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Authors: Pallavi Subhraveti Ron Caspi Peter Midford Peter D Karp An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000091785Cyc: Legionella longbeachae NSW150 Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari sn-glycerol spermidine 3-phosphate putrescine a sulfonate nitrate hydrogencarbonate predicted predicted ABC ABC transporter transporter RS16610 of sn- of spermidine/ glycerol 3- putrescine phosphate a sulfonate nitrate spermidine hydrogencarbonate putrescine sn-glycerol 3-phosphate Amino Acid Degradation Amine and Polyamine Biosynthesis Hormone Biosynthesis Aldehyde Degradation glutaminyl-tRNA gln Aminoacyl-tRNA Charging N 6 -(3-methylbut- a 1-palmitoyl-2- L-alanyl-γ-D- L-alanyl-γ-D- a [bis(guanylyl a [protein] biosynthesis via transamidation core a peptide with homospermidine homospermidine indole-3-acetate L-leucine degradation I a sulfurated 2-en-1-yl)- acyl-sn-glycerol glutamyl-meso-2,6- glutamyl-meso- UDP-N-acetyl- a [glutamine- γ-L-glutamyl- Polyprenyl Biosynthesis L-proline degradation I L-tyrosine degradation I methylglyoxal degradation I oligosaccharide- ATP molybdopterin) cys a type IV prepilin gly an N-terminal C-terminal glu biosynthesis II L-arginine degradation [sulfur carrier] 37 synthetase]- ATP biosynthesis I biosynthesis TCA cycle TCA cycle I (prokaryotic) adenosine lipid A (E. coli 3-phosphate diaminopimeloyl- UDP-N-acetyl- diaminopimelate α-D-muramate cofactor D-alanine L-alanine L-glutamate biotin II (AST pathway) L-tyrosine glu IV (bacteria) L-histidine degradation I in tRNA K-12 core type) D-alanine α-D-muramate chaperone]- putrescine putrescine (indole-3-yl) octaprenyl di-trans,poly-cis leu methylglyoxal diphosphate -undecaprenyl acetyl-CoA pro tyr (no GlcNAc) UDP-N- L-cysteine prepilin glutathione aminopeptidase homospermidine homospermidine acetonitrile arg lactoylglutathione tRNA (N6-isopentenyl 30S tyr tyr nitrile hydratase bifunctional acetylmuramate:L- bifunctional [glutamate- peptidase: synthetase: N: pepN biotin-- synthase: synthase: biosynthesis phosphate biosynthesis arginine N- his lyase: UDP-N- ribosomal RS12835 gln subunit beta: 4-methyl-2- proline adenosine(37)-C2)- lipid IV(A) alanyl-gamma-D- -ammonia ligase]- [acetyl-CoA- LLO_RS16880 LLO_RS16880 (2E,6E)-farnesyl (2E,6E)-farnesyl oxaloacetate 3-(4- LLO_RS17315 acetylmuramate:L- IscS subfamily LLO_RS08110 LLO_RS17480 aminopeptidase protein sym- sym- LLO_RS09720 IPP IPP succinyltransferase: histidine (R)-S- methylthiotransferase adenylyl-L-tyrosine carboxylase] trp trp an L-glutamyl- diphosphate diphosphate 2-methylcitrate oxopentanoate dehydrogenase/L- hydroxyphenyl) palmitoyltransferase alanyl-gamma-D- glutamyl- meso- cysteine prepilin glutathione N: pepN S6--L- tyr tyr (indol-3-yl) 2 LLO_RS08720 ammonia- lactoylglutathione MiaB: miaB imidazole Gln homospermidine homospermidine N -succinyl- glutamate gamma- PagP: pagP diaminopimelate phosphorylase/ ligase: [tRNA ] acetamide synthase: prpC pyruvate lyase: hutH glutamyl- meso- desulfurase: peptidase: synthase: glutamate RS12840 L-arginine semialdehyde [+ 2 isozymes] ligase: mpl [glutamate-- LLO_RS10545 glycerol isoprenyl malate dehydrogenase:citrate (Si)-synthase: gltA urocanate hydroxyacylglutathione diaminopimelate LLO_RS11720 LLO_RS08195 gshB ligase: rimK Asp-tRNA(Asn) amidase: octaprenyl 4-hydroxyphenylpyruvate ammonia-ligase] trp trp phosphate LLO_RS12985 N-succinylarginine dehydrogenase hydrolase: gloB 6 a 2-acyl-sn a hepta- ligase: mpl /Glu-tRNA(Gln) LLO_RS08515 diphosphate transferase: 3-methylbutanoyl- dioxygenase: hppD N -(3-methylbut- cysteine ala a peptide V-type ATP