or homorepeats, are polypeptide segments found in proteins that contain stretches of identical amino acid residues. Although abnormal homorepeat expansions are linked to pathologies such as neurodegenerative diseases, homorepeats are prevalent in eukaryotic proteomes, suggesting that they are important for normal physiology. In this Review, we discuss recent advances in our understanding of the biological functions of homorepeats, which range from facilitating subcellular protein localization to mediating interactions between proteins across diverse cellular pathways. We explore how the functional diversity of homorepeat-containing proteins could be linked to the ability of homorepeats to adopt different structural conformations, an ability influenced by repeat composition, repeat length and the nature of flanking sequences. We conclude by highlighting how an understanding of homorepeats will help us better characterize and develop therapeutics against the human diseases to which they contribute.
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Affiliation(s)
- Sreenivas Chavali
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India.
| | - Anjali K Singh
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
| | - Balaji Santhanam
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA.
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17
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Bondos SE, Geraldo Mendes G, Jons A. Context-dependent HOX transcription factor function in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:225-262. [PMID: 32828467 DOI: 10.1016/bs.pmbts.2020.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
During animal development, HOX transcription factors determine the fate of developing tissues to generate diverse organs and appendages. The power of these proteins is striking: mis-expressing a HOX protein causes homeotic transformation of one body part into another. During development, HOX proteins interpret their cellular context through protein interactions, alternative splicing, and post-translational modifications to regulate cell proliferation, cell death, cell migration, cell differentiation, and angiogenesis. Although mutation and/or mis-expression of HOX proteins during development can be lethal, changes in HOX proteins that do not pattern vital organs can result in survivable malformations. In adults, mutation and/or mis-expression of HOX proteins disrupts their gene regulatory networks, deregulating cell behaviors and leading to arthritis and cancer. On the molecular level, HOX proteins are composed of DNA binding homeodomain, and large regions of unstructured, or intrinsically disordered, protein sequence. The primary roles of HOX proteins in arthritis and cancer suggest that mutations associated with these diseases in both the structured and disordered regions of HOX proteins can have substantial functional effects. These insights lead to new questions critical for understanding and manipulating HOX function in physiological and pathological conditions.
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Affiliation(s)
- Sarah E Bondos
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX, United States.
| | - Gabriela Geraldo Mendes
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX, United States
| | - Amanda Jons
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX, United States
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18
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Fu SJ, Zhang JL, Chen SJ, Chen HH, Liu YL, Xu HJ. Functional analysis of Ultrabithorax in the wing-dimorphic planthopper Nilaparvata lugens (Stål, 1854) (Hemiptera: Delphacidae). Gene 2020; 737:144446. [DOI: 10.1016/j.gene.2020.144446] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 01/24/2023]
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19
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Rivera-Colón AG, Westerman EL, Van Belleghem SM, Monteiro A, Papa R. Multiple Loci Control Eyespot Number Variation on the Hindwings of Bicyclus anynana Butterflies. Genetics 2020; 214:1059-1078. [PMID: 32019848 PMCID: PMC7153931 DOI: 10.1534/genetics.120.303059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 12/26/2020] [Indexed: 11/18/2022] Open
Abstract
The underlying genetic changes that regulate the appearance and disappearance of repeated traits, or serial homologs, remain poorly understood. One hypothesis is that variation in genomic regions flanking master regulatory genes, also known as input-output genes, controls variation in trait number, making the locus of evolution almost predictable. Another hypothesis implicates genetic variation in up- or downstream loci of master control genes. Here, we use the butterfly Bicyclus anynana, a species that exhibits natural variation in eyespot number on the dorsal hindwing, to test these two hypotheses. We first estimated the heritability of dorsal hindwing eyespot number by breeding multiple butterfly families differing in eyespot number and regressing eyespot numbers of offspring on midparent values. We then estimated the number and identity of independent genetic loci contributing to eyespot number variation by performing a genome-wide association study with restriction site-associated DNA sequencing from multiple individuals varying in number of eyespots sampled across a freely breeding laboratory population. We found that dorsal hindwing eyespot number has a moderately high heritability of ∼0.50 and is characterized by a polygenic architecture. Previously identified genomic regions involved in eyespot development, and novel ones, display high association with dorsal hindwing eyespot number, suggesting that homolog number variation is likely determined by regulatory changes at multiple loci that build the trait, and not by variation at single master regulators or input-output genes.
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Affiliation(s)
- Angel G Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois, Urbana-Champaign, Illinois 61801
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, 00925, Puerto Rico
| | - Erica L Westerman
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701
| | - Steven M Van Belleghem
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, 00925, Puerto Rico
| | - Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore 117543
- Yale-NUS College, Singapore 138609
| | - Riccardo Papa
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, 00925, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan, 00926, Puerto Rico
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20
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Pelassa I, Cibelli M, Villeri V, Lilliu E, Vaglietti S, Olocco F, Ghirardi M, Montarolo PG, Corà D, Fiumara F. Compound Dynamics and Combinatorial Patterns of Amino Acid Repeats Encode a System of Evolutionary and Developmental Markers. Genome Biol Evol 2020; 11:3159-3178. [PMID: 31589292 PMCID: PMC6839033 DOI: 10.1093/gbe/evz216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2019] [Indexed: 01/05/2023] Open
Abstract
Homopolymeric amino acid repeats (AARs) like polyalanine (polyA) and polyglutamine (polyQ) in some developmental proteins (DPs) regulate certain aspects of organismal morphology and behavior, suggesting an evolutionary role for AARs as developmental "tuning knobs." It is still unclear, however, whether these are occasional protein-specific phenomena or hints at the existence of a whole AAR-based regulatory system in DPs. Using novel approaches to trace their functional and evolutionary history, we find quantitative evidence supporting a generalized, combinatorial role of AARs in developmental processes with evolutionary implications. We observe nonrandom AAR distributions and combinations in HOX and other DPs, as well as in their interactomes, defining elements of a proteome-wide combinatorial functional code whereby different AARs and their combinations appear preferentially in proteins involved in the development of specific organs/systems. Such functional associations can be either static or display detectable evolutionary dynamics. These findings suggest that progressive changes in AAR occurrence/combination, by altering embryonic development, may have contributed to taxonomic divergence, leaving detectable traces in the evolutionary history of proteomes. Consistent with this hypothesis, we find that the evolutionary trajectories of the 20 AARs in eukaryotic proteomes are highly interrelated and their individual or compound dynamics can sharply mark taxonomic boundaries, or display clock-like trends, carrying overall a strong phylogenetic signal. These findings provide quantitative evidence and an interpretive framework outlining a combinatorial system of AARs whose compound dynamics mark at the same time DP functions and evolutionary transitions.
