Genome Mining Reveals the Genus

Total Page:16

File Type:pdf, Size:1020Kb

Genome Mining Reveals the Genus Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides Monique Royer, Ralf Koebnik, Melanie Marguerettaz, Valerie Barbe, Guillaume P. Robin, Chrystelle Brin, Sebastien Carrere, Camila Gomez, Manuela Huegelland, Ginka H. Voeller, et al. To cite this version: Monique Royer, Ralf Koebnik, Melanie Marguerettaz, Valerie Barbe, Guillaume P. Robin, et al.. Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non- ribosomally synthesized peptides. BMC Genomics, BioMed Central, 2013, 14, 10.1186/1471-2164-14- 658. hal-01209938 HAL Id: hal-01209938 https://hal.archives-ouvertes.fr/hal-01209938 Submitted on 29 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Royer et al. BMC Genomics 2013, 14:658 http://www.biomedcentral.com/1471-2164/14/658 RESEARCH ARTICLE Open Access Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides Monique Royer1, Ralf Koebnik2, Mélanie Marguerettaz1, Valérie Barbe3, Guillaume P Robin2, Chrystelle Brin4, Sébastien Carrere5, Camila Gomez1, Manuela Hügelland6, Ginka H Völler6, Julie Noëll1, Isabelle Pieretti1, Saskia Rausch6, Valérie Verdier2, Stéphane Poussier7, Philippe Rott1, Roderich D Süssmuth6 and Stéphane Cociancich1* Abstract Background: Various bacteria can use non-ribosomal peptide synthesis (NRPS) to produce peptides or other small molecules. Conserved features within the NRPS machinery allow the type, and sometimes even the structure, of the synthesized polypeptide to be predicted. Thus, bacterial genome mining via in silico analyses of NRPS genes offers an attractive opportunity to uncover new bioactive non-ribosomally synthesized peptides. Xanthomonas is a large genus of Gram-negative bacteria that cause disease in hundreds of plant species. To date, the only known small molecule synthesized by NRPS in this genus is albicidin produced by Xanthomonas albilineans. This study aims to estimate the biosynthetic potential of Xanthomonas spp. by in silico analyses of NRPS genes with unknown function recently identified in the sequenced genomes of X. albilineans and related species of Xanthomonas. Results: We performed in silico analyses of NRPS genes present in all published genome sequences of Xanthomonas spp., as well as in unpublished draft genome sequences of Xanthomonas oryzae pv. oryzae strain BAI3 and Xanthomonas spp. strain XaS3. These two latter strains, together with X. albilineans strain GPE PC73 and X. oryzae pv. oryzae strains X8-1A and X11-5A, possess novel NRPS gene clusters and share related NRPS-associated genes such as those required for the biosynthesis of non-proteinogenic amino acids or the secretion of peptides. In silico prediction of peptide structures according to NRPS architecture suggests eight different peptides, each specific to its producing strain. Interestingly, these eight peptides cannot be assigned to any known gene cluster or related to known compounds from natural product databases. PCR screening of a collection of 94 plant pathogenic bacteria indicates that these novel NRPS gene clusters are specific to the genus Xanthomonas and are also present in Xanthomonas translucens and X. oryzae pv. oryzicola. Further genome mining revealed other novel NRPS genes specific to X. oryzae pv. oryzicola or Xanthomonas sacchari. Conclusions: This study revealed the significant potential of the genus Xanthomonas to produce new non-ribosomally synthesized peptides. Interestingly, this biosynthetic potential seems to be specific to strains of Xanthomonas associated with monocotyledonous plants, suggesting a putative involvement of non-ribosomally synthesized peptides in plant-bacteria interactions. * Correspondence: [email protected] 1CIRAD, UMR BGPI, Montpellier Cedex 5, F-34398, France Full list of author information is available at the end of the article © 2013 Royer et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Royer et al. BMC Genomics 2013, 14:658 Page 2 of 19 http://www.biomedcentral.com/1471-2164/14/658 Background The A-domains are the gatekeepers of biosynthesis of Various bacteria, most prominently belonging to the orders the polypeptide due to the specificity of substrate binding Bacillales, Pseudomonadales or Actinomycetales, use non- pockets of NRPSs for their cognate substrates. Compared ribosomal peptide synthesis (NRPS) to produce peptides to the 22 proteinogenic amino acids used in ribosomal or other small molecules. These molecules exhibit broad protein synthesis, the utilization of hundreds of different structural diversity and display biological activities that non-proteinogenic amino acids