An Endosymbiont's Journey Through Metamorphosis of Its Insect Host
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Spatial and morphological reorganization of endosymbiosis during metamorphosis accommodates adult metabolic requirements in a weevil Justin Mairea,1, Nicolas Parisota, Mariana Galvao Ferrarinia, Agnès Valliera, Benjamin Gilletb, Sandrine Hughesb, Séverine Balmanda, Carole Vincent-Monégata, Anna Zaidman-Rémya,2, and Abdelaziz Heddia,2 aUMR0203, Biologie Fonctionnelle, Insectes et Interactions (BF2i), Institut National des Sciences Appliquées de Lyon (INSA-Lyon), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Lyon (Univ Lyon), F-69621 Villeurbanne, France; and bUMR5242, Institut de Génomique Fonctionnelle de Lyon (IGFL), Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon (Univ Lyon), F-69007 Lyon, France Edited by John R. Pringle, Stanford University Medical Center, Stanford, CA, and approved June 25, 2020 (received for review April 15, 2020) Bacterial intracellular symbiosis (endosymbiosis) is widespread in allows adaptive decoupling: for example, task specialization of nature and impacts many biological processes. In holometabolous growth at the larval stage versus reproduction at the adult stage symbiotic insects, metamorphosis entails a complete and abrupt (9, 10). However, metamorphosis is also associated with con- internal reorganization that creates a constraint for endosymbiont straints, including higher susceptibility to predators and patho- transmission from larvae to adults. To assess how endosymbiosis gens, as well as the conservation and adaptation of beneficial copes—and potentially evolves—throughout this major host-tissue symbionts (9, 11). In hemimetabolous insects, the relative mor- reorganization, we used the association between the cereal weevil phological stability associated with incomplete metamorphosis is Sitophilus oryzae and the bacterium Sodalis pierantonius as a model believed to facilitate symbiont maintenance and transmission system. -
Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements
Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280 -
The Role of the Microbiome in Oral Squamous Cell Carcinoma with Insight Into the Microbiome–Treatment Axis
International Journal of Molecular Sciences Review The Role of the Microbiome in Oral Squamous Cell Carcinoma with Insight into the Microbiome–Treatment Axis Amel Sami 1,2, Imad Elimairi 2,* , Catherine Stanton 1,3, R. Paul Ross 1 and C. Anthony Ryan 4 1 APC Microbiome Ireland, School of Microbiology, University College Cork, Cork T12 YN60, Ireland; [email protected] (A.S.); [email protected] (C.S.); [email protected] (R.P.R.) 2 Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, National Ribat University, Nile Street, Khartoum 1111, Sudan 3 Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61 C996, Ireland 4 Department of Paediatrics and Child Health, University College Cork, Cork T12 DFK4, Ireland; [email protected] * Correspondence: [email protected] Received: 30 August 2020; Accepted: 12 October 2020; Published: 29 October 2020 Abstract: Oral squamous cell carcinoma (OSCC) is one of the leading presentations of head and neck cancer (HNC). The first part of this review will describe the highlights of the oral microbiome in health and normal development while demonstrating how both the oral and gut microbiome can map OSCC development, progression, treatment and the potential side effects associated with its management. We then scope the dynamics of the various microorganisms of the oral cavity, including bacteria, mycoplasma, fungi, archaea and viruses, and describe the characteristic roles they may play in OSCC development. We also highlight how the human immunodeficiency viruses (HIV) may impinge on the host microbiome and increase the burden of oral premalignant lesions and OSCC in patients with HIV. Finally, we summarise current insights into the microbiome–treatment axis pertaining to OSCC, and show how the microbiome is affected by radiotherapy, chemotherapy, immunotherapy and also how these therapies are affected by the state of the microbiome, potentially determining the success or failure of some of these treatments. -
Evidence Supporting an Antimicrobial Origin of Targeting Peptides to Endosymbiotic Organelles