synthase: PutA: putA urocanate 5'-deoxyadenosine an unsulfurated adenylyltransferase: + + synthase: LLO_RS13650 malate dehydrogenase: dihydrolase: astB (S)-1-pyrroline- 2-en-1-yl)-2- met -glycerol 3- acylated core UDP-N-acetyl- desulfurase: a [protein] C- biotinyl-5'- H H hisF hisH amidotransferase: amidase: CoA hydratase: (R)-lactate [sulfur carrier] glnE a cleaved type synthase LLO_RS13530 LLO_RS14435 2 5-carboxylate homogentisate (methylsulfanyl) phosphate oligosaccharide UDP-N-acetylmuramoyl- α-D-muramoyl- LLO_RS15510 a peptide norophthalmate terminal α-L- adenylate gatC gatA gatB LLO_RS08535 isovaleryl-CoA N -succinyl- LLO_RS07520 IV prepilin [+ 7 isozymes] di-trans,octa-cis (S)-malate citrate adenosine 37 lipid A (E. coli γ L-alanyl-γ-D- glutamate-α- a 5-phosphooxy- octaprenyl dehydrogenase: L-ornithine L-alanyl- -D- (indol-3-yl)acetate -undecaprenyl homogentisate 4-imidazolone- in tRNA K-12 type) glutamyl-meso-2,6- a [glutamine L-glutamate ammonium L-glutamyl- diphosphate LLO_RS05520 glutamyl-meso-2,6- a [bis(guanylyl 1,2-dioxygenase: + F0F1 ATP + Gln diphosphate 5-propanoate synthetase]-O H H [tRNA ] synthase: aconitate hydratase: diaminopimeloyl- diaminopimelate ala molybdopterin) 3-methylcrotonyl- LLO_RS05895 4 -(5'-adenylyl) synthase LLO_RS02325 L-glutamate-5- imidazolonepropionase: pyruvate D-alanine cofactor LLO_RS16895 CoA N 2 -succinyl- 4-maleyl- -L-tyrosine Asp-tRNA(Asn) [+ 4 isozymes] semialdehyde LLO_RS04200 chaperone]-S- class II fumarate methylcrotonoyl- L-glutamate 5- /Glu-tRNA(Gln) all-trans- di-trans,octa-cis acetoacetate sulfanyl-L-cysteine hydratase: fumC CoA carboxylase: semialdehyde bifunctional N-formimino- met RS05480 met amidotransferase: octaprenyl -undecaprenyl fumarate maleylacetoacetate cis-aconitate LLO_RS05505 succinylglutamate- proline gatC gatA gatB diphosphate phosphate aconitate hydratase: isomerase: maiA L-glutamate semialdehyde dehydrogenase/L- a mature peptidoglycan a carboxy- a [glutamine L-alanyl-γ-D- L-alanyl-γ-D- LLO_RS02325 3-methylglutaconyl- a [DNA]-3'- a 5'-phospho- + formimidoylglutamase: NAD + menadione NADH H an acyl-CoA H O a D-tyrosyl- succinate dehydrogenase dehydrogenase: glutamate gamma- 4-fumaryl- (meso-diaminopimelate adenylated- synthetase]-O glutamyl-meso-2,6- glutamyl-L-lysyl- 2 ser sec thr thr [+ 4 isozymes] CoA Secondary Metabolite hydroxyl [DNA] cys [tRNA Tyr ] ATP roseoflavin a tRNA an L-glutaminyl- LLO_RS04190 4 flavoprotein subunit: sdhA astD semialdehyde acetoacetate containing) [ThiS sulfur- -(5'-adenylyl) diaminopimeloyl- D-alanyl-D-alanine RS13265 [tRNA Gln ] methylglutaconyl- Degradation 5'-phosphate 2 dehydrogenase -L-tyrosine tRNA charging CoA hydratase: N - carrier protein] D-alanine serine serine glu DNA ligase: NADH-quinone tol-pal system- LLO_RS05500 succinylglutamate PutA: putA myo-inositol degradation I lytic murein penicillin- D-tyrosyl- serine- LLO_RS05160 oxidoreductase: associated a sugar RS14200 a sugar succinate D-threo-isocitrate transglycosylase LD- binding tRNA(Tyr) bifunctional -tRNA IscS subfamily LLO_RS01430 bifunctional [glutamate- acyl-CoA gln Gln NADP-dependent isocitrate HMG-CoA glu fumarate NAD- riboflavin a tRNA myo-inositol B: mltB cysteine -ammonia ligase]- carboxypeptidase: protein deacylase: ligase: Ala asp ser dependent LLO_RS01435 thioesterase: a tRNA ala tRNA asp ser a tRNA dehydrogenase: icd LLO_RS02355 2: mrdA LLO_RS05405 kinase/FAD serS elongator ADP-forming succinate- hydroxymethylglutaryl- [+ 4 isozymes] DNA ligase desulfurase: nuoE nuoF adenylyl-L-tyrosine ybgC phe a tRNA Phe gly a tRNA Gly met initiator tRNA Met met thr a tRNA Thr asn tRNA Asn pro a tRNA Pro val a tRNA Val lys