has been described for range from adaptation to unfavorable environments, com- NRPS. Each substrate binding pocket of NRPSs is specific munication or competition with other microorganisms for its amino acid substrate, and predictive models based in their natural habitat, or even to action as virulence fac- on domain arrangement and on the sequence of modules tors (for review [1,2]). Non-ribosomal peptide synthetases have been deduced. The predictive power of these models (NRPSs) are megaenzymes, usually with a multimodular has been refined from sequence analyses of NRPS structure, that catalyze the non-ribosomal assembly of pep- A-domains with known specificity combined with exam- tides from proteinogenic and non-proteinogenic amino ples of crystal structures of A-domains [9-11], thus identi- acids [3,4]. A basic module consists of an adenylation do- fying amino acid residues crucial for A-domain specificity. main (A-domain) responsible for amino acid activation; a These models postulate specificity-conferring signatures peptidyl carrier protein domain (PCP-domain)—usually for NRPS A-domains consisting of ten critical amino acid adjacent to the A-domain—for thioesterification of the ac- residues putatively involved in amino acid or aryl acid sub- tivated amino acid; a condensation domain (C-domain), strate specificity. The number of NRPS modules and their which performs transpeptidation between the upstream domain organization within the enzymes determine the and downstream peptidyl and amino acyl thioesters to structure of the final peptide product. Using in silico ana- elongate the growing peptide chain. In addition to this lyses of the NRPS genes, these conserved features within basic subset of core domains, each NRPS system also has a the NRPS machinery allow prediction of the type, and chain-terminating thioesterase domain (TE-domain) that is sometimes even the structure, of the synthesized polypep- responsible for detachment of the mature polypeptide. tide. It is therefore possible to investigate the biosynthetic Typically, NRPS initiation modules lack a C-domain potential of a given bacterium by analysis of the architec- [3]. The exceptions are initiation modules of NRPS in- ture of its NRPS gene clusters. volved in biosynthesis of cyclic lipopeptides [5]. C- The transfer of a phosphopantetheinyl group to PCP- domains present in these initiation modules catalyze domains is required for posttranslational activation of N-acylation of the first amino acid with a fatty acid NRPSs. Inactive apo-NRPSs are converted to their active (with a β-hydroxy-carboxylic acid). Phylogenetic ana- holo-forms by transfer of the 4′-phosphopantetheinyl lyses of C-domains in NRPSs showed that C-domains (P-pant) moiety of coenzyme A to the sidechain hydroxyl of initiation modules, termed starter C-domains, segre- of a serine residue in the PCP-domains. The P-pant moi- gate in a separate phylogenetic clade distant from the ety serves to tether covalently the growing polypeptide C-domains of elongation NRPS modules [6]. In addition being assembled by NRPSs. Transfer of the P-pant moiety to the essential domains mentioned above (A, PCP, C and from coenzyme A to a serine residue is catalyzed by TE), optional auxiliary domains such as epimerization (E) 4′-phosphopantetheinyl transferase (PPTase). PPTases are or heterocyclization (Cy) domains can be found within involved not only in posttranslational activation of NRPS some NRPS modules. Commonly, epimerization domains but also in posttranslational activation of fatty acid and are located C-terminally of PCP-domains and perform polyketide synthases that do not contain PCP-domains epimerization of the last amino acid of the adjacent but instead have acyl carrier protein (ACP) domains. All peptidyl-thioester. Interestingly, biochemical data showed PPTases are recognized by a common signature sequence that C-domains involved in assembly of arthrofactin (V/I)G(I/V)D …x40-45… (F/W)(S/C/T)xKE(S/A)xxK, but not only catalyze transpeptidation between the up- overall sequence similarities are low [12-15]. Carrier
Recommended publications
  • Glycine Transaminase 1. Identification of The
