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1. Tricin-lignins: occurrence and quantitation of tricin in relation to phylogeny.

Author

Lan W, Rencoret J, Lu F, Karlen SD, Smith BG, Harris PJ, Del Río JC, and Ralph J

Subjects
Chromatography, Liquid, Mass Spectrometry, Poaceae classification, Poaceae metabolism, Flavonoids metabolism, Lignin metabolism, Phylogeny
Abstract

Tricin [5,7-dihydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-4H-chromen-4-one], a flavone, was recently established as an authentic monomer in grass lignification that likely functions as a nucleation site. It is linked onto lignin as an aryl alkyl ether by radical coupling with monolignols or their acylated analogs. However, the level of tricin that incorporates into lignin remains unclear. Herein, three lignin characterization methods: acidolysis; thioacidolysis; and derivatization followed by reductive cleavage; were applied to quantitatively assess the amount of lignin-integrated tricin. Their efficiencies at cleaving the tricin-(4'-O-β)-ether bonds and the degradation of tricin under the corresponding reaction conditions were evaluated. A hexadeuterated tricin analog was synthesized as an internal standard for accurate quantitation purposes. Thioacidolysis proved to be the most efficient method, liberating more than 91% of the tricin with little degradation. A survey of different seed-plant species for the occurrence and content of tricin showed that it is widely distributed in the lignin from species in the family Poaceae (order Poales). Tricin occurs at low levels in some commelinid monocotyledon families outside the Poaceae, such as the Arecaceae (the palms, order Arecales) and Bromeliaceae (Poales), and the non-commelinid monocotyledon family Orchidaceae (Orchidales). One eudicotyledon was found to have tricin (Medicago sativa, Fabaceae). The content of lignin-integrated tricin is much higher than the extractable tricin level in all cases. Lignins, including waste lignin streams from biomass processing, could therefore provide a large and alternative source of this valuable flavone, reducing the costs, and encouraging studies into its application beyond its current roles., (© 2016 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Published
2016
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2. The challenge of West Nile virus in Europe: knowledge gaps and research priorities

Author

Sebastian Ulbert, Norbert Nowotny, Ana Moreno, Luisa Barzon, N. Pardigon, Penelope Koraka, Antonio Tenorio, Miguel Ángel Jiménez-Clavero, Jordi Figuerola, Paolo Cordioli, Niek N. Sanders, Byron E. E. Martina, Annapaola Rizzoli, Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), Centro de Investigacion en Sanidad Animal (INIA-CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Universita degli Studi di Padova, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna 'Bruno Ubertini' (IZSLER), Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Erasmus University Medical Center [Rotterdam] (Erasmus MC), University of Veterinary Medicine [Vienna] (Vetmeduni), Sultan Qaboos University (SQU), Institut Pasteur [Paris], Universiteit Gent = Ghent University [Belgium] (UGENT), Fraunhofer Institute for Cell Therapy and Immunology (Fraunhofer IZI), Fraunhofer (Fraunhofer-Gesellschaft), Instituto de Salud Carlos III [Madrid] (ISC), This paper is the product of a cooperative action promoted by the Coordinators and delegates of the EU funded projects on West Nile virus under the 7th European Programme, in particular the EuroWestNile project (www.eurowestnile.org, GA n. 261391), the EDENext project (www.edenext.eu , GA n. 261504) the Wings project (www.west-nile-shield-project.eu , GA n. 261426), and the Vectorie project (www.vectorie.eu , GA n. 261466). This study was partially funded by EU grant FP7-261504 EDENext and is catalogued by the EDENext Steering Committee as EDENext 142 (http://www.edenext.eu). AR was partially funded by the Autonomous Province of Trento grant LExEM (http://www.lexem.eu). The contents of this publication are the sole responsibility of the authors and don't necessarily reflect the views of the European Commission., This paper is dedicated to the memory of our wonderful colleague and friend, Dr Paolo Cordioli, who recently passed away. We thank the European Centre for Disease Prevention and Control (ECDC) for supporting this initiative and for promoting a stronger integration between public health and research in Europe. We also thank Dr Jolanta Kolodziejek of the Institute of Virology, University of Veterinary Medicine Vienna for establishing the phylogenetic trees and Matteo Marcantonio of the GIS/RS platform at the Edmund Mach Foundation for preparing the map in Figure 1, European Project: 261391,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,EUROWESTNILE(2011), European Project: 261504,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,EDENEXT(2011), European Project: 261426,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,WINGS(2011), European Project: 261466,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,VECTORIE(2010), Virology, Università degli Studi di Padova = University of Padua (Unipd), Institut Pasteur [Paris] (IP), Universiteit Gent = Ghent University (UGENT), and Publica