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Affiliation(s)
- Ilaria Pelassa
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Italy
| | - Marica Cibelli
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Italy
| | - Veronica Villeri
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Italy
| | - Elena Lilliu
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Italy
| | - Serena Vaglietti
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Italy
| | - Federica Olocco
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Italy
| | - Mirella Ghirardi
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Italy.,National Institute of Neuroscience (INN), Torino, Italy
| | - Pier Giorgio Montarolo
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Italy.,National Institute of Neuroscience (INN), Torino, Italy
| | - Davide Corà
- Department of Translational Medicine, Piemonte Orientale University, Novara, Italy.,Center for Translational Research on Autoimmune and Allergic Disease (CAAD), Novara, Italy
| | - Ferdinando Fiumara
- Department of Neuroscience Rita Levi Montalcini, University of Torino, Italy.,National Institute of Neuroscience (INN), Torino, Italy
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21
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Kavouras M, Malandrakis EE, Danis T, Blom E, Anastassiadis K, Panagiotaki P, Exadactylos A. Hox Genes Polymorphism Depicts Developmental Disruption of Common Sole Eggs. Open Life Sci 2019; 14:549-563. [PMID: 33817191 PMCID: PMC7874752 DOI: 10.1515/biol-2019-0061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 11/22/2019] [Indexed: 12/31/2022] Open
Abstract
In sole aquaculture production, consistency in the quality of produced eggs throughout the year is unpredictable. Hox genes have a crucial role in controlling embryonic development and their genetic variation could alter the phenotype dramatically. In teleosts genome duplication led paralog hox genes to become diverged. Direct association of polymorphism in hoxa1a, hoxa2a & hoxa2b of Solea solea with egg viability indicates hoxa2b as a potential genetic marker. High Resolution Melt (HRM) analysis was carried out in 52 viable and 61 non-viable eggs collected at 54±6 hours post fertilization (hpf). Allelic and genotypic frequencies of polymorphism were analyzed and results illustrated a significantly increased risk for non-viability for minor alleles and their homozygous genotypes. Haplotype analysis demonstrated a significant recessive effect on the risk of non-viability, by increasing the odds of disrupting embryonic development up to three-fold. Phylogenetic analysis showed that the paralog genes hoxa2a and hoxa2b, are separated distinctly in two clades and presented a significant ω variation, revealing their diverged evolutionary rate.
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Affiliation(s)
| | - Emmanouil E. Malandrakis
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Fytokou str, Volos, Greece
| | - Theodoros Danis
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Fytokou str, Volos, Greece
| | - Ewout Blom
- Wageningen Marine Research, Wageningen University & Research, IJmuiden, The Netherlands
| | | | - Panagiota Panagiotaki
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Fytokou str, Volos, Greece
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22
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Primon M, Hunter KD, Pandha HS, Morgan R. Kinase Regulation of HOX Transcription Factors. Cancers (Basel) 2019; 11:cancers11040508. [PMID: 30974835 PMCID: PMC6521248 DOI: 10.3390/cancers11040508] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/02/2019] [Accepted: 04/07/2019] [Indexed: 01/03/2023] Open
Abstract
The HOX genes are a group of homeodomain-containing transcription factors that play important regulatory roles in early development, including the establishment of cell and tissue identity. HOX expression is generally reduced in adult cells but is frequently re-established as an early event in tumour formation and supports an oncogenic phenotype. HOX transcription factors are also involved in cell cycle regulation and DNA repair, along with normal adult physiological process including stem cell renewal. There have been extensive studies on the mechanism by which HOX proteins regulate transcription, with particular emphasis on their interaction with cofactors such as Pre-B-cell Leukaemia Homeobox (PBX) and Myeloid Ecotropic Viral Integration Site 1 (MEIS). However, significantly less is known of how the activity of HOX proteins is regulated. There is growing evidence that phosphorylation may play an important role in this context, and in this review, we draw together a number of important studies published over the last 20 years, and discuss the relevance of phosphorylation in the regulation and function of HOX proteins in development, evolution, cell cycle regulation, and cancer.
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Affiliation(s)
- Monika Primon
- Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, Bradford BD7 1DP, UK.
| | - Keith D Hunter
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, University of Sheffield, Sheffield S10 2TN, UK.
| | - Hardev S Pandha
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
| | - Richard Morgan
- Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, Bradford BD7 1DP, UK.
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23
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Redundant and Cryptic Enhancer Activities of the Drosophila yellow Gene. Genetics 2019; 212:343-360. [PMID: 30842209 DOI: 10.1534/genetics.119.301985] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 02/25/2019] [Indexed: 11/18/2022] Open
Abstract
Cis-regulatory sequences known as enhancers play a key role in regulating gene expression. Evolutionary changes in these DNA sequences contribute to phenotypic evolution. The Drosophila yellow gene, which is required for pigmentation, has emerged as a model system for understanding how cis-regulatory sequences evolve, providing some of the most detailed insights available into how activities of orthologous enhancers have diverged between species. Here, we examine the evolution of yellow cis-regulatory sequences on a broader scale, by comparing the distribution and function of yellow enhancer activities throughout the 5' intergenic and intronic sequences of Drosophila melanogaster, D. pseudoobscura, and D. willistoni We find that cis-regulatory sequences driving expression in a particular tissue are not as modular as previously described, but rather have many redundant and cryptic enhancer activities distributed throughout the regions surveyed. Interestingly, cryptic enhancer activities of sequences from one species often drove patterns of expression observed in other species, suggesting that the frequent evolutionary changes in yellow expression observed among Drosophila species may be facilitated by gaining and losing repression of preexisting cis-regulatory sequences.
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24
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RepEx: A web server to extract sequence repeats from protein and DNA sequences. Comput Biol Chem 2018; 78:424-430. [PMID: 30598392 DOI: 10.1016/j.compbiolchem.2018.12.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 12/25/2018] [Indexed: 11/20/2022]
Abstract
Evolution builds up new genetic material from existing ones, not in random, but in highly ordered and eloquent patterns. Most of these sequence repeats are revelatory of valuable information contributing to areas of disease research and function of macromolecules, to name a few. In the age of next generation genome sequencing, rapid and efficient extraction of all unbiased sequence repeats from macromolecules is the need of the hour. In view of this reckoning, an online web-based computing server, RepEx, has been developed to extract and display all possible repeats for DNA and protein sequences. Apart from exact or identical repeats, the server has been designed adeptly to identify and extract degenerate, inverted, everted and mirror repeats from both DNA and protein sequences. The server has striking output displays, featuring interactive graphs and comprehensive output files. In addition, RepEx has been accoutered with an easy-to-use interface and search filters to facilitate a user-defined query or search and is freely available and accessible via the World Wide Web at http://bioserver2.physics.iisc.ac.in/RepEx/.