cells Article Evidence Supporting an Antimicrobial Origin of Targeting Peptides to Endosymbiotic Organelles Clotilde Garrido y, Oliver D. Caspari y , Yves Choquet , Francis-André Wollman and Ingrid Lafontaine * UMR7141, Institut de Biologie Physico-Chimique (CNRS/Sorbonne Université), 13 Rue Pierre et Marie Curie, 75005 Paris, France; [email protected] (C.G.); [email protected] (O.D.C.); [email protected] (Y.C.); [email protected] (F.-A.W.) * Correspondence: [email protected] These authors contributed equally to this work. y Received: 19 June 2020; Accepted: 24 July 2020; Published: 28 July 2020 Abstract: Mitochondria and chloroplasts emerged from primary endosymbiosis. Most proteins of the endosymbiont were subsequently expressed in the nucleo-cytosol of the host and organelle-targeted via the acquisition of N-terminal presequences, whose evolutionary origin remains enigmatic. Using a quantitative assessment of their physico-chemical properties, we show that organelle targeting peptides, which are distinct from signal peptides targeting other subcellular compartments, group with a subset of antimicrobial peptides. We demonstrate that extant antimicrobial peptides target a fluorescent reporter to either the mitochondria or the chloroplast in the green alga Chlamydomonas reinhardtii and, conversely, that extant targeting peptides still display antimicrobial activity. Thus, we provide strong computational and functional evidence for an evolutionary link between organelle-targeting and antimicrobial peptides. Our results support the view that resistance of bacterial progenitors of organelles to the attack of host antimicrobial peptides has been instrumental in eukaryogenesis and in the emergence of photosynthetic eukaryotes. Keywords: Chlamydomonas; targeting peptides; antimicrobial peptides; primary endosymbiosis; import into organelles; chloroplast; mitochondrion 1. -
Small Genome Symbiont Underlies Cuticle Hardness in Beetles
Small genome symbiont underlies cuticle hardness in beetles Hisashi Anbutsua,b,1,2, Minoru Moriyamaa,1, Naruo Nikohc,1, Takahiro Hosokawaa,d, Ryo Futahashia, Masahiko Tanahashia, Xian-Ying Menga, Takashi Kuriwadae,f, Naoki Morig, Kenshiro Oshimah, Masahira Hattorih,i, Manabu Fujiej, Noriyuki Satohk, Taro Maedal, Shuji Shigenobul, Ryuichi Kogaa, and Takema Fukatsua,m,n,2 aBioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan; bComputational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo 169-8555, Japan; cDepartment of Liberal Arts, The Open University of Japan, Chiba 261-8586, Japan; dFaculty of Science, Kyushu University, Fukuoka 819-0395, Japan; eNational Agriculture and Food Research Organization, Kyushu Okinawa Agricultural Research Center, Okinawa 901-0336, Japan; fFaculty of Education, Kagoshima University, Kagoshima 890-0065, Japan; gDivision of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; hGraduate School of Frontier Sciences, University of Tokyo, Chiba 277-8561, Japan; iGraduate School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan; jDNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan; kMarine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan; lNIBB Core Research Facilities, National Institute for Basic Biology, Okazaki 444-8585, Japan; mDepartment of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan; and nGraduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan Edited by Nancy A. Moran, University of Texas at Austin, Austin, TX, and approved August 28, 2017 (received for review July 19, 2017) Beetles, representing the majority of the insect species diversity, are symbiont transmission over evolutionary time (4, 6, 7). -
Temporal Dynamics of the Gut Bacteriome and Mycobiome in the Weanling Pig