Subjects
Health Knowledge, Attitudes, Practice, Veterinary medicine, Economic growth, WNV STRAINS, Epidemiology, viruses, MESH: Health Knowledge, Attitudes, Practice, medicine.disease_cause, Disease Outbreaks, EXPERIMENTAL-INFECTION, ENVELOPE PROTEIN, Neuroinvasive disease, Medicine and Health Sciences, MESH: Genetic Variation, MESH: Disease Outbreaks, MESH: Phylogeny, Phylogeny, media_common, EARLY WARNING SYSTEM, biology, SUBSTITUTION, AMINO-ACID, 3. Good health, Europe, MESH: Research, Geography, Population Surveillance, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, West Nile virus, SPARROWS PASSER-DOMESTICUS, media_common.quotation_subject, Ecology (disciplines), MESH: Population Surveillance, SDG 3 - Good Health and Well-being, Virology, medicine, Humans, media_common.cataloged_instance, Veterinary Sciences, European union, TIME RT-PCR, Settore VET/06 - PARASSITOLOGIA E MALATTIE PARASSITARIE DEGLI ANIMALI, MESH: West Nile virus, MESH: West Nile Fever, MESH: Humans, Research, LINEAGE 1 STRAIN, Public Health, Environmental and Occupational Health, Genetic Variation, Outbreak, biology.organism_classification, USUTU VIRUS, Early warning system, MESH: Europe, CULEX-PIPIENS MOSQUITOS, Usutu virus, West Nile Fever, Diversity (politics)
Abstract

West Nile virus (WNV) is continuously spreading across Europe, and other continents, i.e. North and South America and many other regions of the world. Despite the overall sporadic nature of outbreaks with cases of West Nile neuroinvasive disease (WNND) in Europe, the spillover events have increased and the virus has been introduced into new areas. The high genetic diversity of the virus, with remarkable phenotypic variation, and its endemic circulation in several countries, require an intensification of the integrated and multidisciplinary research efforts built under the 7th Framework Programme of the European Union (FP7). It is important to better clarify several aspects of WNV circulation in Europe, including its ecology, genomic diversity, pathogenicity, transmissibility, diagnosis and control options, under different environmental and socio-economic scenarios. Identifying WNV endemic as well as infection-free areas is becoming a need for the development of human vaccines and therapeutics and the application of blood and organs safety regulations. This review, produced as a joint initiative among European experts and based on analysis of 118 scientific papers published between 2004 and 2014, provides the state of knowledge on WNV and highlights the existing knowledge and research gaps that need to be addressed with high priority in Europe and neighbouring countries.

Published
2015

3. Presence of Recombinant Bat Coronavirus GCCDC1 in Cambodian Bats

Author

Feng Zhu, Veasna Duong, Xiao Fang Lim, Vibol Hul, Tanu Chawla, Lucy Keatts, Tracey Goldstein, Alexandre Hassanin, Vuong Tan Tu, Philippe Buchy, October M. Sessions, Lin-Fa Wang, Philippe Dussart, Danielle E. Anderson, Duke-NUS Medical School [Singapore], Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Wildlife Conservation Society (WCS), University of California [Davis] (UC Davis), University of California (UC), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Vietnam Academy of Science and Technology (VAST), University of Melbourne, and DEA and L-FW were supported by Grants NRF2012NRFCRP001-056 and NRF2016NRF-NSFC002-013 from the Singapore National Research Foundation. This study was made possible by the generous support of the American people through the United States Agency for International Development (USAID) Emerging Pandemic Threats PREDICT project (cooperative agreement number GHN-A-OO-09-00010-00 and AID-OAA-A-14-00102). The contents of this paper are the responsibility of the authors and do not necessarily reflect the views of the US Agency for International Development or the US Government. The fieldwork was supported in part by the National Authority for Preah Vihear, UNESCO, 'Société des amis du Muséum et du Jardin des Plantes', and the Muséum national d’Histoire naturelle.