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25
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Mikhaleva Y, Skinnes R, Sumic S, Thompson EM, Chourrout D. Development of the house secreting epithelium, a major innovation of tunicate larvaceans, involves multiple homeodomain transcription factors. Dev Biol 2018; 443:117-126. [DOI: 10.1016/j.ydbio.2018.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 07/27/2018] [Accepted: 09/05/2018] [Indexed: 01/24/2023]
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26
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Qiu J, Wang W, Hu S, Wang Y, Sun W, Hu J, Gan X, Wang J. Molecular cloning, characterization and expression analysis of C/EBP α, β and δ in adipose-related tissues and adipocyte of duck ( Anas platyrhynchos ). Comp Biochem Physiol B Biochem Mol Biol 2018; 221-222:29-43. [DOI: 10.1016/j.cbpb.2018.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 04/14/2018] [Accepted: 04/16/2018] [Indexed: 12/17/2022]
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27
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Al Khatib A, Siomava N, Iannini A, Posnien N, Casares F. Specific expression and function of the Six3 optix in Drosophila serially homologous organs. Biol Open 2017. [PMID: 28642242 PMCID: PMC5576073 DOI: 10.1242/bio.023606] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Organ size and pattern results from the integration of two positional information systems. One global information system, encoded by the Hox genes, links organ type with position along the main body axis. Within specific organs, local information is conveyed by signaling molecules that regulate organ growth and pattern. The mesothoracic (T2) wing and the metathoracic (T3) haltere of Drosophila represent a paradigmatic example of this coordination. The Hox gene Ultrabithorax (Ubx), expressed in the developing T3, selects haltere identity by, among other processes, modulating the production and signaling efficiency of Dpp, a BMP2-like molecule that acts as a major regulator of size and pattern. However, the mechanisms of the Hox-signal integration in this well-studied system are incomplete. Here, we have investigated this issue by studying the expression and function of the Six3 transcription factor optix during Drosophila wing and haltere development. We find that in both organs, Dpp defines the expression domain of optix through repression, and that the specific position of this domain in wing and haltere seems to reflect the differential signaling profile among these organs. We show that optix expression in wing and haltere primordia is conserved beyond Drosophila in other higher diptera. In Drosophila, optix is necessary for the growth of wing and haltere. In the wing, optix is required for the growth of the most anterior/proximal region (the ‘marginal cell’) and for the correct formation of sensory structures along the proximal anterior wing margin; the halteres of optix mutants are also significantly reduced. In addition, in the haltere, optix is necessary for the suppression of sensory bristles. Summary: The position of the Six3 optix is regulated by the Dpp pathway during wing and haltere development, and controls the size of both serially homologous organs.
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Affiliation(s)
- Amer Al Khatib
- Department of Gene Regulation and Morphogenesis, Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo de Olavide University-JA, 41013 Seville, Spain.,Department of Biology, University of Florence, I-50019, Florence, Italy
| | - Natalia Siomava
- Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Goettingen Center for Molecular Biosciences (GZMB), Department of Developmental Biology, University of Goettingen, 37077 Goettingen, Germany
| | - Antonella Iannini
- Department of Gene Regulation and Morphogenesis, Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo de Olavide University-JA, 41013 Seville, Spain
| | - Nico Posnien
- Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Goettingen Center for Molecular Biosciences (GZMB), Department of Developmental Biology, University of Goettingen, 37077 Goettingen, Germany
| | - Fernando Casares
- Department of Gene Regulation and Morphogenesis, Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo de Olavide University-JA, 41013 Seville, Spain
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28
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Constraints and consequences of the emergence of amino acid repeats in eukaryotic proteins. Nat Struct Mol Biol 2017; 24:765-777. [PMID: 28805808 DOI: 10.1038/nsmb.3441] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/23/2017] [Indexed: 12/21/2022]
Abstract
Proteins with amino acid homorepeats have the potential to be detrimental to cells and are often associated with human diseases. Why, then, are homorepeats prevalent in eukaryotic proteomes? In yeast, homorepeats are enriched in proteins that are essential and pleiotropic and that buffer environmental insults. The presence of homorepeats increases the functional versatility of proteins by mediating protein interactions and facilitating spatial organization in a repeat-dependent manner. During evolution, homorepeats are preferentially retained in proteins with stringent proteostasis, which might minimize repeat-associated detrimental effects such as unregulated phase separation and protein aggregation. Their presence facilitates rapid protein divergence through accumulation of amino acid substitutions, which often affect linear motifs and post-translational-modification sites. These substitutions may result in rewiring protein interaction and signaling networks. Thus, homorepeats are distinct modules that are often retained in stringently regulated proteins. Their presence facilitates rapid exploration of the genotype-phenotype landscape of a population, thereby contributing to adaptation and fitness.
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29
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Ritzman TB, Banovich N, Buss KP, Guida J, Rubel MA, Pinney J, Khang B, Ravosa MJ, Stone AC. Facing the facts: The Runx2 gene is associated with variation in facial morphology in primates. J Hum Evol 2017; 111:139-151. [PMID: 28874267 DOI: 10.1016/j.jhevol.2017.06.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 06/22/2017] [Accepted: 06/28/2017] [Indexed: 12/31/2022]
Abstract
The phylogenetic and adaptive factors that cause variation in primate facial form-including differences among the major primate clades and variation related to feeding and/or social behavior-are relatively well understood. However, comparatively little is known about the genetic mechanisms that underlie diversity in facial form in primates. Because it is essential for osteoblastic differentiation and skeletal development, the runt-related transcription factor 2 (Runx2) is one gene that may play a role in these genetic mechanisms. Specifically, polymorphisms in the QA ratio (determined by the ratio of the number of polyglutamines to polyalanines in one functional domain of Runx2) have been shown to be correlated with variation in facial length and orientation in other mammal groups. However, to date, the relationship between variation in this gene and variation in facial form in primates has not been explicitly tested. To test the hypothesis that the QA ratio is correlated with facial form in primates, the current study quantified the QA ratio, facial length, and facial angle in a sample of 33 primate species and tested for correlation using phylogenetic generalized least squares. The results indicate that the QA ratio of the Runx2 gene is positively correlated with variation in relative facial length in anthropoid primates. However, no correlation was found in strepsirrhines, and there was no correlation between facial angle and the QA ratio in any groups. These results suggest that, in primates, the QA ratio of the Runx2 gene may play a role in modulating facial size, but not facial orientation. This study therefore provides important clues about the genetic and developmental mechanisms that may underlie variation in facial form in primates.
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Affiliation(s)
- Terrence B Ritzman
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA; Department of Archaeology, University of Cape Town, Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, Cape Town, South Africa; School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.
| | - Nicholas Banovich
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA; Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Kaitlin P Buss
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Jennifer Guida
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA; School of Public Health, University of Maryland, College Park, MD, USA
| | - Meagan A Rubel
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer Pinney
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Bao Khang
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Matthew J Ravosa
- Department of Biological Sciences, University of Notre Dame, South Bend, IN, USA; Department of Aerospace and Mechanical Engineering, University of Notre Dame, South Bend, IN, USA; Department of Anthropology, University of Notre Dame, South Bend, IN, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA; Center for Bioarchaeological Research, ASU, Tempe, AZ, USA; Institute of Human Origins, ASU, Tempe, AZ, USA
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30
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Ortiz-Lombardia M, Foos N, Maurel-Zaffran C, Saurin AJ, Graba Y. Hox functional diversity: Novel insights from flexible motif folding and plastic protein interaction. Bioessays 2017; 39. [PMID: 28092121 DOI: 10.1002/bies.201600246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
How the formidable diversity of forms emerges from developmental and evolutionary processes is one of the most fascinating questions in biology. The homeodomain-containing Hox proteins were recognized early on as major actors in diversifying animal body plans. The molecular mechanisms underlying how this transcription factor family controls a large array of context- and cell-specific biological functions is, however, still poorly understood. Clues to functional diversity have emerged from studies exploring how Hox protein activity is controlled through interactions with PBC class proteins, also evolutionary conserved HD-containing proteins. Recent structural data and molecular dynamic simulations add further mechanistic insights into Hox protein mode of action, suggesting that flexible folding of protein motifs allows for plastic protein interaction. As we discuss in this review, these findings define a novel type of Hox-PBC interaction, weak and dynamic instead of strong and static, hence providing novel clues to understanding Hox transcriptional specificity and diversity.