    SAFETY DATA SHEET glycine transaminase Not for Private Therapeutic Use! 1. Identification of the Substance/preparation and of the company/undertaking 1.1 Identification of the Product: glycine transaminase (EXWM-2880) 1.2 Manufacture/Supplier Identification: Creative Enzymes 45-1 Ramsey Road Shirley, NY 11967, USA Tel: 1-631-562-8517 1-516-512-3133 Fax: 1-631-938-8127 E-mail: [email protected] Website: www.creative-enzymes.com 1.3 Relevant identified uses of the substance or mixture and uses advised against Identified uses: For research use only, not for human or veterinary use. 1.4 Emergency telephone number Emergency Phone #: +1-800-424-9300 (CHEMTREC Within USA and Canada) +1-703-527-3887 (CHEMTREC Outside USA and Canada) 2. Hazards Identification Physical/chemical hazards :n/a Human health hazards: Not specific hazard 3. EC No. / CAS No. EC No.:EC 2.6.1.4 CAS No.: 9032-99-9 4. First Aid Measures 4.1 Inhalation: If inhaled, remove to fresh air. If not breathing, give artificial respiration. If breathing is difficult, give oxygen. Get medical attention. 4.2 Ingestion: Do NOT induce vomiting unless directed to do so by medical personnel. Never give anything by mouth to an Unconscious person. If large quantities of this material are swallowed, call a physician immediately. Loosentight clothing such as a collar, tie, belt or waistband. Ingestion: Do NOT induce vomiting unless directed to do so by medical personnel. Never give anything by mouth to an Unconscious person. If large quantities of this material are swallowed, call a physician immediately.
    [Show full text]
  • Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
    Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341
    [Show full text]
  • Como As Enzimas Agem?
    O que são enzimas? Catalizadores biológicos - Aceleram reações químicas específicas sem a formação de produtos colaterais PRODUTO SUBSTRATO COMPLEXO SITIO ATIVO ENZIMA SUBSTRATO Características das enzimas 1 - Grande maioria das enzimas são proteínas (algumas moléculas de RNA tem atividade catalítica) 2 - Funcionam em soluções aquosas diluídas, em condições muito suaves de temperatura e pH (mM, pH neutro, 25 a 37oC) Pepsina estômago – pH 2 Enzimas de organismos hipertermófilos (crescem em ambientes quentes) atuam a 95oC 3 - Apresentam alto grau de especificidade por seus reagentes (substratos) Molécula que se liga ao sítio ativo Região da enzima e que vai sofrer onde ocorre a a ação da reação = sítio ativo enzima = substrato 4 - Peso molecular: varia de 12.000 à 1 milhão daltons (Da), são portanto muito grandes quando comparadas ao substrato. 5 - A atividade catalítica das Enzimas depende da integridade de sua conformação protéica nativa – local de atividade catalítica (sitio ativo) Sítio ativo e toda a molécula proporciona um ambiente adequado para ocorrer a reação química desejada sobre o substrato A atividade de algumas enzimas podem depender de outros componentes não proteicos Enzima ativa = Holoenzimas Parte protéica das enzimas + cofator Apoenzima ou apoproteína •Íon inorgânico •Molécula complexa (coenzima) Covalentemente ligados à apoenzima GRUPO PROSTÉTICO COFATORES Elemento com ação complementar ao sitio ativo as enzimas que auxiliam na formação de um ambiente ideal para ocorrer a reação química ou participam diretamente dela
    [Show full text]
  • Genome Mining Reveals the Genus Xanthomonas to Be A
    Royer et al. BMC Genomics 2013, 14:658 http://www.biomedcentral.com/1471-2164/14/658 RESEARCH ARTICLE Open Access Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides Monique Royer1, Ralf Koebnik2, Mélanie Marguerettaz1, Valérie Barbe3, Guillaume P Robin2, Chrystelle Brin4, Sébastien Carrere5, Camila Gomez1, Manuela Hügelland6, Ginka H Völler6, Julie Noëll1, Isabelle Pieretti1, Saskia Rausch6, Valérie Verdier2, Stéphane Poussier7, Philippe Rott1, Roderich D Süssmuth6 and Stéphane Cociancich1* Abstract Background: Various bacteria can use non-ribosomal peptide synthesis (NRPS) to produce peptides or other small molecules. Conserved features within the NRPS machinery allow the type, and sometimes even the structure, of the synthesized polypeptide to be predicted. Thus, bacterial genome mining via in silico analyses of NRPS genes offers an attractive opportunity to uncover new bioactive non-ribosomally synthesized peptides. Xanthomonas is a large genus of Gram-negative bacteria that cause disease in hundreds of plant species. To date, the only known small molecule synthesized by NRPS in this genus is albicidin produced by Xanthomonas albilineans. This study aims to estimate the biosynthetic potential of Xanthomonas spp. by in silico analyses of NRPS genes with unknown function recently identified in the sequenced genomes of X. albilineans and related species of Xanthomonas. Results: We performed in silico analyses of NRPS genes present in all published genome sequences of Xanthomonas spp., as well as in unpublished draft genome sequences of Xanthomonas oryzae pv. oryzae strain BAI3 and Xanthomonas spp. strain XaS3. These two latter strains, together with X. albilineans strain GPE PC73 and X.