microorganisms Article Temporal Dynamics of the Gut Bacteriome and Mycobiome in the Weanling Pig Ann M. Arfken, Juli Foster Frey and Katie Lynn Summers * Animal Biosciences and Biotechnology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA; [email protected] (A.M.A.); [email protected] (J.F.F.) * Correspondence: [email protected]; Tel.: +1-301-504-8760 Received: 27 April 2020; Accepted: 4 June 2020; Published: 9 June 2020 Abstract: Weaning is a period of environmental changes and stress that results in significant alterations to the piglet gut microbiome and is associated with a predisposition to disease, making potential interventions of interest to the swine industry. In other animals, interactions between the bacteriome and mycobiome can result in altered nutrient absorption and susceptibility to disease, but these interactions remain poorly understood in pigs. Recently, we assessed the colonization dynamics of fungi and bacteria in the gastrointestinal tract of piglets at a single time point post-weaning (day 35) and inferred interactions were found between fungal and bacterial members of the porcine gut ecosystem. In this study, we performed a longitudinal assessment of the fecal bacteriome and mycobiome of piglets from birth through the weaning transition. Piglet feces in this study showed a dramatic shift over time in the bacterial and fungal communities, as well as an increase in network connectivity between the two kingdoms. The piglet fecal bacteriome showed a relatively stable and predictable pattern of development from Bacteroidaceae to Prevotellaceae, as seen in other studies, while the mycobiome demonstrated a loss in diversity over time with a post-weaning population dominated by Saccharomycetaceae. -
The Photosynthetic Endosymbiont in Cryptomonad Cells Produces Both Chloroplast and Cytoplasmic-Type Ribosomes
Journal of Cell Science 107, 649-657 (1994) 649 Printed in Great Britain © The Company of Biologists Limited 1994 JCS6601 The photosynthetic endosymbiont in cryptomonad cells produces both chloroplast and cytoplasmic-type ribosomes Geoffrey I. McFadden1,*, Paul R. Gilson1 and Susan E. Douglas2 1Plant Cell Biology Research Centre, School of Botany, University of Melbourne, Parkville, Victoria, 3052, Australia 2Institute of Marine Biosciences, National Research Council of Canada, 1411 Oxford St, Halifax, Nova Scotia B3H 3Z1, Canada *Author for correspondence SUMMARY Cryptomonad algae contain a photosynthetic, eukaryotic tion machinery. We also localized transcripts of the host endosymbiont. The endosymbiont is much reduced but nucleus rRNA gene. These transcripts were found in the retains a small nucleus. DNA from this endosymbiont nucleolus of the host nucleus, and throughout the host nucleus encodes rRNAs, and it is presumed that these cytoplasm, but never in the endosymbiont compartment. rRNAs are incorporated into ribosomes. Surrounding the Our rRNA localizations indicate that the cryptomonad cell endosymbiont nucleus is a small volume of cytoplasm produces two different of sets of cytoplasmic-type proposed to be the vestigial cytoplasm of the endosymbiont. ribosomes in two separate subcellular compartments. The If this compartment is indeed the endosymbiont’s results suggest that there is no exchange of rRNAs between cytoplasm, it would be expected to contain ribosomes with these compartments. We also used the probe specific for the components encoded by the endosymbiont nucleus. In this endosymbiont rRNA gene to identify chromosomes from paper, we used in situ hybridization to localize rRNAs the endosymbiont nucleus in pulsed field gel electrophore- encoded by the endosymbiont nucleus of the cryptomonad sis. -
Identification and Characterisation of Endogenous Avian Leukosis Virus Subgroup E (ALVE) Insertions in Chicken Whole Genome Sequencing Data Andrew S
Mason et al. Mobile DNA (2020) 11:22 https://doi.org/10.1186/s13100-020-00216-w RESEARCH Open Access Identification and characterisation of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in chicken whole genome sequencing data Andrew S. Mason1,2* , Ashlee R. Lund3, Paul M. Hocking1ˆ, Janet E. Fulton3† and David W. Burt1,4† Abstract Background: Endogenous retroviruses (ERVs) are the remnants of retroviral infections which can elicit prolonged genomic and immunological stress on their host organism. In chickens, endogenous Avian Leukosis Virus subgroup E (ALVE) expression has been associated with reductions in muscle growth rate and egg production, as well as providing the potential for novel recombinant viruses. However, ALVEs can remain in commercial stock due to their incomplete identification and association with desirable traits, such as ALVE21 and slow feathering. The availability of whole genome sequencing (WGS) data facilitates high-throughput identification and characterisation of these retroviral remnants. Results: We have developed