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Affiliation(s)
- Miguel Ortiz-Lombardia
- Aix-Marseille-Université, CNRS UMR 7257, AFMB, Marseille, France.,Aix-Marseille-Université, CNRS UMR 7256, AFMB, Marseille, France
| | - Nicolas Foos
- Aix-Marseille-Université, CNRS UMR 7257, AFMB, Marseille, France
| | | | - Andrew J Saurin
- Aix-Marseille-Université, CNRS UMR 7288, case 907, IBDM, Marseille, France
| | - Yacine Graba
- Aix-Marseille-Université, CNRS UMR 7288, case 907, IBDM, Marseille, France
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31
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The genome of the Gulf pipefish enables understanding of evolutionary innovations. Genome Biol 2016; 17:258. [PMID: 27993155 PMCID: PMC5168715 DOI: 10.1186/s13059-016-1126-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 12/05/2016] [Indexed: 11/10/2022] Open
Abstract
Background Evolutionary origins of derived morphologies ultimately stem from changes in protein structure, gene regulation, and gene content. A well-assembled, annotated reference genome is a central resource for pursuing these molecular phenomena underlying phenotypic evolution. We explored the genome of the Gulf pipefish (Syngnathus scovelli), which belongs to family Syngnathidae (pipefishes, seahorses, and seadragons). These fishes have dramatically derived bodies and a remarkable novelty among vertebrates, the male brood pouch. Results We produce a reference genome, condensed into chromosomes, for the Gulf pipefish. Gene losses and other changes have occurred in pipefish hox and dlx clusters and in the tbx and pitx gene families, candidate mechanisms for the evolution of syngnathid traits, including an elongated axis and the loss of ribs, pelvic fins, and teeth. We measure gene expression changes in pregnant versus non-pregnant brood pouch tissue and characterize the genomic organization of duplicated metalloprotease genes (patristacins) recruited into the function of this novel structure. Phylogenetic inference using ultraconserved sequences provides an alternative hypothesis for the relationship between orders Syngnathiformes and Scombriformes. Comparisons of chromosome structure among percomorphs show that chromosome number in a pipefish ancestor became reduced via chromosomal fusions. Conclusions The collected findings from this first syngnathid reference genome open a window into the genomic underpinnings of highly derived morphologies, demonstrating that de novo production of high quality and useful reference genomes is within reach of even small research groups. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1126-6) contains supplementary material, which is available to authorized users.
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32
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Single Amino Acid Repeats in the Proteome World: Structural, Functional, and Evolutionary Insights. PLoS One 2016; 11:e0166854. [PMID: 27893794 PMCID: PMC5125637 DOI: 10.1371/journal.pone.0166854] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 11/05/2016] [Indexed: 12/15/2022] Open
Abstract
Microsatellites or simple sequence repeats (SSR) are abundant, highly diverse stretches of short DNA repeats present in all genomes. Tandem mono/tri/hexanucleotide repeats in the coding regions contribute to single amino acids repeats (SAARs) in the proteome. While SSRs in the coding region always result in amino acid repeats, a majority of SAARs arise due to a combination of various codons representing the same amino acid and not as a consequence of SSR events. Certain amino acids are abundant in repeat regions indicating a positive selection pressure behind the accumulation of SAARs. By analysing 22 proteomes including the human proteome, we explored the functional and structural relationship of amino acid repeats in an evolutionary context. Only ~15% of repeats are present in any known functional domain, while ~74% of repeats are present in the disordered regions, suggesting that SAARs add to the functionality of proteins by providing flexibility, stability and act as linker elements between domains. Comparison of SAAR containing proteins across species reveals that while shorter repeats are conserved among orthologs, proteins with longer repeats, >15 amino acids, are unique to the respective organism. Lysine repeats are well conserved among orthologs with respect to their length and number of occurrences in a protein. Other amino acids such as glutamic acid, proline, serine and alanine repeats are generally conserved among the orthologs with varying repeat lengths. These findings suggest that SAARs have accumulated in the proteome under positive selection pressure and that they provide flexibility for optimal folding of functional/structural domains of proteins. The insights gained from our observations can help in effective designing and engineering of proteins with novel features.
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33
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Percival-Smith A. Non-specificity of transcription factor function in Drosophila melanogaster. Dev Genes Evol 2016; 227:25-39. [PMID: 27848019 DOI: 10.1007/s00427-016-0566-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 11/03/2016] [Indexed: 10/20/2022]
Abstract
A major problem in developmental genetics is how HOX transcription factors, like Proboscipedia (PB) and Ultrabithorax (UBX), regulate distinct programs of gene expression to result in a proboscis versus a haltere, respectively, when the DNA-binding homeodomain (HD) of HOX transcription factors recognizes similar DNA-binding sequences. Indeed, the lack of DNA-binding specificity is a problem for all transcription factors (TFs), as the DNA-binding domains generally recognize small targets of five to six bases in length. Although not the initial intent of the study, I found extensive non-specificity of TF function. Multiple TFs including HOX and HD-containing and non-HD-containing TFs induced both wingless and eyeless phenotypes. The TFs Labial (LAB), Deformed (DFD), Fushi tarazu (FTZ), and Squeeze (SQZ) induced ectopic larval thoracic (T) 1 beard formation in T2 and T3. The TF Doublesex male (DSXM) rescued the reduced maxillary palp pb phenotype. These examples of non-specificity of TF function across classes of TFs, combined with previous observations, compromise the implicit, initial assumption often made that an intrinsic mechanism of TF specificity is important for function. Interestingly, the functional complementation of the pb phenotype may suggest a larger role for regulation of expression of TFs in restriction of function as opposed to an intrinsic specificity of TF function. These observations have major ramifications for analysis of functional conservation in evolution and development.
