1
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Gil J, Rosin LF, Navarrete E, Chowdhury N, Abraham S, Cornilleau G, Lei EP, Mozziconacci J, Mirny LA, Muller H, Drinnenberg IA. Unique territorial and compartmental organization of chromosomes in the holocentric silkmoth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557757. [PMID: 37745315 PMCID: PMC10515926 DOI: 10.1101/2023.09.14.557757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The hallmarks of chromosome organization in multicellular eukaryotes are chromosome territories (CT), chromatin compartments, and insulated domains, including topologically associated domains (TADs). Yet, most of these elements of chromosome organization are derived from analyses of a limited set of model organisms, while large eukaryotic groups, including insects, remain mostly unexplored. Here we combine Hi-C, biophysical modeling, and microscopy to characterize the 3D genome architecture of the silkworm, Bombyx mori. In contrast to other eukaryotes, B. mori chromosomes form highly separated territories. Similar to other eukaryotes, B. mori chromosomes segregate into active A and inactive B compartments, yet unlike in vertebrate systems, contacts between euchromatic A regions appear to be a strong driver of compartmentalization. Remarkably, we also identify a third compartment, called secluded S, with a unique contact pattern. Each S region shows prominent short-range self-contacts and is remarkably devoid of contacts with the rest of the chromosome, including other S regions. Compartment S hosts a unique combination of genetic and epigenetic features, localizes towards the periphery of CTs, and shows developmental plasticity. Biophysical modeling reveals that the formation of such secluded domains requires highly localized loop extrusion within them, along with a low level of extrusion in A and B. Our Hi-C data supports predicted genome-wide and localized extrusion. Such a broad, non-uniform distribution of extruders has not been seen in other organisms. Overall, our analyses support loop extrusion in insects and highlight the evolutionary plasticity of 3D genome organization, driven by a new combination of known processes.
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Martín-Zamora FM, Davies BE, Donnellan RD, Guynes K, Martín-Durán JM. Functional genomics in Spiralia. Brief Funct Genomics 2023; 22:487-497. [PMID: 37981859 PMCID: PMC10658182 DOI: 10.1093/bfgp/elad036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/12/2023] [Accepted: 07/25/2023] [Indexed: 11/21/2023] Open
Abstract
Our understanding of the mechanisms that modulate gene expression in animals is strongly biased by studying a handful of model species that mainly belong to three groups: Insecta, Nematoda and Vertebrata. However, over half of the animal phyla belong to Spiralia, a morphologically and ecologically diverse animal clade with many species of economic and biomedical importance. Therefore, investigating genome regulation in this group is central to uncovering ancestral and derived features in genome functioning in animals, which can also be of significant societal impact. Here, we focus on five aspects of gene expression regulation to review our current knowledge of functional genomics in Spiralia. Although some fields, such as single-cell transcriptomics, are becoming more common, the study of chromatin accessibility, DNA methylation, histone post-translational modifications and genome architecture are still in their infancy. Recent efforts to generate chromosome-scale reference genome assemblies for greater species diversity and optimise state-of-the-art approaches for emerging spiralian research systems will address the existing knowledge gaps in functional genomics in this animal group.
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Affiliation(s)
- Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Billie E Davies
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Rory D Donnellan
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Kero Guynes
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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3
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Acemel RD, Lupiáñez DG. Evolution of 3D chromatin organization at different scales. Curr Opin Genet Dev 2023; 78:102019. [PMID: 36603519 DOI: 10.1016/j.gde.2022.102019] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 01/04/2023]
Abstract
Most animal genomes fold in 3D chromatin domains called topologically associated domains (TADs) that facilitate interactions between cis-regulatory elements (CREs) and promoters. Owing to their critical role in the control of developmental gene expression, we explore how TADs have shaped animal evolution. In the light of recent studies that profile TADs in disparate animal lineages, we discuss their phylogenetic distribution and the mechanisms that underlie their formation. We present evidence indicating that TADs are plastic entities composed of genomic strata of different ages: ancient cores are combined with newer regions and brought into extant TADs through genomic rearrangements. We highlight that newly incorporated TAD strata enable the establishment of new CRE-promoter interactions and in turn new expression patterns that can drive phenotypical innovation. We further highlight how subtle changes in chromatin folding may fine-tune the expression levels of developmental genes and hold a potential for evolutionary significance.