    [Show full text]
  • Mai Motomontant De Llu to Mo Na Mini
    MAIMOTOMONTANT US009828618B2 DE LLU TO MO NA MINI (12 ) United States Patent ( 10 ) Patent No. : US 9 ,828 ,618 B2 Hidesaki et al. (45 ) Date of Patent: *Nov . 28 , 2017 (54 ) MICROORGANISM HAVING CARBON EP 2 738 247 Al 6 / 2014 DIOXIDE FIXATION CYCLE INTRODUCED TW 201311889 3 / 2013 THEREINTO WO WO - 2009 /046929 A2 4 / 2009 WO WO - 2009 /094485 A1 7 / 2009 WO WO - 2010 /071697 A1 6 / 2010 ( 71 ) Applicant: Mitsui Chemicals , Inc . , Tokyo ( JP ) WO WO - 2011 /099006 A2 8 / 2011 ( 72 ) Inventors: Tomonori Hidesaki, Singapore (SG ) ; WO WO 2013 /018734 A12 / 2013 Ryota Fujii, Chiba ( JP ); Yoshiko Matsumoto , Mobara ( JP ) ; Anjali OTHER PUBLICATIONS Madhavan , Singapore ( SG ) ; Su Sun Wendisch et al. , Current Opinion in Microbiology 2006, vol . 9 , p . Chong, Singapore ( SG ) 268 - 274 . * Chistoserdova et al. , Journal of Bacteriology , 1994 , vol. 176 , No . ( 73 ) Assignee : MITSUI CHEMICALS , INC . , Tokyo 23 , p . 7398 - 7404. * ( JP ) Schneider et al. , The Journal of Biological Chemistry , 2012 , vol . 287 , No. 1 , p . 757 - 766 Only . * ( * ) Notice : Subject to any disclaimer , the term of this Office Action issued in Chinese Patent Application No . patent is extended or adjusted under 35 201480002416 . 5 dated Jun . 23 , 2016 . U . S .C . 154 (b ) by 0 days . Erb et al. , “ The Apparent Malate Synthase Activity of Rhodobacter sphaeroides is Due to Two Paralogous Enzymes , (3S ) -Malyl - Co This patent is subject to a terminal dis enzyme A (COA ) B -Methylmalyl - CoA Lyase and (3S ) -Malyl -CoA claimer . Thioesterase ” , J . Bacteriol, Sep . 2009 , pp . 1249 - 1258 , vol. 192 , No . (21 ) Appl. No. : 14 /428 , 928 Yim et al.