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34
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Karaz S, Courgeon M, Lepetit H, Bruno E, Pannone R, Tarallo A, Thouzé F, Kerner P, Vervoort M, Causeret F, Pierani A, D'Onofrio G. Neuronal fate specification by the Dbx1 transcription factor is linked to the evolutionary acquisition of a novel functional domain. EvoDevo 2016; 7:18. [PMID: 27525057 PMCID: PMC4983035 DOI: 10.1186/s13227-016-0055-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/27/2016] [Indexed: 12/18/2022] Open
Abstract
Background Dbx1 is a homeodomain transcription factor involved in neuronal fate specification belonging to a widely conserved family among bilaterians. In mammals, Dbx1 was proposed to act as a transcriptional repressor by interacting with the Groucho corepressors to allow the specification of neurons involved in essential biological functions such as locomotion or breathing. Results Sequence alignments of Dbx1 proteins from different species allowed us to identify two conserved domains related to the Groucho-dependent Engrailed repressor domain (RD), as well as a newly described domain composed of clusterized acidic residues at the C-terminus (Cter) which is present in tetrapods but also several invertebrates. Using a heterologous luciferase assay, we showed that the two putative repressor domains behave as such in a Groucho-dependent manner, whereas the Cter does not bear any intrinsic transcriptional activity. Consistently with in vitro data, we found that both RDs are involved in cell fate specification using in vivo electroporation experiments in the chick spinal cord. Surprisingly, we show that the Cter domain is required for Dbx1 function in vivo, acting as a modulator of its repressive activity and/or imparting specificity. Conclusion Our results strongly suggest that the presence of a Cter domain among tetrapods is essential for Dbx1 to regulate neuronal diversity and, in turn, nervous system complexity. Electronic supplementary material The online version of this article (doi:10.1186/s13227-016-0055-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sonia Karaz
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Maximilien Courgeon
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Hélène Lepetit
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Eugenia Bruno
- Dept. BEOM, Stazione Zoologica A. Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Raimondo Pannone
- Dept. BEOM, Stazione Zoologica A. Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Andrea Tarallo
- Dept. BEOM, Stazione Zoologica A. Dohrn, Villa Comunale, 80121 Naples, Italy
| | - France Thouzé
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Pierre Kerner
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Michel Vervoort
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Frédéric Causeret
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Alessandra Pierani
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Giuseppe D'Onofrio
- Dept. BEOM, Stazione Zoologica A. Dohrn, Villa Comunale, 80121 Naples, Italy
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Shimada MK, Sanbonmatsu R, Yamaguchi-Kabata Y, Yamasaki C, Suzuki Y, Chakraborty R, Gojobori T, Imanishi T. Selection pressure on human STR loci and its relevance in repeat expansion disease. Mol Genet Genomics 2016; 291:1851-69. [PMID: 27290643 DOI: 10.1007/s00438-016-1219-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 05/21/2016] [Indexed: 12/30/2022]
Abstract
Short Tandem Repeats (STRs) comprise repeats of one to several base pairs. Because of the high mutability due to strand slippage during DNA synthesis, rapid evolutionary change in the number of repeating units directly shapes the range of repeat-number variation according to selection pressure. However, the remaining questions include: Why are STRs causing repeat expansion diseases maintained in the human population; and why are these limited to neurodegenerative diseases? By evaluating the genome-wide selection pressure on STRs using the database we constructed, we identified two different patterns of relationship in repeat-number polymorphisms between DNA and amino-acid sequences, although both patterns are evolutionary consequences of avoiding the formation of harmful long STRs. First, a mixture of degenerate codons is represented in poly-proline (poly-P) repeats. Second, long poly-glutamine (poly-Q) repeats are favored at the protein level; however, at the DNA level, STRs encoding long poly-Qs are frequently divided by synonymous SNPs. Furthermore, significant enrichments of apoptosis and neurodevelopment were biological processes found specifically in genes encoding poly-Qs with repeat polymorphism. This suggests the existence of a specific molecular function for polymorphic and/or long poly-Q stretches. Given that the poly-Qs causing expansion diseases were longer than other poly-Qs, even in healthy subjects, our results indicate that the evolutionary benefits of long and/or polymorphic poly-Q stretches outweigh the risks of long CAG repeats predisposing to pathological hyper-expansions. Molecular pathways in neurodevelopment requiring long and polymorphic poly-Q stretches may provide a clue to understanding why poly-Q expansion diseases are limited to neurodegenerative diseases.
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Affiliation(s)
- Makoto K Shimada
- Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan. .,National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi Koto-ku, Tokyo, 135-0064, Japan. .,Japan Biological Informatics Consortium, 10F TIME24 Building, 2-4-32 Aomi, Koto-ku, Tokyo, 135-8073, Japan.
| | - Ryoko Sanbonmatsu
- Japan Biological Informatics Consortium, 10F TIME24 Building, 2-4-32 Aomi, Koto-ku, Tokyo, 135-8073, Japan
| | - Yumi Yamaguchi-Kabata
- National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi Koto-ku, Tokyo, 135-0064, Japan.,Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
| | - Chisato Yamasaki
- National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi Koto-ku, Tokyo, 135-0064, Japan.,Japan Biological Informatics Consortium, 10F TIME24 Building, 2-4-32 Aomi, Koto-ku, Tokyo, 135-8073, Japan
| | - Yoshiyuki Suzuki
- Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya, Aichi, 467-8501, Japan
| | - Ranajit Chakraborty
- Health Science Center, University of North Texas, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA
| | - Takashi Gojobori
- National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi Koto-ku, Tokyo, 135-0064, Japan.,Computational Bioscience Research Center, King Abdullah University of Science and Technology, Ibn Al-Haytham Building (West), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Tadashi Imanishi
- National Institute of Advanced Industrial Science and Technology, 2-3-26 Aomi Koto-ku, Tokyo, 135-0064, Japan.,Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
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36
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A Derived Allosteric Switch Underlies the Evolution of Conditional Cooperativity between HOXA11 and FOXO1. Cell Rep 2016; 15:2097-2108. [DOI: 10.1016/j.celrep.2016.04.088] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 02/23/2016] [Accepted: 04/26/2016] [Indexed: 12/11/2022] Open
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37
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Takiya S, Tsubota T, Kimoto M. Regulation of Silk Genes by Hox and Homeodomain Proteins in the Terminal Differentiated Silk Gland of the Silkworm Bombyx mori. J Dev Biol 2016; 4:E19. [PMID: 29615585 PMCID: PMC5831788 DOI: 10.3390/jdb4020019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/08/2016] [Accepted: 05/17/2016] [Indexed: 12/15/2022] Open
Abstract
The silk gland of the silkworm Bombyx mori is a long tubular organ that is divided into several subparts along its anteroposterior (AP) axis. As a trait of terminal differentiation of the silk gland, several silk protein genes are expressed with unique regional specificities. Most of the Hox and some of the homeobox genes are also expressed in the differentiated silk gland with regional specificities. The expression patterns of Hox genes in the silk gland roughly correspond to those in embryogenesis showing "colinearity". The central Hox class protein Antennapedia (Antp) directly regulates the expression of several middle silk gland-specific silk genes, whereas the Lin-1/Isl-1/Mec3 (LIM)-homeodomain transcriptional factor Arrowhead (Awh) regulates the expression of posterior silk gland-specific genes for silk fiber proteins. We summarize our results and discuss the usefulness of the silk gland of Bombyx mori for analyzing the function of Hox genes. Further analyses of the regulatory mechanisms underlying the region-specific expression of silk genes will provide novel insights into the molecular bases for target-gene selection and regulation by Hox and homeodomain proteins.
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Affiliation(s)
- Shigeharu Takiya
- Shigeharu Takiya, Division of Biological Sciences and Center for Genome Dynamics, Faculty of Science, Hokkaido University, North 10, West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.
- Graduate School of Life Science, Hokkaido University, North 10, West 8, Kita-ku, Sapporo 060-0810, Japan.
| | - Takuya Tsubota
- Transgenic Silkworm Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan.
| | - Mai Kimoto
- Graduate School of Life Science, Hokkaido University, North 10, West 8, Kita-ku, Sapporo 060-0810, Japan.
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38
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Rezsohazy R, Saurin AJ, Maurel-Zaffran C, Graba Y. Cellular and molecular insights into Hox protein action. Development 2016; 142:1212-27. [PMID: 25804734 DOI: 10.1242/dev.109785] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hox genes encode homeodomain transcription factors that control morphogenesis and have established functions in development and evolution. Hox proteins have remained enigmatic with regard to the molecular mechanisms that endow them with specific and diverse functions, and to the cellular functions that they control. Here, we review recent examples of Hox-controlled cellular functions that highlight their versatile and highly context-dependent activity. This provides the setting to discuss how Hox proteins control morphogenesis and organogenesis. We then summarise the molecular modalities underlying Hox protein function, in particular in light of current models of transcription factor function. Finally, we discuss how functional divergence between Hox proteins might be achieved to give rise to the many facets of their action.