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Kohli M, Letsch H, Greve C, Béthoux O, Deregnaucourt I, Liu S, Zhou X, Donath A, Mayer C, Podsiadlowski L, Gunkel S, Machida R, Niehuis O, Rust J, Wappler T, Yu X, Misof B, Ware J. Evolutionary history and divergence times of Odonata (dragonflies and damselflies) revealed through transcriptomics. iScience 2021; 24:103324. [PMID: 34805787 PMCID: PMC8586788 DOI: 10.1016/j.isci.2021.103324] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 05/14/2021] [Accepted: 10/19/2021] [Indexed: 11/22/2022] Open
Abstract
Dragonflies and damselflies are among the earliest flying insects with extant representatives. However, unraveling details of their long evolutionary history, such as egg laying (oviposition) strategies, is impeded by unresolved phylogenetic relationships, particularly in damselflies. Here we present a transcriptome-based phylogenetic reconstruction of Odonata, analyzing 2,980 protein-coding genes in 105 species representing nearly all the order's families. All damselfly and most dragonfly families are recovered as monophyletic. Our data suggest a sister relationship between dragonfly families of Gomphidae and Petaluridae. According to our divergence time estimates, both crown-Zygoptera and -Anisoptera arose during the late Triassic. Egg-laying with a reduced ovipositor apparently evolved in dragonflies during the late Jurassic/early Cretaceous. Lastly, we also test the impact of fossil choice and placement, particularly, of the extinct fossil species, †Triassolestodes asiaticus, and †Proterogomphus renateae on divergence time estimates. We find placement of †Proterogomphus renateae to be much more impactful than †Triassolestodes asiaticus.
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Affiliation(s)
- Manpreet Kohli
- Department of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Harald Letsch
- Department for Animal Biodiversity, Universität Wien, Vienna, Austria
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Olivier Béthoux
- CR2P (Centre de Recherche en Paléontologie – Paris), MNHN – CNRS – Sorbonne Université, Paris, France
| | - Isabelle Deregnaucourt
- CR2P (Centre de Recherche en Paléontologie – Paris), MNHN – CNRS – Sorbonne Université, Paris, France
| | - Shanlin Liu
- Department of Entomology, China Agricultural University,Beijing 100193, People’s Republic of China
| | - Xin Zhou
- Department of Entomology, China Agricultural University,Beijing 100193, People’s Republic of China
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Christoph Mayer
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Simon Gunkel
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Ryuichiro Machida
- Sugadaira Research Station, Mountain Research Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano, Japan
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University, Freiburg, Germany
| | - Jes Rust
- Palaeontology Section, Institute of Geosciences, Rheinische Friedrich-Wilhelms Universität Bonn, Bonn 53115, Germany
| | - Torsten Wappler
- Palaeontology Section, Institute of Geosciences, Rheinische Friedrich-Wilhelms Universität Bonn, Bonn 53115, Germany
| | - Xin Yu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Bernhard Misof
- Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Jessica Ware
- Department of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
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5
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Szucsich NU, Bartel D, Blanke A, Böhm A, Donath A, Fukui M, Grove S, Liu S, Macek O, Machida R, Misof B, Nakagaki Y, Podsiadlowski L, Sekiya K, Tomizuka S, Von Reumont BM, Waterhouse RM, Walzl M, Meng G, Zhou X, Pass G, Meusemann K. Four myriapod relatives - but who are sisters? No end to debates on relationships among the four major myriapod subgroups. BMC Evol Biol 2020; 20:144. [PMID: 33148176 PMCID: PMC7640414 DOI: 10.1186/s12862-020-01699-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 09/30/2020] [Indexed: 11/20/2022] Open
Abstract
Background Phylogenetic relationships among the myriapod subgroups Chilopoda, Diplopoda, Symphyla and Pauropoda are still not robustly resolved. The first phylogenomic study covering all subgroups resolved phylogenetic relationships congruently to morphological evidence but is in conflict with most previously published phylogenetic trees based on diverse molecular data. Outgroup choice and long-branch attraction effects were stated as possible explanations for these incongruencies. In this study, we addressed these issues by extending the myriapod and outgroup taxon sampling using transcriptome data. Results We generated new transcriptome data of 42 panarthropod species, including all four myriapod subgroups and additional outgroup taxa. Our taxon sampling was complemented by published transcriptome and genome data resulting in a supermatrix covering 59 species. We compiled two data sets, the first with a full coverage of genes per species (292 single-copy protein-coding genes), the second with a less stringent coverage (988 genes). We inferred phylogenetic relationships among myriapods using different data types, tree inference, and quartet computation approaches. Our results unambiguously support monophyletic Mandibulata and Myriapoda. Our analyses clearly showed that there is strong signal for a single unrooted topology, but a sensitivity of the position of the internal root on the choice of outgroups. However, we observe strong evidence for a clade Pauropoda+Symphyla, as well as for a clade Chilopoda+Diplopoda. Conclusions Our best quartet topology is incongruent with current morphological phylogenies which were supported in another phylogenomic study. AU tests and quartet mapping reject the quartet topology congruent to trees inferred with morphological characters. Moreover, quartet mapping shows that confounding signal present in the data set is sufficient to explain the weak signal for the quartet topology derived from morphological characters. Although outgroup choice affects results, our study could narrow possible trees to derivatives of a single quartet topology. For highly disputed relationships, we propose to apply a series of tests (AU and quartet mapping), since results of such tests allow to narrow down possible relationships and to rule out confounding signal.