obsERVer, a new bioinformatic ERV identification pipeline which can identify ALVEs in WGS data without further sequencing. With this pipeline, 20 ALVEs were identified across eight elite layer lines from Hy-Line International, including four novel integrations and characterisation of a fast feathered phenotypic revertant that still contained ALVE21. These bioinformatically detected sites were subsequently validated using new high- throughput KASP assays, which showed that obsERVer was highly precise and exhibited a 0% false discovery rate. A further fifty-seven diverse chicken WGS datasets were analysed for their ALVE content, identifying a total of 322 integration sites, over 80% of which were novel. Like exogenous ALV, ALVEs show site preference for proximity to protein-coding genes, but also exhibit signs of selection against deleterious integrations within genes. -
Ecophysiological Plasticity and Bacteriome Shift in the Seagrass Halophila Stipulacea Along a Depth Gradient in the Northern Red Sea
fpls-07-02015 January 4, 2017 Time: 15:45 # 1 ORIGINAL RESEARCH published: 05 January 2017 doi: 10.3389/fpls.2016.02015 Ecophysiological Plasticity and Bacteriome Shift in the Seagrass Halophila stipulacea along a Depth Gradient in the Northern Red Sea Alice Rotini1*†, Astrid Y. Mejia1†, Rodrigo Costa2, Luciana Migliore1 and Gidon Winters3* 1 Department of Biology, Tor Vergata University, Rome, Italy, 2 Department of Bioengineering (iBB), Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal, 3 The Dead Sea-Arava Science Center, Neve Zohar, Israel Halophila stipulacea is a small tropical seagrass species. It is the dominant seagrass species in the Gulf of Aqaba (GoA; northern Red Sea), where it grows in both shallow and deep environments (1–50 m depth). Native to the Red Sea, Persian Gulf, and Indian Ocean, this species has invaded the Mediterranean and has recently established itself in the Caribbean Sea. Due to its invasive nature, there is growing interest to understand Edited by: this species’ capacity to adapt to new conditions, which might be attributed to its ability Julia Cooke, Open University, UK to thrive in a broad range of ecological niches. In this study, a multidisciplinary approach Reviewed by: was used to depict variations in morphology, biochemistry (pigment and phenol content) Stephen Summers, and epiphytic bacterial communities along a depth gradient (4–28 m) in the GoA. Along Heriot-Watt University, UK Lara Beth Ainley, this gradient, H. stipulacea increased leaf area and pigment contents (Chlorophyll a and Macquarie University, Australia b, total Carotenoids), while total phenol contents were mostly uniform. H. stipulacea *Correspondence: displayed a well conserved core bacteriome, as assessed by 454-pyrosequencing Gidon Winters of 16S rRNA gene reads amplified from metagenomic DNA. -
The Origin of Plastids By: Cheong Xin Chan, Ph.D
A Collaborative Learning Space for Science ABOUT FACULTY STUDENTS INTERMEDIATE CELL ORIGINS AND METABOLISM | Lead Editor: Gary Cote, Mario De Tullio The Origin of Plastids By: Cheong Xin Chan, Ph.D. & Debashish Bhattacharya, Ph.D. (Rutgers, The State University of New Jersey) © 2010 Nature Education Citation: Chan, C. X. & Bhattacharya, D. (2010) The Origin of Plastids. Nature Education 3(9):84 Plastids are core components of photosynthesis in plants and algae. Scientists are currently debating the events leading to the appearance of plastids in eukaryotic cells. Organelles, called plastids, are the main sites of photosynthesis in eukaryotic cells. Chloroplasts, as well as any other pigment containing cytoplasmic organelles that enables the harvesting and conversion of light and carbon dioxide into food and energy, are plastids. Found mainly in eukaryotic cells, plastids can be grouped into two distinctive types depending on their membrane structure: primary plastids and secondary plastids. Primary plastids are found in most algae and plants, and secondary, more-complex plastids are typically found in plankton, such as diatoms and dinoflagellates. Exploring the origin of plastids is an exciting field of research because it enhances our understanding of the basis of photosynthesis in green plants, our primary food source on planet Earth. Primary Plastids and Endosymbiosis Where did plastids originate? Their origin is explained by endosymbiosis, the act of a unicellular heterotrophic protist engulfing a free-living photosynthetic cyanobacterium and retaining it, instead of digesting it in the food vacuole (Margulis 1970; McFadden 2001; Kutschera & Niklas 2005). The captured cell (the endosymbiont) was then reduced to a functional organelle bound by two membranes, and was transmitted vertically to subsequent generations. -