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Affiliation(s)
- René Rezsohazy
- Institut des Sciences de la Vie, Université Catholique de Louvain, Louvain-la-Neuve B-1348, Belgium
| | - Andrew J Saurin
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille 13288, Cedex 09, France
| | | | - Yacine Graba
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille 13288, Cedex 09, France
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39
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Wu R, Liu Q, Zhang P, Liang D. Tandem amino acid repeats in the green anole (Anolis carolinensis) and other squamates may have a role in increasing genetic variability. BMC Genomics 2016; 17:109. [PMID: 26868501 PMCID: PMC4751654 DOI: 10.1186/s12864-016-2430-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 02/02/2016] [Indexed: 01/04/2023] Open
Abstract
Background Tandem amino acid repeats are characterised by the consecutive recurrence of a single amino acid. They exhibit high rates of length mutations in addition to point mutations and have been proposed to be involved in genetic plasticity. Squamate reptiles (lizards and snakes) diversify in both morphology and physiology. The underlying mechanism is yet to be understood. In a previous phylogenomic analysis of reptiles, the density of tandem repeats in an anole lizard diverged heavily from that of the other reptiles. To gain further insight into the tandem amino acid repeats in squamates, we analysed the repeat content in the green anole (Anolis carolinensis) proteome and compared the amino acid repeats in a large orthologous protein data set from six vertebrates (the Western clawed frog, the green anole, the Chinese softshell turtle, the zebra finch, mouse and human). Results Our results revealed that the number of amino acid repeats in the green anole exceeded those found in the other five species studied. Species-only repeats were found in high proportion in the green anole but not in the other five species, suggesting that the green anole had gained many amino acid repeats in either the Anolis or the squamate lineage. Since the amino acid repeat containing genes in the green anole were highly enriched in genes related to transcription and development, an important family of developmental genes, i.e., the Hox family, was further studied in a wide collection of squamates. Abundant amino acid repeats were also observed, implying the general high tolerance of amino acid repeats in squamates. A particular enrichment of amino acid repeats was observed in the central class Hox genes that are known to be responsible for defining cervical to lumbar regions. Conclusions Our study suggests that the abundant amino acid repeats in the green anole, and possibly in other squamates, may play a role in increasing the genetic variability, and contribute to the evolutionary diversity of this clade. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2430-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Riga Wu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.
| | - Qingfeng Liu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.
| | - Peng Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.
| | - Dan Liang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.
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40
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Londe S, Monnin T, Cornette R, Debat V, Fisher BL, Molet M. Phenotypic plasticity and modularity allow for the production of novel mosaic phenotypes in ants. EvoDevo 2015; 6:36. [PMID: 26629324 PMCID: PMC4666092 DOI: 10.1186/s13227-015-0031-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 11/12/2015] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The origin of discrete novelties remains unclear. Some authors suggest that qualitative phenotypic changes may result from the reorganization of preexisting phenotypic traits during development (i.e., developmental recombination) following genetic or environmental changes. Because ants combine high modularity with extreme phenotypic plasticity (queen and worker castes), their diversified castes could have evolved by developmental recombination. We performed a quantitative morphometric study to investigate the developmental origins of novel phenotypes in the ant Mystrium rogeri, which occasionally produces anomalous 'intercastes.' Our analysis compared the variation of six morphological modules with body size using a large sample of intercastes. RESULTS We confirmed that intercastes are conspicuous mosaics that recombine queen and worker modules. In addition, we found that many other individuals traditionally classified as workers or queens also exhibit some level of mosaicism. The six modules had distinct profiles of variation suggesting that each module responds differentially to factors that control body size and polyphenism. Mosaicism appears to result from each module responding differently yet in an ordered and predictable manner to intermediate levels of inducing factors that control polyphenism. The order of module response determines which mosaic combinations are produced. CONCLUSIONS Because the frequency of mosaics and their canalization around a particular phenotype may evolve by selection on standing genetic variation that affects the plastic response (i.e., genetic accommodation), developmental recombination is likely to play an important role in the evolution of novel castes in ants. Indeed, we found that most mosaics have queen-like head and gaster but a worker-like thorax congruent with the morphology of ergatoid queens and soldiers, respectively. Ergatoid queens of M. oberthueri, a sister species of M. rogeri, could have evolved from intercastes produced ancestrally through such a process.
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Affiliation(s)
- Sylvain Londe
- />UMR 7618 Institute of Ecology and Environmental Sciences of Paris, Sorbonne Universités, UPMC Univ Paris 06, 7 quai St Bernard, 75 252 Paris, France
| | - Thibaud Monnin
- />UMR 7618 Institute of Ecology and Environmental Sciences of Paris, Sorbonne Universités, UPMC Univ Paris 06, 7 quai St Bernard, 75 252 Paris, France
| | - Raphaël Cornette
- />Département Systématique et Évolution, Muséum National d’Histoire Naturelle; CNRS UMR 7205, Institut de Systématique, Evolution, Biodiversité, Paris, France
| | - Vincent Debat
- />Département Systématique et Évolution, Muséum National d’Histoire Naturelle; CNRS UMR 7205, Institut de Systématique, Evolution, Biodiversité, Paris, France
| | - Brian L. Fisher
- />Department of Entomology, California Academy of Sciences, Golden Gate Park, 55 Music Concourse Drive, San Francisco, CA 94118 USA
| | - Mathieu Molet
- />UMR 7618 Institute of Ecology and Environmental Sciences of Paris, Sorbonne Universités, UPMC Univ Paris 06, 7 quai St Bernard, 75 252 Paris, France
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41
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Pick L. Hox genes, evo-devo, and the case of the ftz gene. Chromosoma 2015; 125:535-51. [PMID: 26596987 DOI: 10.1007/s00412-015-0553-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/11/2015] [Accepted: 10/15/2015] [Indexed: 12/29/2022]
Abstract
The discovery of the broad conservation of embryonic regulatory genes across animal phyla, launched by the cloning of homeotic genes in the 1980s, was a founding event in the field of evolutionary developmental biology (evo-devo). While it had long been known that fundamental cellular processes, commonly referred to as housekeeping functions, are shared by animals and plants across the planet-processes such as the storage of information in genomic DNA, transcription, translation and the machinery for these processes, universal codon usage, and metabolic enzymes-Hox genes were different: mutations in these genes caused "bizarre" homeotic transformations of insect body parts that were certainly interesting but were expected to be idiosyncratic. The isolation of the genes responsible for these bizarre phenotypes turned out to be highly conserved Hox genes that play roles in embryonic patterning throughout Metazoa. How Hox genes have changed to promote the development of diverse body plans remains a central issue of the field of evo-devo today. For this Memorial article series, I review events around the discovery of the broad evolutionary conservation of Hox genes and the impact of this discovery on the field of developmental biology. I highlight studies carried out in Walter Gehring's lab and by former lab members that have continued to push the field forward, raising new questions and forging new approaches to understand the evolution of developmental mechanisms.
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Affiliation(s)
- Leslie Pick
- Department of Entomology and Program in Molecular and Cell Biology, University of Maryland, College Park, MD, 20742, USA.