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Affiliation(s)
- Nikolaus U Szucsich
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria. .,Central Research Laboratories, Natural History Museum of Vienna, A-1010, Vienna, Austria.
| | - Daniela Bartel
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria
| | - Alexander Blanke
- Institute for Zoology, Biocenter, University of Cologne, D-50674, Cologne, Germany.,Institute of Evolutionary Biology and Animal Ecology, University of Bonn, D-53121, Bonn, Germany
| | - Alexander Böhm
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany
| | - Makiko Fukui
- Department of Biology, Graduate School of Science and Engineering, Ehime University, Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Simon Grove
- Invertebrate Zoology, Collections and Research Facility, Tasmanian Museum and Art Gallery, Rosny, Tasmania, 7018, Australia
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Oliver Macek
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria.,Central Research Laboratories, Natural History Museum of Vienna, A-1010, Vienna, Austria
| | - Ryuichiro Machida
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda, Nagano, 386-2204, Japan
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany
| | - Yasutaka Nakagaki
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda, Nagano, 386-2204, Japan
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany
| | - Kaoru Sekiya
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda, Nagano, 386-2204, Japan
| | | | - Björn M Von Reumont
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE TBG), Senckenberganlage 25, 60325, Frankfurt, Germany.,Animal Venomics, Institute for Insect Biotechnology, University of Giessen, Heinrich Buff Ring 26-32, D-35394, Giessen, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Manfred Walzl
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria
| | - Guanliang Meng
- Centre of Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Günther Pass
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria
| | - Karen Meusemann
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany. .,Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), University of Freiburg, D-79104, Freiburg, Germany. .,Australian National Insect Collection, National Research Collections Australia, CSIRO, ACT, Canberra, 2601, Australia.
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6
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Vizueta J, Escuer P, Frías-López C, Guirao-Rico S, Hering L, Mayer G, Rozas J, Sánchez-Gracia A. Evolutionary History of Major Chemosensory Gene Families across Panarthropoda. Mol Biol Evol 2020; 37:3601-3615. [DOI: 10.1093/molbev/msaa197] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abstract
Chemosensory perception is a fundamental biological process of particular relevance in basic and applied arthropod research. However, apart from insects, there is little knowledge of specific molecules involved in this system, which is restricted to a few taxa with uneven phylogenetic sampling across lineages. From an evolutionary perspective, onychophorans (velvet worms) and tardigrades (water bears) are of special interest since they represent the closest living relatives of arthropods, altogether comprising the Panarthropoda. To get insights into the evolutionary origin and diversification of the chemosensory gene repertoire in panarthropods, we sequenced the antenna- and head-specific transcriptomes of the velvet worm Euperipatoides rowelli and analyzed members of all major chemosensory families in representative genomes of onychophorans, tardigrades, and arthropods. Our results suggest that the NPC2 gene family was the only family encoding soluble proteins in the panarthropod ancestor and that onychophorans might have lost many arthropod-like chemoreceptors, including the highly conserved IR25a receptor of protostomes. On the other hand, the eutardigrade genomes lack genes encoding the DEG-ENaC and CD36-sensory neuron membrane proteins, the chemosensory members of which have been retained in arthropods; these losses might be related to lineage-specific adaptive strategies of tardigrades to survive extreme environmental conditions. Although the results of this study need to be further substantiated by an increased taxon sampling, our findings shed light on the diversification of chemosensory gene families in Panarthropoda and contribute to a better understanding of the evolution of animal chemical senses.