    [Show full text]
  • O O2 Enzymes Available from Sigma Enzymes Available from Sigma
    COO 2.7.1.15 Ribokinase OXIDOREDUCTASES CONH2 COO 2.7.1.16 Ribulokinase 1.1.1.1 Alcohol dehydrogenase BLOOD GROUP + O O + O O 1.1.1.3 Homoserine dehydrogenase HYALURONIC ACID DERMATAN ALGINATES O-ANTIGENS STARCH GLYCOGEN CH COO N COO 2.7.1.17 Xylulokinase P GLYCOPROTEINS SUBSTANCES 2 OH N + COO 1.1.1.8 Glycerol-3-phosphate dehydrogenase Ribose -O - P - O - P - O- Adenosine(P) Ribose - O - P - O - P - O -Adenosine NICOTINATE 2.7.1.19 Phosphoribulokinase GANGLIOSIDES PEPTIDO- CH OH CH OH N 1 + COO 1.1.1.9 D-Xylulose reductase 2 2 NH .2.1 2.7.1.24 Dephospho-CoA kinase O CHITIN CHONDROITIN PECTIN INULIN CELLULOSE O O NH O O O O Ribose- P 2.4 N N RP 1.1.1.10 l-Xylulose reductase MUCINS GLYCAN 6.3.5.1 2.7.7.18 2.7.1.25 Adenylylsulfate kinase CH2OH HO Indoleacetate Indoxyl + 1.1.1.14 l-Iditol dehydrogenase L O O O Desamino-NAD Nicotinate- Quinolinate- A 2.7.1.28 Triokinase O O 1.1.1.132 HO (Auxin) NAD(P) 6.3.1.5 2.4.2.19 1.1.1.19 Glucuronate reductase CHOH - 2.4.1.68 CH3 OH OH OH nucleotide 2.7.1.30 Glycerol kinase Y - COO nucleotide 2.7.1.31 Glycerate kinase 1.1.1.21 Aldehyde reductase AcNH CHOH COO 6.3.2.7-10 2.4.1.69 O 1.2.3.7 2.4.2.19 R OPPT OH OH + 1.1.1.22 UDPglucose dehydrogenase 2.4.99.7 HO O OPPU HO 2.7.1.32 Choline kinase S CH2OH 6.3.2.13 OH OPPU CH HO CH2CH(NH3)COO HO CH CH NH HO CH2CH2NHCOCH3 CH O CH CH NHCOCH COO 1.1.1.23 Histidinol dehydrogenase OPC 2.4.1.17 3 2.4.1.29 CH CHO 2 2 2 3 2 2 3 O 2.7.1.33 Pantothenate kinase CH3CH NHAC OH OH OH LACTOSE 2 COO 1.1.1.25 Shikimate dehydrogenase A HO HO OPPG CH OH 2.7.1.34 Pantetheine kinase UDP- TDP-Rhamnose 2 NH NH NH NH N M 2.7.1.36 Mevalonate kinase 1.1.1.27 Lactate dehydrogenase HO COO- GDP- 2.4.1.21 O NH NH 4.1.1.28 2.3.1.5 2.1.1.4 1.1.1.29 Glycerate dehydrogenase C UDP-N-Ac-Muramate Iduronate OH 2.4.1.1 2.4.1.11 HO 5-Hydroxy- 5-Hydroxytryptamine N-Acetyl-serotonin N-Acetyl-5-O-methyl-serotonin Quinolinate 2.7.1.39 Homoserine kinase Mannuronate CH3 etc.
    [Show full text]
  • Information to Users
    INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandardm a r g ins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand corner and continuing from left to right in equal sections with small overlaps. Each original is also photographed in one exposure and is included in reduced form at the back of the book. Photographs included in the original manuscript have been reproduced xerographically in this copy. Higher quality 6" x 9" black and white photographic prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UMI directly to order. University Microfilms International A Bell & Howell Information Company 300 North Zeeb Road. Ann Arbor. Ml 48106-1346 USA 313/761-4700 800/521-0600 Order Number 91S0S67 Studies on the metabolism of oxalate, glyoxylate, glycolate and glycine by peroxisomes and mitochondria from rat liver Sutherland, Steven Thomas, Ph.D.