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42
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Stampfel G, Kazmar T, Frank O, Wienerroither S, Reiter F, Stark A. Transcriptional regulators form diverse groups with context-dependent regulatory functions. Nature 2015; 528:147-51. [PMID: 26550828 DOI: 10.1038/nature15545] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 09/02/2015] [Indexed: 12/25/2022]
Abstract
One of the most important questions in biology is how transcription factors (TFs) and cofactors control enhancer function and thus gene expression. Enhancer activation usually requires combinations of several TFs, indicating that TFs function synergistically and combinatorially. However, while TF binding has been extensively studied, little is known about how combinations of TFs and cofactors control enhancer function once they are bound. It is typically unclear which TFs participate in combinatorial enhancer activation, whether different TFs form functionally distinct groups, or if certain TFs might substitute for each other in defined enhancer contexts. Here we assess the potential regulatory contributions of TFs and cofactors to combinatorial enhancer control with enhancer complementation assays. We recruited GAL4-DNA-binding-domain fusions of 812 Drosophila TFs and cofactors to 24 enhancer contexts and measured enhancer activities by 82,752 luciferase assays in S2 cells. Most factors were functional in at least one context, yet their contributions differed between contexts and varied from repression to activation (up to 289-fold) for individual factors. Based on functional similarities across contexts, we define 15 groups of TFs that differ in developmental functions and protein sequence features. Similar TFs can substitute for each other, enabling enhancer re-engineering by exchanging TF motifs, and TF-cofactor pairs cooperate during enhancer control and interact physically. Overall, we show that activators and repressors can have diverse regulatory functions that typically depend on the enhancer context. The systematic functional characterization of TFs and cofactors should further our understanding of combinatorial enhancer control and gene regulation.
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Affiliation(s)
- Gerald Stampfel
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Tomáš Kazmar
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Olga Frank
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Sebastian Wienerroither
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Franziska Reiter
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
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43
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The elimination of an adult segment by the Hox gene Abdominal-B. Mech Dev 2015; 138 Pt 2:210-217. [DOI: 10.1016/j.mod.2015.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 07/31/2015] [Accepted: 08/01/2015] [Indexed: 11/19/2022]
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44
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Bondos SE, Swint-Kruse L, Matthews KS. Flexibility and Disorder in Gene Regulation: LacI/GalR and Hox Proteins. J Biol Chem 2015; 290:24669-77. [PMID: 26342073 DOI: 10.1074/jbc.r115.685032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
To modulate transcription, a variety of input signals must be sensed by genetic regulatory proteins. In these proteins, flexibility and disorder are emerging as common themes. Prokaryotic regulators generally have short, flexible segments, whereas eukaryotic regulators have extended regions that lack predicted secondary structure (intrinsic disorder). Two examples illustrate the impact of flexibility and disorder on gene regulation: the prokaryotic LacI/GalR family, with detailed information from studies on LacI, and the eukaryotic family of Hox proteins, with specific insights from investigations of Ultrabithorax (Ubx). The widespread importance of structural disorder in gene regulatory proteins may derive from the need for flexibility in signal response and, particularly in eukaryotes, in protein partner selection.
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Affiliation(s)
- Sarah E Bondos
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843
| | - Liskin Swint-Kruse
- the Department of Biochemistry and Molecular Biology, the University of Kansas Medical Center, Kansas City, Kansas 66160, and
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45
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Radó-Trilla N, Arató K, Pegueroles C, Raya A, de la Luna S, Albà MM. Key Role of Amino Acid Repeat Expansions in the Functional Diversification of Duplicated Transcription Factors. Mol Biol Evol 2015; 32:2263-72. [PMID: 25931513 PMCID: PMC4540963 DOI: 10.1093/molbev/msv103] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The high regulatory complexity of vertebrates has been related to two rounds of whole genome duplication (2R-WGD) that occurred before the divergence of the major vertebrate groups. Following these events, many developmental transcription factors (TFs) were retained in multiple copies and subsequently specialized in diverse functions, whereas others reverted to their singleton state. TFs are known to be generally rich in amino acid repeats or low-complexity regions (LCRs), such as polyalanine or polyglutamine runs, which can evolve rapidly and potentially influence the transcriptional activity of the protein. Here we test the hypothesis that LCRs have played a major role in the diversification of TF gene duplicates. We find that nearly half of the TF gene families originated during the 2R-WGD contains LCRs. The number of gene duplicates with LCRs is 155 out of 550 analyzed (28%), about twice as many as the number of single copy genes with LCRs (15 out of 115, 13%). In addition, duplicated TFs preferentially accumulate certain LCR types, the most prominent of which are alanine repeats. We experimentally test the role of alanine-rich LCRs in two different TF gene families, PHOX2A/PHOX2B and LHX2/LHX9. In both cases, the presence of the alanine-rich LCR in one of the copies (PHOX2B and LHX2) significantly increases the capacity of the TF to activate transcription. Taken together, the results provide strong evidence that LCRs are important driving forces of evolutionary change in duplicated genes.
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Affiliation(s)
- Núria Radó-Trilla
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Krisztina Arató
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain Centre for Genomic Regulation (CRG), Barcelona, Spain Centro de Investigación Biomèdica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Cinta Pegueroles
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Barcelona, Spain Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Alicia Raya
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain Centre for Genomic Regulation (CRG), Barcelona, Spain Centro de Investigación Biomèdica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Susana de la Luna
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain Centre for Genomic Regulation (CRG), Barcelona, Spain Centro de Investigación Biomèdica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - M Mar Albà
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Barcelona, Spain Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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46
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Singarete ME, Grizante MB, Milograna SR, Nery MF, Kin K, Wagner GP, Kohlsdorf T. Molecular evolution of HoxA13 and the multiple origins of limbless morphologies in amphibians and reptiles. Genet Mol Biol 2015; 38:255-62. [PMID: 26500429 PMCID: PMC4612600 DOI: 10.1590/s1415-475738320150039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/23/2015] [Indexed: 03/03/2023] Open
Abstract
Developmental processes and their results, morphological characters, are inherited through transmission of genes regulating development. While there is ample evidence that cis-regulatory elements tend to be modular, with sequence segments dedicated to different roles, the situation for proteins is less clear, being particularly complex for transcription factors with multiple functions. Some motifs mediating protein-protein interactions may be exclusive to particular developmental roles, but it is also possible that motifs are mostly shared among different processes. Here we focus on HoxA13, a protein essential for limb development. We asked whether the HoxA13 amino acid sequence evolved similarly in three limbless clades: Gymnophiona, Amphisbaenia and Serpentes. We explored variation in ω (dN/dS) using a maximum-likelihood framework and HoxA13sequences from 47 species. Comparisons of evolutionary models provided low ω global values and no evidence that HoxA13 experienced relaxed selection in limbless clades. Branch-site models failed to detect evidence for positive selection acting on any site along branches of Amphisbaena and Gymnophiona, while three sites were identified in Serpentes. Examination of alignments did not reveal consistent sequence differences between limbed and limbless species. We conclude that HoxA13 has no modules exclusive to limb development, which may be explained by its involvement in multiple developmental processes.