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Affiliation(s)
- Joel Vizueta
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Paula Escuer
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristina Frías-López
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | | | - Lars Hering
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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7
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Overlapping but Distinct Sequences Play Roles in the Insulator and Promoter Activities of the Drosophila BEAF-Dependent scs' Insulator. Genetics 2020; 215:1003-1012. [PMID: 32554599 DOI: 10.1534/genetics.120.303344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/16/2020] [Indexed: 12/30/2022] Open
Abstract
Chromatin domain insulators are thought to help partition the genome into genetic units called topologically associating domains (TADs). In Drosophila, TADs are often separated by inter-TAD regions containing active housekeeping genes and associated insulator binding proteins. This raises the question of whether insulator binding proteins are involved primarily in chromosomal TAD architecture or gene activation, or if these two activities are linked. The Boundary Element-Associated Factor of 32 kDa (BEAF-32, or BEAF for short) is usually found in inter-TADs. BEAF was discovered based on binding to the scs' insulator, and is important for the insulator activity of scs' and other BEAF binding sites. There are divergent promoters in scs' with a BEAF binding site by each. Here, we dissect the scs' insulator to identify DNA sequences important for insulator and promoter activity, focusing on the half of scs' with a high affinity BEAF binding site. We find that the BEAF binding site is important for both insulator and promoter activity, as is another sequence we refer to as LS4. Aside from that, different sequences play roles in insulator and promoter activity. So while there is overlap and BEAF is important for both, insulator and promoter activity can be separated.
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8
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Dong Y, Avva SVSP, Maharjan M, Jacobi J, Hart CM. Promoter-Proximal Chromatin Domain Insulator Protein BEAF Mediates Local and Long-Range Communication with a Transcription Factor and Directly Activates a Housekeeping Promoter in Drosophila. Genetics 2020; 215:89-101. [PMID: 32179582 PMCID: PMC7198264 DOI: 10.1534/genetics.120.303144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/12/2020] [Indexed: 12/23/2022] Open
Abstract
BEAF (Boundary Element-Associated Factor) was originally identified as a Drosophila melanogaster chromatin domain insulator-binding protein, suggesting a role in gene regulation through chromatin organization and dynamics. Genome-wide mapping found that BEAF usually binds near transcription start sites, often of housekeeping genes, suggesting a role in promoter function. This would be a nontraditional role for an insulator-binding protein. To gain insight into molecular mechanisms of BEAF function, we identified interacting proteins using yeast two-hybrid assays. Here, we focus on the transcription factor Serendipity δ (Sry-δ). Interactions were confirmed in pull-down experiments using bacterially expressed proteins, by bimolecular fluorescence complementation, and in a genetic assay in transgenic flies. Sry-δ interacted with promoter-proximal BEAF both when bound to DNA adjacent to BEAF or > 2-kb upstream to activate a reporter gene in transient transfection experiments. The interaction between BEAF and Sry-δ was detected using both a minimal developmental promoter (y) and a housekeeping promoter (RpS12), while BEAF alone strongly activated the housekeeping promoter. These two functions for BEAF implicate it in playing a direct role in gene regulation at hundreds of BEAF-associated promoters.
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Affiliation(s)
- Yuankai Dong
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - S V Satya Prakash Avva
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Mukesh Maharjan
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Janice Jacobi
- Hayward Genetics Center, Tulane University, New Orleans, Louisiana 70112
| | - Craig M Hart
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
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9
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Meusemann K, Korb J, Schughart M, Staubach F. No Evidence for Single-Copy Immune-Gene Specific Signals of Selection in Termites. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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10
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Shelomi M, Wipfler B, Zhou X, Pauchet Y. Multifunctional cellulase enzymes are ancestral in Polyneoptera. INSECT MOLECULAR BIOLOGY 2020; 29:124-135. [PMID: 31449690 DOI: 10.1111/imb.12614] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/02/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
Many hemimetabolous insects produce their own cellulase enzymes from the glycoside hydrolase family 9, first observed in termites and cockroaches. Phasmatodea have multiple cellulases, some of which are multifunctional and can degrade xylan or xyloglucan. To discover when these abilities evolved, we identified cellulases from the Polyneoptera sampled by the 1000 Insect Transcriptome and Evolution (1KITE) project, including all cockroach and termite transcriptomes. We hoped to identify what role enzyme substrate specificities had in the evolution of dietary specification, such as leaf-feeding or wood-feeding. Putative cellulases were identified from the transcriptomes and analysed phylogenetically. All cellulases were amplified from an exemplar set of Polyneoptera species using rapid amplification of cDNA ends PCR and heterologously expressed in an insect cell line, then tested against different polysaccharides for their digestive abilities. We identified several multifunctional xyloglucanolytic enzymes across Polyneoptera, plus a large group of cellulase-like enzymes found in nearly all insect orders with no discernible digestive ability. Multifunctional xylanolytic cellulases remain unique to Phasmatodea. The presence or absence of multifunctional enzymes does not impact dietary specification, but rather having multiple, multifunctional cellulase genes is an ancestral state for Polyneoptera and possibly Insecta. The prevalence of multifunctional cellulases in other animals demands further investigation.