Inflammatory Bacteriome Featuring Fusobacterium Nucleatum and Pseudomonas Aeruginosa Identified in Association with Oral Squamous Cell Carcinoma
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 6 March 2017 doi:10.20944/preprints201703.0024.v1 Peer-reviewed version available at Scientific Reports 2017, 7, , 1834; doi:10.1038/s41598-017-02079-3 Inflammatory Bacteriome Featuring Fusobacterium nucleatum and Pseudomonas aeruginosa Identified in Association with Oral Squamous Cell Carcinoma Nezar Noor Al-hebshi 1,2,*, Akram Thabet Nasher 3, Mohamed Yousef Maryoud 1, Husham E. Homeida 1, Tsute Chen 4, Ali Mohamed Idris 1 and Newell W Johnson 5 1 Department of Maxillofacial Surgery and Diagnostic Sciences, College of Dentistry, Jazan University, Jazan, Saudi Arabia. 2 Kornberg School of Dentistry, Temple University, Philadelphia, PA, USA. 3 Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Sana’a University, Yemen. 4 Department of Microbiology, Forsyth Institute, Cambridge, MA, USA. 5 Menzies Health Institute Queensland and School of Dentistry and Oral Health, Griffith University, Queensland, Australia. *Corresponding authors: Nezar Noor Al-hebshi, Kornberg School of Dentistry, Temple University, 3223 N Board Street, Philadelphia 19462, PA, USA. Email: [email protected] Abstract: Studies on the possible association between bacteria and oral squamous cell carcinoma (OSCC) remain inconclusive, largely due to methodological variations/limitations. The objective of this study was to characterize the species composition as well as functional attributes of the bacteriome associated with OSCC. DNA obtained from 20 fresh OSCC biopsies (cases) and 20 deep-epithelium swabs (matched control subjects) were sequenced for the V1-V3 region using Illumina’s 2x300 bp chemistry. High quality, non-chimeric merged reads were classified to species level using a prioritized BLASTN-algorithm. Downstream analyses were performed using QIIME, PICRUSt, and LEfSe. -
Restriction-Modification Systems As Mobile Genetic Elements in the Evolution of an Intracellular Symbiont
Restriction-Modification Systems as Mobile Genetic Elements in the Evolution of an Intracellular Symbiont Hao Zheng,y,1 Carsten Dietrich,y,1 Yuichi Hongoh,2 and Andreas Brune*,1 1Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany 2Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Japan yThese authors contributed equally to this work. *Corresponding author: E-mail: [email protected]. Associate editor: Eduardo Rocha Abstract Long-term vertical transmission of intracellular bacteria causes massive genomic erosion and results in extremely small genomes, particularly in ancient symbionts. Genome reduction is typically preceded by the accumulation of pseudogenes and proliferation of mobile genetic elements, which are responsible for chromosome rearrangements during the initial stage of endosymbiosis. We compared the genomes of an endosymbiont of termite gut flagellates, “Candidatus Endomicrobium trichonymphae,” and its free-living relative Endomicrobium proavitum anddiscoveredmanyremnants of restriction-modification (R-M) systems that are consistently associated with genome rearrangements in the endosym- biont genome. The rearrangements include apparent insertions, transpositions, and the duplication of a genomic region; there was no evidence of transposon structures or other mobile elements. Our study reveals a so far unrecognized mechanism for genome rearrangements in intracellular symbionts and sheds new light on the general role of R-M systems in genome evolution. Key words: restriction-modification system, CRISPR-Cas system, mobile genetic elements, endosymbiont, genome reduction. Mutualistic symbioses between bacteria and eukaryotes are indicate that it is still in an early stage of genome reduction ubiquitous in nature, and they can greatly affect the genomes (Hongoh et al. 2008).