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Authors: Carol A Fulcher Anamika Kothari Ron Caspi Maneesh Yadav An online version of this diagram is available through BioCyc.org and may be used for analysis of omics datasets. Lines in the diagram correspond to reactions; nodes correspond to metabolites. Markus Krummenacker Ingrid Keseler Pathways are colored according to their cellular function, such as biosynthesis of cofactors. Mtbh37rvCyc: Mycobacterium tuberculosis H37Rv Cellular Overview Reactions not assigned to any pathway are in the far right of the cytoplasm. Suzanne Paley Peter D Karp In the membrane are transporters (with arrows) and other membrane proteins. a dimycocerosyl a mycobacterial phthiocerol sulfolipid connections between pathways are omitted for legibility. Rv3237c Rv1490 Rv0068 LpqS Rv2729c Rv2042c Rv1006 Rv2901c LppX Rv1181 Rv1245c Rv0574c Rv3186 Rv3213c IniA PhoP Rv2998 Rv3779 CpsA Rv3173c KdpD Rv1075c Rv3691 Rv2690c Rv1639c Rv0968 SepF Rv3694c Rv2693c Rv1627c LpqN Rv0628c Rv1785c Rv0383c Rv1518 Rv0846c Rv0523c Rv2414c Rv3558 Rv0338c DppA Rv2994 Rv0849 Rv2715 Rv1648 Rv0897c ClpB Rv2942 Rv2963 Rv3271c GcpE Rv3885c RpsA Rv3055 Rv0463 Rv0398c Rv2551c Rv1753c Rv0613c Rv3474 Rv1254 Rv0460 Rv0364 Rv0999 Rv1671 Rv1988 Rv3000 Rv3657c Rv2144c TatA SupB CydD Rv0088 Rv3325 Rv1087A Rv3632 Rv3823c NusA Rv0246 Rv2732c Rv3401 Rv0774c Rv2185c SecA Rv2446c Rv0927c Rv3789 Rv1194c Rv1145 Rv1787 Rv1882c Rv3346c Rv0048c SigK Rv3723 Rv0064 Rv1172c Rv2644c Rv3738c Rv1546 Rv3018c Rv0826 Rv3394c Rv0093c Rv3035 Rv2676c Rv0842 Rv0490 UspC Rv3770c Rv1578c Rv0146 Rv3067 Rv0874c Rv0519c Rv1610 Rv0177 Rv1626 MbtD InfC Rv0566c Rv0207c EspR Rv3131 Rv1428c Rv1754c a dimycocerosyl a mycobacterial phthiocerol sulfolipid Rv2198c Rv1050 Rv1091 Rv2600 Cofactor, Prosthetic Group, Electron Carrier, and Vitamin Biosynthesis Detoxification DnaJ Amine and Degradation/Utilization/ Fatty Acid and Lipid Biosynthesis Assimilation - Other Polyamine γ a ring-opened 7- β-D-glucose an oxidized L-alanyl- -D- a [protein]-L- adenosylcobalamin biosynthesis II (aerobic) Biosynthesis L-arabinitol 8-oxo-(d)GTP detoxification II cob(II)yrinate roseoflavin 6-phosphate glutamyl-L-lysyl- ditrans,octacis- proline (ω = 180) mycothiol flavin biosynthesis I (bacteria and plants) superpathway of adenosylcobalamin salvage from cobinamide I thiamine diphosphate adenosylcobalamin NAD salvage pathway I (PNC VI cycle) thiamine diphosphate Fermentation mixed acid fermentation reactive oxygen species degradation oxidized GTP and octane oxidation methylguanine in DNA ATP ATP coenzyme F 420 trans, trans-farnesyl superpathway of mycolate biosynthesis a,c-diamide 5’-phosphate D-alanyl-D-alanine undecaprenyldiphospho- oxidation biosynthesis I (E.

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Bacteria Belonging to Pseudomonas Typographi Sp. Nov. from the Bark Beetle Ips Typographus Have Genomic Potential to Aid in the Host Ecology
insects Article Bacteria Belonging to Pseudomonas typographi sp. nov. from the Bark Beetle Ips typographus Have Genomic Potential to Aid in the Host Ecology Ezequiel Peral-Aranega 1,2 , Zaki Saati-Santamaría 1,2 , Miroslav Kolaˇrik 3,4, Raúl Rivas 1,2,5 and Paula García-Fraile 1,2,4,5,* 1 Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; [email protected] (E.P.-A.); [email protected] (Z.S.-S.); [email protected] (R.R.) 2 Spanish-Portuguese Institute for Agricultural Research (CIALE), 37185 Salamanca, Spain 3 Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague, Czech Republic; [email protected] 4 Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic 5 Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain * Correspondence: [email protected] Received: 4 July 2020; Accepted: 1 September 2020; Published: 3 September 2020 Simple Summary: European Bark Beetle (Ips typographus) is a pest that affects dead and weakened spruce trees. Under certain environmental conditions, it has massive outbreaks, resulting in attacks of healthy trees, becoming a forest pest. It has been proposed that the bark beetle’s microbiome plays a key role in the insect’s ecology, providing nutrients, inhibiting pathogens, and degrading tree defense compounds, among other probable traits. During a study of bacterial associates from I. typographus, we isolated three strains identified as Pseudomonas from different beetle life stages. In this work, we aimed to reveal the taxonomic status of these bacterial strains and to sequence and annotate their genomes to mine possible traits related to a role within the bark beetle holobiont.
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