a tRNA Lys cys a tRNA Cys glu a tRNA glu his a tRNA His trp a tRNA Trp ile a tRNA Ile leu a tRNA Leu arg a tRNA Arg tyr a tRNA Tyr inositol 2- synthetase: a sugar RS11370 a sugar Met -CoA ligase: sucC sucD glu LLO_RS11720 phosphorylase/ LD- [+ 2 isozymes] tRNA glutamine-- CoA lyase: L-citrulline degradation dehydrogenase: LigA: ligA LLO_RS01450 [+ 3 isozymes] ribF a mature peptidoglycan cysteine [glutamate-- carboxypeptidase: alanine- tRNA ligase/ aspartate- serine- LLO_RS05490 a mature peptidoglycan nuoH nuoI an L-seryl- iolG γ ammonia-ligase] γ a tRNA Tyr with (L-alanyl- -D- strand (non- desulfurase: LLO_RS01465 LLO_RS03860 L-alanyl- -D- D-tyrosine sec phenylalanine- glycine--tRNA methionine-- methionine-- threonine- asparagine- proline-- valine-- -tRNA lysine- YqeY domain cysteine-- glutamate- histidine- -tRNA tryptophan-- isoleucine- leucine-- arginine-- tyrosine-- -tRNA acetoacetate L-methionine degradation roseoflavin [tRNA ] L-citrulline glutamyl-meso-2,6- reducing terminus) [DNA] NMN LLO_RS15510 nuoK nuoN adenylyltransferase: glutamyl-L- D-ala a carboxylate sulfate RS13435 sulfate -tRNA ligase: ligase: glyQ tRNA ligase: tRNA ligase: -tRNA -tRNA tRNA ligase: tRNA ligase: ligase: -tRNA fusion protein: tRNA ligase: -tRNA -tRNA ligase: tRNA ligase: -tRNA tRNA ligase: tRNA ligase: tRNA ligase: ligase: succinyl-CoA 2-oxoglutarate I (to L-homocysteine) scyllo-inosose adenine ornithine diaminopimeloyl-D- AMP glnE L-alanyl-γ-D- lysyl-D-alanine pheS pheT LLO_RS05430 LLO_RS01010 LLO_RS01010 ligase: thrS ligase: asnS LLO_RS04140 LLO_RS04215 alaS ligase: lysS LLO_RS06005 LLO_RS06010 ligase: gltX ligase: hisS aspS LLO_RS09060 ligase: ileS LLO_RS11855 LLO_RS12750 LLO_RS13340 serS dinucleotide alanine) tetrapeptide L-serine degradation met carbamoyltransferase: myo-inosose-2 a thiocarboxylated- D-ala glutamyl-meso- an L-methionyl- argF dehydratase: iolE ala [ThiS sulfur-
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    ABSTRACT BOZDAG, AHMET. Investigation of Methanol and Formaldehyde Metabolism in Bacillus methanolicus.(Under the direction of Prof. Michael C. Flickinger). Bacillus methanolicus is a Gram-positive aerobic methylotroph growing optimally at 50-53 °C. Wild-type strains of B. methanolicus have been reported to secrete 58 g/l of L- glutamate in fed-batch cultures. Mutants of B. methanolicus created via classical mutangenesis can secrete 37 g/l of L-lysine, at 50 °C. The genes required for methylotrophyin B. methanolicus are encoded by an endogenous plasmid, pBM19 in strain MGA3, except for hexulose phosphate synthase (hps) and phosphohexuloisomerase (phi) which are encoded on the chromosome.It is a promising candidate for industrial production of chemical intermediates or amino acids from methanol. B. methanolicus employs the ribulose monophospate (RuMP) pathway to assimilate the carbon derived from the methanol, but enzymes that dissimilate carbon are not identified, although formaldehyde and formate were identified as intermediates by 13C NMR. It is important to understand how methanol is oxidized to formaldehyde and then, to formate and carbon dioxide. This study aims to elucidate the methanol dissimilation pathway of B. methanolicus. Growth rates of B. methanolicus MGA3 were assessed on methanol, mannitol, and glucose as a substrate. B. methanolicus achieved maximum growth rate, µmax, when growing on 25 mM methanol, 0.65±0.007 h-1, and it gradually decreased to 0.231±0.004 h-1 at 2Mmethanol concentration which demonstrates substrate inhibition. The maximum growth rates (µmax) of B. methanolicus MGA3 on mannitol and glucose are 0.532±0.002 and 0.336±0.003 h-1, respectively.