    [Show full text]
  • Nucleotide Sequence and Predicted Functions of the Entire Sinorhizobium Meliloti Psyma Megaplasmid
    Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid Melanie J. Barnetta, Robert F. Fishera, Ted Jonesb, Caridad Kompb, A. Pia Abolab, Fre´ de´ rique Barloy-Hublerc, Leah Bowserb, Delphine Capelac,d,e, Francis Galibertc,Je´ roˆ me Gouzyd, Mani Gurjalb, Andrea Honga, Lucas Huizarb, Richard W. Hymanb, Daniel Kahnd, Michael L. Kahnf, Sue Kalmanb,g, David H. Keatinga,h, Curtis Palmb, Melicent C. Pecka, Raymond Surzyckib,i, Derek H. Wellsa, Kuo-Chen Yeha,h,j, Ronald W. Davisb, Nancy A. Federspielb,k, and Sharon R. Longa,h,l aDepartment of Biological Sciences, and hHoward Hughes Medical Institute, Stanford University, Stanford, CA 94305; bStanford Center for DNA Sequencing and Technology, 855 California Avenue, Palo Alto, CA 94304; cLaboratoire de Ge´ne´ tique et De´veloppement, Faculte´deMe´ decine, 2 Avenue du Pr. Le´on Bernard, F-35043 Rennes Cedex, France; dLaboratoire de Biologie Mole´culaire de Relations Plantes–Microorganisms, Unite´Mixte de Recherche, 215 Institut National de la Recherche Agronomique–Centre National de la Recherche Scientifique, F-31326 Castanet Tolosan, France; and fInstitute of Biological Chemistry, Washington State University, Pullman, WA 99164 Contributed by Sharon R. Long, June 12, 2001 The symbiotic nitrogen-fixing soil bacterium Sinorhizobium me- pSymA provide versatility to S. meliloti and may be adaptive in liloti contains three replicons: pSymA, pSymB, and the chromo- both the free-living and symbiotic states. some. We report here the complete 1,354,226-nt sequence of pSymA. In addition to a large fraction of the genes known to be Materials and Methods specifically involved in symbiosis, pSymA contains genes likely to Library Construction and Sequencing.
    [Show full text]
  • DEEPT Genomics) Reveals Misclassification of Xanthomonas Species Complexes Into Xylella, Stenotrophomonas and Pseudoxanthomonas
    bioRxiv preprint doi: https://doi.org/10.1101/2020.02.04.933507; this version posted February 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Deep phylo-taxono-genomics (DEEPT genomics) reveals misclassification of Xanthomonas species complexes into Xylella, Stenotrophomonas and Pseudoxanthomonas Kanika Bansal1,^, Sanjeet Kumar1,$,^, Amandeep Kaur1, Shikha Sharma1, Prashant Patil1,#, Prabhu B. Patil1,* 1Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh. $Present address: Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. #Present address: Department of Microbiology, School of Medicine, University of Washington, Seattle, WA, USA. ^Equal Contribution *Corresponding author Running Title: Comprehensive phylo-taxono-genomics of Xanthomonas and its relatives. Correspondence: Prabhu B. Patil Email: [email protected] Principal Scientist CSIR- Institute of Microbial Technology Sector 39-A, Chandigarh, India- 160036 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.04.933507; this version posted February 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Genus Xanthomonas encompasses specialized group of phytopathogenic bacteria with genera Xylella, Stenotrophomonas and Pseudoxanthomonas being its closest relatives. While species of genera Xanthomonas and Xylella are known as serious phytopathogens, members of other two genera are found in diverse habitats with metabolic versatility of biotechnological importance. Few species of Stenotrophomonas are multidrug resistant opportunistic nosocomial pathogens. In the present study, we report genomic resource of genus Pseudoxanthomonas and further in-depth comparative studies with publically available genome resources of other three genera.
    [Show full text]
  • The Thermodynamics of the Krebs Cycle and Related Compounds
    The Thermodynamics of the Krebs Cycle and Related Compounds Cite as: Journal of Physical and Chemical Reference Data 19, 1049 (1990); https:// doi.org/10.1063/1.555878 Submitted: 16 June 1988 . Published Online: 15 October 2009 Stanley L. Miller, and David Smith-Magowan ARTICLES YOU MAY BE INTERESTED IN Erratum: Heat Capacities and Entropies of Organic Compounds in the Condensed Phase [J. Phys. Chem. Ref. Data 13, Suppl. 1 (1984)] Journal of Physical and Chemical Reference Data 19, 1075 (1990); https:// doi.org/10.1063/1.555861 Selected Values of Heats of Combustion and Heats of Formation of Organic Compounds Containing the Elements C, H, N, O, P, and S. Journal of Physical and Chemical Reference Data 1, 221 (1972); https:// doi.org/10.1063/1.3253099 Thermodynamics of Enzyme-Catalyzed Reactions: Part 7—2007 Update Journal of Physical and Chemical Reference Data 36, 1347 (2007); https:// doi.org/10.1063/1.2789450 Journal of Physical and Chemical Reference Data 19, 1049 (1990); https://doi.org/10.1063/1.555878 19, 1049 © 1990 American Institute of Physics for the National Institute of Standards and Technology. The Thermodynamics of the Krebs Cycle and Related Compounds Stanley L. Miller Department of Chemistry (B-017), University of California San Diego, La Jolla. California 92093 and David Smith-Magowana Chemical Thermodynamics Division. National Bureau of Standards. Gaithersburg. Maryland 20899 Received June 16, 1988; revised manuscript received March 20, 1990 A survey is made of the enthalpies of formation, third law entropies and Gibbs energies available for Krebs cycle and related compounds. These include formate, acetate, succinate, fumarate, glycine, alanine, aspartate and glutamate.