Subjects
Recombination, Genetic, China, Coronaviridae, Coronaviridae Infections, [SDV]Life Sciences [q-bio], viruses, bats, coronavirus, virus diseases, cross-species transmission, Genome, Viral, zoonosis, recombination, respiratory tract diseases, Evolution, Molecular, Phylogeography, co-infection, Infectious Diseases, Chiroptera, Virology, Animals, GCCDC1, Cambodia, Phylogeny, Disease Reservoirs
Abstract

International audience; Bats have been recognized as an exceptional viral reservoir, especially for coronaviruses. At least three bat zoonotic coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have been shown to cause severe diseases in humans and it is expected more will emerge. One of the major features of CoVs is that they are all highly prone to recombination. An extreme example is the insertion of the P10 gene from reoviruses in the bat CoV GCCDC1, first discovered in Rousettus leschenaultii bats in China. Here, we report the detection of GCCDC1 in four different bat species (Eonycteris spelaea, Cynopterus sphinx, Rhinolophus shameli and Rousettus sp.) in Cambodia. This finding demonstrates a much broader geographic and bat species range for this virus and indicates common cross-species transmission. Interestingly, one of the bat samples showed a co-infection with an Alpha CoV most closely related to RsYN14, a virus recently discovered in the same genus (Rhinolophus) of bat in Yunnan, China, 2020. Taken together, our latest findings highlight the need to conduct active surveillance in bats to assess the risk of emerging CoVs, especially in Southeast Asia.

Published
2022

4. Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes

Author

Panagiotis S. Adam, Simonetta Gribaldo, Guillaume Borrel, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris] (IP), Université Paris Diderot - Paris 7 (UPD7), P.S.A. is supported by a PhD fellowship from Paris Diderot University and by funds from the PhD Programme 'Frontières du Vivant (FdV)–Programme Bettencourt.' G.B. is a recipient of a Roux-Cantarini fellowship from the Institut Pasteur. S.G. acknowledges funding from the French National Agency for Research Grant ArchEvol (ANR-16-CE02-0005-01)., We thank Alexander Probst for feedback on an earlier version of the paper, and two anonymous reviewers whose comments helped improve clarity and correctness of the manuscript., ANR-16-CE02-0005,Arch-Evol,Approches phylogenomiques pour étudier l'origine et évolution des Archées(2016), and Institut Pasteur [Paris]

Subjects
0301 basic medicine, Enzyme complex, MESH: Genome, Archaeal, LUCA, [SDV]Life Sciences [q-bio], MESH: Genome, Bacterial, Genome, Corrections, chemistry.chemical_compound, Genome, Archaeal, MESH: Multienzyme Complexes/genetics, methanogens, Phylogeny, MESH: Phylogeny, Genetics, Carbon Monoxide, Multidisciplinary, Last universal ancestor, Carbon fixation, Acetyl-CoA, MESH: Carbon Cycle, Aldehyde Oxidoreductases, Biological Evolution, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, PNAS Plus, MESH: Bacteria/enzymology, Wood–Ljungdahl pathway, Wood-Ljungdahl pathway, MESH: Aldehyde Oxidoreductases/metabolism, Carbon monoxide dehydrogenase, 030106 microbiology, MESH: Bacteria/genetics, Acetate-CoA Ligase, Bacterial genome size, Biology, MESH: Biological Evolution, MESH: Aldehyde Oxidoreductases/genetics, Carbon Cycle, 03 medical and health sciences, MESH: Carbon Monoxide/metabolism, Multienzyme Complexes, MESH: Archaea/genetics, evolution, MESH: Acetate-CoA Ligase/metabolism, MESH: Multienzyme Complexes/metabolism, MESH: Archaea/enzymology, Bacteria, MESH: Acetate-CoA Ligase/genetics, Archaea, acetogens, 030104 developmental biology, chemistry, biology.protein, Genome, Bacterial
Abstract