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Affiliation(s)
- M Shelomi
- Department of Entomology, National Taiwan University, Taipei, Taiwan
| | - B Wipfler
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - X Zhou
- Department of Entomology, China Agricultural University, Beijing, China
| | - Y Pauchet
- Department of Entomology, Max-Planck Institute für chemische Ökologie, Jena, Germany
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11
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Jiang F, Liu Q, Liu X, Wang XH, Kang L. Genomic data reveal high conservation but divergent evolutionary pattern of Polycomb/Trithorax group genes in arthropods. INSECT SCIENCE 2019; 26:20-34. [PMID: 29127737 DOI: 10.1111/1744-7917.12558] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 11/04/2017] [Accepted: 11/05/2017] [Indexed: 06/07/2023]
Abstract
Epigenetic gene control is maintained by chromatin-associated Polycomb group (PcG) and Trithorax group (TrxG) genes, which act antagonistically via the interplay between PcG and TrxG regulation to generate silenced or permissive transcriptional states. In this study, we searched for PcG/TrxG genes in 180 arthropod genomes, covering all the sequenced arthropod genomes at the time of conducting this study, to perform a global investigation of PcG/TrxG genes in a phylogenetic frame. Results of ancestral state reconstruction analysis revealed that the ancestor of arthropod species has an almost complete repertoire of PcG/TrxG genes, and most of these genes were seldom lost above order level. The domain diversity analysis indicated that the PcG/TrxG genes show variable extent of domain structure changes; some of these changes could be associated with lineage-specific events. The likelihood ratio tests for selection pressure detected a number of PcG/TrxG genes which underwent episodic positive selection on the branch leading to the insects with holometabolous development. These results suggest that, despite their high conservation across arthropod species, different members of PcG/TrxG genes showed considerable differences in domain structure and sequence divergence in arthropod evolution. Our cross species comparisons using large-scale genomic data provide insights into divergent evolutionary pattern on highly conserved genes in arthropods.
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Affiliation(s)
- Feng Jiang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Qing Liu
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Xiang Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xian-Hui Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Le Kang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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12
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Melnikova L, Kostyuchenko M, Parshikov A, Georgiev P, Golovnin A. Role of Su(Hw) zinc finger 10 and interaction with CP190 and Mod(mdg4) proteins in recruiting the Su(Hw) complex to chromatin sites in Drosophila. PLoS One 2018; 13:e0193497. [PMID: 29474480 PMCID: PMC5825117 DOI: 10.1371/journal.pone.0193497] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 02/12/2018] [Indexed: 02/07/2023] Open
Abstract
Su(Hw) belongs to the class of proteins that organize chromosome architecture and boundaries/insulators between regulatory domains. This protein contains a cluster of 12 zinc finger domains most of which are responsible for binding to three different modules in the consensus site. Su(Hw) forms a complex with CP190 and Mod(mdg4)-67.2 proteins that binds to well-known Drosophila insulators. To understand how Su(Hw) performs its activities and binds to specific sites in chromatin, we have examined the previously described su(Hw)f mutation that disrupts the 10th zinc finger (ZF10) responsible for Su(Hw) binding to the upstream module. The results have shown that Su(Hw)f loses the ability to interact with CP190 in the absence of DNA. In contrast, complete deletion of ZF10 does not prevent the interaction between Su(Hw)Δ10 and CP190. Having studied insulator complex formation in different mutant backgrounds, we conclude that both association with CP190 and Mod(mdg4)-67.2 partners and proper organization of DNA binding site are essential for the efficient recruitment of the Su(Hw) complex to chromatin insulators.
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Affiliation(s)
- Larisa Melnikova
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Margarita Kostyuchenko
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Parshikov
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail: (AG); (PG)
| | - Anton Golovnin
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail: (AG); (PG)
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