  • Planctomycetes Attached to Algal Surfaces: Insight Into Their Genomes

    Planctomycetes Attached to Algal Surfaces: Insight Into Their Genomes

    MSc 2.º CICLO FCUP 2015 into Planctomycetes their Planctomycetes genomes attached attached to algal surfaces: Insight into to algal their genomes surfaces Mafalda Seabra Faria : Insight : Dissertação de Mestrado apresentada à Faculdade de Ciências da Universidade do Porto Laboratório de Ecofisiologia Microbiana da Universidade do Porto Biologia Celular e Molecular 2014/2015 Mafalda Seabra Faria Seabra Mafalda I FCUP Planctomycetes attached to algal surfaces: Insight into their genomes Planctomycetes attached to algal surfaces: Insight into their genomes Mafalda Seabra Faria Mestrado em Biologia Celular e Molecular Biologia 2015 Orientador Olga Maria Oliveira da Silva Lage, Professora Auxiliar, Faculdade de Ciências da Universidade do Porto Co-orientador Jens Harder, Senior Scientist and Professor, Max Planck Institute for Marine Microbiology FCUP II Planctomycetes attached to algal surfaces: Insight into their genomes Todas as correções determinadas pelo júri, e só essas, foram efetuadas. O Presidente do Júri, Porto, ______/______/_________ FCUP III Planctomycetes attached to algal surfaces: Insight into their genomes FCUP IV Planctomycetes attached to algal surfaces: Insight into their genomes “Tell me and I forget, teach me and I may remember, involve me and I learn.” Benjamin Franklin FCUP V Planctomycetes attached to algal surfaces: Insight into their genomes FCUP VI Planctomycetes attached to algal surfaces: Insight into their genomes Acknowledgements Foremost, I would like to express my sincere gratitude to my supervisor Professor
  • SI Table 1. Assessment of Genome Completeness

    SI Table 1. Assessment of Genome Completeness

    SI Table 1. Assessment of Genome Completeness COG family IMG gene object identifier Conserved gene set Large subunit ribosomal proteins COG0081 2062288324 Ribosomal protein L1 COG0244 2062347387 Ribosomal protein L10 COG0080 2062288323 Ribosomal protein L11 COG0102 Absent Ribosomal protein L13 COG0093 2062418832 Ribosomal protein L14 COG0200 2062418826 Ribosomal protein L15 COG0197 2062418838 Ribosomal protein L16/L10E COG0203 2062418836 Ribosomal protein L17 COG0256 2062418829 Ribosomal protein L18 COG0335 2062273558 Ribosomal protein L19 COG0090 2062418842 Ribosomal protein L2 COG0292 2062350539 Ribosomal protein L20 COG0261 2062142780 Ribosomal protein L21 COG0091 2062418840 Ribosomal protein L22 COG0089 2062138283 Ribosomal protein L23 COG0198 2062418834 Ribosomal protein L24 COG1825 2062269715 Ribosomal protein L25 (general stress protein Ctc) COG0211 2062142779 Ribosomal protein L27 COG0227 Absent Ribosomal protein L28 COG0255 2062418837 Ribosomal protein L29 COG0087 2062154483 Ribosomal protein L3 COG1841 2062335748 Ribosomal protein L30/L7E COG0254 Absent Ribosomal protein L31 COG0333 Absent Ribosomal protein L32 COG0267 Absent Ribosomal protein L33 COG0230 Absent Ribosomal protein L34 COG0291 2062350538 Ribosomal protein L35 COG0257 Absent Ribosomal protein L36 COG0088 2062138282 Ribosomal protein L4 COG0094 2062418833 Ribosomal protein L5 COG0097 2062418830 Ribosomal protein L6P/L9E COG0222 2062288326 Ribosomal protein L7/L12 COG0359 2062209880 Ribosomal protein L9 Small subunit ribosomal proteins COG0539 Absent Ribosomal protein