    [Show full text]
  • Manganese Orchestrates a Metabolic Shift Leading to the Increased Bioconversion of Glycerol Into Α-Ketoglutarate
    AIMS Bioengineering, 4(1): 12-27. DOI: 10.3934/bioeng.2017.1.12 Received: 29 Novermber 2016 Accepted: 26 December 2016 Published: 30 December 2016 http://www.aimspress.com/journal/Bioengineering Research article Manganese orchestrates a metabolic shift leading to the increased bioconversion of glycerol into α-ketoglutarate. Azhar A. Alhasawi and Vasu D. Appanna* Faculty of Science and Engineering, Laurentian University, Sudbury, ON, P3E 2C6, Canada * Corresponding: Email: [email protected]; Tel: 705-675-1151 ext: 2112. Abstract: Glycerol is a major by-product of the biodiesel industry and its transformation into value- added products is an ongoing technological challenge. Here we report on the ability of the nutritionally-versatile Pseudomonas fluorescens to synthesize copious amount of α-ketoglutarate (KG) in a glycerol medium supplemented with manganese (Mn). The enhanced production of this keto-acid was mediated by the increased activities of isocitrate dehydrogenase (ICDH)-(NAD)P dependent and aminotransaminases. At stationary phase of growth when the optimal quantity of KG was recorded, these enzymes exhibited maximal activities. Two isoforms of pyruvate carboxylase (PC) that were identified in the Mn-treated cells provided an effective route for the synthesis of oxaloacetate, a metabolite critical in the production of KG. Furthermore, the increased activities of phosphoenol pyruvate carboxylase (PEPC) and pyruvate orthophosphate dikinase (PPDK) ensured the efficacy of this KG-generating metabolic system by supplying pyruvate and ATP from the oxaloacetate synthesized by PC. Mn-exposed whole cells converted 90% of industrial glycerol into KG. This Mn-evoked metabolic network can be optimized into the economic transformation of glycerol into KG.
    [Show full text]
  • Photorespiratory Bypasses Lead to Increased Growth in Arabidopsis Thaliana: Are Predictions Consistent with Experimental Evidence?
    ORIGINAL RESEARCH published: 07 April 2016 doi: 10.3389/fbioe.2016.00031 Photorespiratory Bypasses Lead to Increased Growth in Arabidopsis thaliana: Are Predictions Consistent with Experimental Evidence? Georg Basler1,2† , Anika Küken3† , Alisdair R. Fernie4 and Zoran Nikoloski3* 1 Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA, 2 Department of Environmental Protection, Estación Experimental del Zaidín CSIC, Granada, Spain, 3 Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany, 4 Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany Arguably, the biggest challenge of modern plant systems biology lies in predicting the performance of plant species, and crops in particular, upon different intracellular and external perturbations. Recently, an increased growth of Arabidopsis thaliana plants was Edited by: achieved by introducing two different photorespiratory bypasses via metabolic engi- Patrik R. Jones, neering. Here, we investigate the extent to which these findings match the predictions Imperial College London, UK from constraint-based modeling. To determine the effect of the employed metabolic Reviewed by: Biswapriya Biswavas Misra, network model on the predictions, we perform a comparative analysis involving three University of Florida, USA state-of-the-art metabolic reconstructions of A. thaliana. In addition, we investigate Dong-Yup Lee, three scenarios with
    [Show full text]