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Affiliation(s)
- Marina E Singarete
- Programa de Pós-Graduação em Biologia Celular e Molecular, Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Mariana B Grizante
- School of Life Sciences, Arizona State University, Tempe, AZ, USA. ; Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Sarah R Milograna
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Mariana F Nery
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil. ; Departamento de Genética, Evolução e Bioagentes, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Koryu Kin
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA. ; Department of Obstetrics, Gynecology and Reproductive Sciences, Yale Systems Biology Institute, Yale University, West Haven, CT, USA
| | - Tiana Kohlsdorf
- Programa de Pós-Graduação em Biologia Celular e Molecular, Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil. ; Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
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47
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Saadaoui M, Litim-Mecheri I, Macchi M, Graba Y, Maurel-Zaffran C. A survey of conservation of sea spider and Drosophila Hox protein activities. Mech Dev 2015; 138 Pt 2:73-86. [PMID: 26238019 DOI: 10.1016/j.mod.2015.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/24/2015] [Accepted: 07/25/2015] [Indexed: 01/29/2023]
Abstract
Hox proteins have well-established functions in development and evolution, controlling the final morphology of bilaterian animals. The common phylogenetic origin of Hox proteins and the associated evolutionary diversification of protein sequences provide a unique framework to explore the relationship between changes in protein sequence and function. In this study, we aimed at questioning how sequence variation within arthropod Hox proteins influences function. This was achieved by exploring the functional impact of sequence conservation/divergence of the Hox genes, labial, Sex comb reduced, Deformed, Ultrabithorax and abdominalA from two distant arthropods, the sea spider and the well-studied Drosophila. Results highlight a correlation between sequence conservation within the homeodomain and the degree of functional conservation, and identify a novel functional domain in the Labial protein.
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Affiliation(s)
- Mehdi Saadaoui
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France; Institut de Biologie de l'ENS, 46, rue d'Ulm, 75005 Paris, France
| | - Isma Litim-Mecheri
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France; IGBMC, INSERM U964, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Meiggie Macchi
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France
| | - Yacine Graba
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France
| | - Corinne Maurel-Zaffran
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France
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48
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Rebeiz M, Patel NH, Hinman VF. Unraveling the Tangled Skein: The Evolution of Transcriptional Regulatory Networks in Development. Annu Rev Genomics Hum Genet 2015; 16:103-31. [PMID: 26079281 DOI: 10.1146/annurev-genom-091212-153423] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The molecular and genetic basis for the evolution of anatomical diversity is a major question that has inspired evolutionary and developmental biologists for decades. Because morphology takes form during development, a true comprehension of how anatomical structures evolve requires an understanding of the evolutionary events that alter developmental genetic programs. Vast gene regulatory networks (GRNs) that connect transcription factors to their target regulatory sequences control gene expression in time and space and therefore determine the tissue-specific genetic programs that shape morphological structures. In recent years, many new examples have greatly advanced our understanding of the genetic alterations that modify GRNs to generate newly evolved morphologies. Here, we review several aspects of GRN evolution, including their deep preservation, their mechanisms of alteration, and how they originate to generate novel developmental programs.
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Affiliation(s)
- Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260;
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Lind AL, Wisecaver JH, Smith TD, Feng X, Calvo AM, Rokas A. Examining the evolution of the regulatory circuit controlling secondary metabolism and development in the fungal genus Aspergillus. PLoS Genet 2015; 11:e1005096. [PMID: 25786130 PMCID: PMC4364702 DOI: 10.1371/journal.pgen.1005096] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 02/23/2015] [Indexed: 01/07/2023] Open
Abstract
Filamentous fungi produce diverse secondary metabolites (SMs) essential to their ecology and adaptation. Although each SM is typically produced by only a handful of species, global SM production is governed by widely conserved transcriptional regulators in conjunction with other cellular processes, such as development. We examined the interplay between the taxonomic narrowness of SM distribution and the broad conservation of global regulation of SM and development in Aspergillus, a diverse fungal genus whose members produce well-known SMs such as penicillin and gliotoxin. Evolutionary analysis of the 2,124 genes comprising the 262 SM pathways in four Aspergillus species showed that most SM pathways were species-specific, that the number of SM gene orthologs was significantly lower than that of orthologs in primary metabolism, and that the few conserved SM orthologs typically belonged to non-homologous SM pathways. RNA sequencing of two master transcriptional regulators of SM and development, veA and mtfA, showed that the effects of deletion of each gene, especially veA, on SM pathway regulation were similar in A. fumigatus and A. nidulans, even though the underlying genes and pathways regulated in each species differed. In contrast, examination of the role of these two regulators in development, where 94% of the underlying genes are conserved in both species showed that whereas the role of veA is conserved, mtfA regulates development in the homothallic A. nidulans but not in the heterothallic A. fumigatus. Thus, the regulation of these highly conserved developmental genes is divergent, whereas-despite minimal conservation of target genes and pathways-the global regulation of SM production is largely conserved. We suggest that the evolution of the transcriptional regulation of secondary metabolism in Aspergillus represents a novel type of regulatory circuit rewiring and hypothesize that it has been largely driven by the dramatic turnover of the target genes involved in the process.
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Affiliation(s)
- Abigail L. Lind
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jennifer H. Wisecaver
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Timothy D. Smith
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America
| | - Xuehuan Feng
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America
| | - Ana M. Calvo
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America
| | - Antonis Rokas
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America,Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America,* E-mail:
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50
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Nadimpalli S, Persikov AV, Singh M. Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PLoS Genet 2015; 11:e1005011. [PMID: 25748510 PMCID: PMC4351887 DOI: 10.1371/journal.pgen.1005011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 01/18/2015] [Indexed: 01/17/2023] Open
Abstract
Differences in transcriptional regulatory networks underlie much of the phenotypic variation observed across organisms. Changes to cis-regulatory elements are widely believed to be the predominant means by which regulatory networks evolve, yet examples of regulatory network divergence due to transcription factor (TF) variation have also been observed. To systematically ascertain the extent to which TFs contribute to regulatory divergence, we analyzed the evolution of the largest class of metazoan TFs, Cys2-His2 zinc finger (C2H2-ZF) TFs, across 12 Drosophila species spanning ~45 million years of evolution. Remarkably, we uncovered that a significant fraction of all C2H2-ZF 1-to-1 orthologs in flies exhibit variations that can affect their DNA-binding specificities. In addition to loss and recruitment of C2H2-ZF domains, we found diverging DNA-contacting residues in ~44% of domains shared between D. melanogaster and the other fly species. These diverging DNA-contacting residues, found in ~70% of the D. melanogaster C2H2-ZF genes in our analysis and corresponding to ~26% of all annotated D. melanogaster TFs, show evidence of functional constraint: they tend to be conserved across phylogenetic clades and evolve slower than other diverging residues. These same variations were rarely found as polymorphisms within a population of D. melanogaster flies, indicating their rapid fixation. The predicted specificities of these dynamic domains gradually change across phylogenetic distances, suggesting stepwise evolutionary trajectories for TF divergence. Further, whereas proteins with conserved C2H2-ZF domains are enriched in developmental functions, those with varying domains exhibit no functional enrichments. Our work suggests that a subset of highly dynamic and largely unstudied TFs are a likely source of regulatory variation in Drosophila and other metazoans.
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Affiliation(s)
- Shilpa Nadimpalli
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Anton V. Persikov
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Mona Singh
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
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