Erratum in : Correction for Adam et al., Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes. [Proc Natl Acad Sci U S A. 2018]; International audience; Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ ACS) is a five-subunit enzyme complex responsible for the carbonyl branch of the Wood-Ljungdahl (WL) pathway, considered one of the most ancient metabolisms for anaerobic carbon fixation, but its origin and evolutionary history have been unclear. While traditionally associated with methanogens and acetogens, the presence of CODH/ACS homologs has been reported in a large number of un-cultured anaerobic lineages. Here, we have carried out an exhaustive phylogenomic study of CODH/ACS in over 6,400 archaeal and bacterial genomes. The identification of complete and likely functional CODH/ACS complexes in these genomes significantly expands its distribution in microbial lineages. The CODH/ACS complex displays astounding conservation and vertical inheritance over geological times. Rare intradomain and interdomain transfer events might tie into important functional transitions, including the acquisition of CODH/ACS in some archaeal methanogens not known to fix carbon, the tinkering of the complex in a clade of model bacterial acetogens, or emergence of archaeal-bacterial hybrid complexes. Once these transfers were clearly identified, our results allowed us to infer the presence of a CODH/ACS complex with at least four subunits in the last universal common ancestor (LUCA). Different scenarios on the possible role of ancestral CODH/ACS are discussed. Despite common assumptions, all are equally compatible with an autotrophic, mixotrophic, or heterotrophic LUCA. Functional characterization of CODH/ACS from a larger spectrum of bacterial and archaeal lineages and detailed evolutionary analysis of the WL methyl branch will help resolve this issue.

Published
2018

5. Genome-scale rates of evolutionary change in bacteria

Author

Jane Hawkey, David J. Edwards, Simon Le Hello, Kathryn E. Holt, Mathieu Fourment, Edward C. Holmes, François-Xavier Weill, Sebastián Duchêne, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Centre for Systems Genomics, The University of MelbourneParkville, VIC, Australia., Department of Biochemistry and Molecular Biology, Centre National de Référence - National Reference Center Escherichia coli, Shigella et Salmonella (CNR-ESS), Institut Pasteur [Paris] (IP), This research was funded by the NHMRC (Australia Fellowship#AF30 to E. C. H., Career Development Fellowship #1061409 toK. E. H.). S. D. was supported by a McKenzie fellowship from the University of Melbourne.This paper was supported by the following grant(s):National Health and Medical Research Council 1061409.National Health and Medical Research Council GNT1037231., and Institut Pasteur [Paris]

Subjects
0301 basic medicine, 0106 biological sciences, Mechanisms of Evolution, Evolutionary change, Genome scale, Bacterial genome size, phylogeny, Genome, 010603 evolutionary biology, 01 natural sciences, Orders of magnitude (bit rate), Evolution, Molecular, 03 medical and health sciences, Phylogenetics, evolution, Molecular clock, Evolutionary dynamics, 030304 developmental biology, Whole genome sequencing, Genetics, 0303 health sciences, biology, Bacteria, Models, Genetic, molecular clock, Genetic Variation, General Medicine, biology.organism_classification, Biological Evolution, 030104 developmental biology, Ancient DNA, 13. Climate action, Evolutionary biology, time-dependency, Microbial Evolution and Epidemiology, Mutation, Human genome, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, substitution rates, Genome, Bacterial, Research Paper
Abstract

Estimating the rates at which bacterial genomes evolve is critical to understanding major evolutionary and ecological processes such as disease emergence, long-term host-pathogen associations, and short-term transmission patterns. The surge in bacterial genomic data sets provides a new opportunity to estimate these rates and reveal the factors that shape bacterial evolutionary dynamics. For many organisms estimates of evolutionary rate display an inverse association with the time-scale over which the data are sampled. However, this relationship remains unexplored in bacteria due to the difficulty in estimating genome-wide evolutionary rates, which are impacted by the extent of temporal structure in the data and the prevalence of recombination. We collected 36 whole genome sequence data sets from 16 species of bacterial pathogens to systematically estimate and compare their evolutionary rates and assess the extent of temporal structure in the absence of recombination. The majority (28/36) of data sets possessed sufficient clock-like structure to robustly estimate evolutionary rates. However, in some species reliable estimates were not possible even with “ancient DNA” data sampled over many centuries, suggesting that they evolve very slowly or that they display extensive rate variation among lineages. The robustly estimated evolutionary rates spanned several orders of magnitude, from 10−6 to 10−8 nucleotide substitutions site-1 year-1. This variation was largely attributable to sampling time, which was strongly negatively associated with estimated evolutionary rates, with this relationship best described by an exponential decay curve. To avoid potential estimation biases such time-dependency should be considered when inferring evolutionary time-scales in bacteria.

Published
2016