Dna sequence of both chromosomes of the cholerae pathogen Vibrio cholerae




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títuloDna sequence of both chromosomes of the cholerae pathogen Vibrio cholerae
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Supplementary Information
DNA Sequence of both chromosomes of the cholerae pathogen Vibrio cholerae
John F. Heidelberg*, Jonathan A. Eisen*, William C. Nelson*, Rebecca A. Clayton, Michelle L. Gwinn*, Robert J. Dodson*, Daniel H. Haft*, Erin K. Hickey*, Jeremy D. Peterson*, Lowell Umayam*, Steven R. Gill*, Karen E. Nelson, * Timothy D. Read*, Hervé Tettelin*, Delwood Richardson*, Maria D. Ermolaeva*, Jessica Vamathevan*, Steven Bass*, Haiying Qin*, Iona Dragoi*, Patrick Sellers*, Lisa McDonald*, Teresa Utterback*, Robert D. Fleishmann*, William C. Nierman*, Owen White*, Steven L. Salzberg*, Hamilton O. Smith*††, Rita R. Colwell, John J. Mekalanos, J. Craig Venter*††, Claire M. Fraser*.
* The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA

Center of Marine Biotechnology, University of Maryland Biotechnology Institute, 701 East Pratt St., Baltamore, MD 21202, USA and Department of Cell and Molecular Biology, University of Maryland, College Park, MD 20742, USA
Harvard Medical School, Department of Microbiology and Molecular Genetics, 200 Longwood Ave, Boston, MA 02115, USA

†† Current Address: Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA

Table of contents

Fig. S1 Phylogenetic tree of Transketolase 1 (tktA) homologs

Fig. S2 Phylogenetic tree of serine hydroxymethyltransferase (glyA) homologs

Fig. S3 Phylogenetic tree of ParA homologs

Table S1. Identification of Vibrio cholerae El Tor N16961 genes
Fig. S1. Phylogenetic tree of Transketolase 1 (tktA) homologs. The tree shows the genes of the V. cholerae tktA from the large chromosome and the small chromosome group together, suggesting a recent duplication. Homologs of tktA were identified by BLASTP and PSI-BLAST searches of the NCBI nr database and the TIGR unfinished genomes (http://www.tigr.org). Amino-acid sequences of the proteins were aligned using CLUSTALW and a neighbor-joining phylogenetic tree was generated from the alignment using the Phylip program (using the PAM based distance calculation). Hypervariable regions of the alignment and positions with gaps in many of the sequences were excluded from the analysis. * Preliminary data from unfinished TIGR genome. Abbreviations: AQUAE, Aquifex aeolicus; SYNSP, Synechococcus sp.; ENTFA, Enterococcus faecalis; BACSU, Bacillus subunittilis; DEIRA, Deinococcus radiodurans; HELPY, Helicobacter pylori; MYCGE, Mycoplasma genitalium; MYCPN, Mycoplasma pneumoniae; CHLTE, Chlorobium tepidum; TREPA, Treponema pallidum; RHOCA, Rhodopseudomonas capsulata; NEIME, Neisseria meningitidis; SHEPU, Shewanella putrefaciens; VIBCH, Vibrio cholerae; ECOLI, Escherichia coli; HAEIN, Haemophilus influenzae.




Fig. S2. Phylogenetic tree of serine hydroxymethyltransferase (glyA) homologs. The tree shows the genes of V. cholerae glyA from the large chromosome and the small chromosome group apart, suggesting that one of these two genes was acquired. Homologs of glyA were identified by BLASTP and PSI-BLAST searches of the NCBI nr database and the TIGR unfinished genomes (http://www.tigr.org). Amino-acid sequences of the proteins were aligned using CLUSTALW and a neighbor-joining phylogenetic tree was generated from the alignment using the Phylip program (using the PAM based distance calculation). Hypervariable regions of the alignment and positions with gaps in many of the sequences were excluded from the analysis. Tree. * Preliminary data from unfinished TIGR genome. Abbreviations: MYCGE, Mycoplasma genitalium; MYCPN, Mycoplasma pneumoniae; BORBU, Borrelia burgdorferi; HELPY, Helicobacter pylori; CAMJE, Campylobacter jejuni; RICPR, Rickettsia prowazekii; METEX, Methylobacterium extorquens; BRAJA, Bradyrhizobium japonicum; HYPME, Hyphomicrobium methylovorum; VIBCH, Vibrio cholerae; SYNSP, Synechococcus sp.; ENTFA, Enterococcus faecalis; STRPN, Streptococcus pneumoniae; STAAU, Staphylococcus aureus; BACSU, Bacillus subunittilis; NEIGO, Neisseria gonorrhoeae; NEIME, Neisseria meningitidis; ACTAC, Actinobacillus actinomycetemcomitans; HAEIN Haemophilus influenzae; ACIRA, Acinetobacter radioresistens; SHEPU, Shewanella putrefaciens; SALTY, Salmonella typhimurium; ECOLI, Escherichia coli; CHLTR, Chlamydia trachomatis; CHLPN, Chlamydia pneumoniae; STRCO, Streptomyces coelicolor; CORS1, Corynebacterium sp.; MYCTU, Mycobacterium tuberculosis; MYCLE, Mycobacterium leprae; AQUAE, Aquifex aeolicus; ARCFU, Archaeoglobus fulgidus; METJA, Methanococcus jannaschii; METTH, Methanobacterium thermoautotrophicum; METTM, Methanobacterium thermoautotrophicum (strain Marburg / DSM 2133).





Fig. S3. Phylogenetic tree of ParA homologs. The tree shows the grouping of the V. cholerae ParA from the large chromosome with other chromosomal ParAs, and the grouping of the V. cholerae ParA from the small chromosome with plasmid, phage, and megaplasmid ParAs, suggesting that the small chromosome may have originated as a plasmid or megaplasmid. Homologs of ParA were identified by BLASTP and PSI-BLAST searches of the NCBI nr database. Amino-acid sequences of the proteins were aligned using CLUSTALW and a neighbor-joining phylogenetic tree was generated from the alignment using the Phylip program (using the PAM based distance calculation). Hypervariable regions of the alignment and positions with gaps in many of the sequences were excluded from the analysis. The V. cholerae ParA homologs are underlined. Proposed ParA subunitfamilies are highlighted. Abbreviations: BORBU, Borrelia burgdorferi; PYRAB, Pyrococcus abyssi; PYRHO, Pyrococcus horikoshii; METJA, Methanococcus jannaschii; ENTFA, Enterococcus faecalis; ECOLI, Escherichia coli; PSEPU, Pseudomonas putida; PSEAE, Pseudomonas aeruginosa; VIBCH, Vibrio cholerae; STRCO, Streptomyces coelicolor; MYCTU, Mycobacterium tuberculosis; MYCLE, Mycobacterium leprae; DEIRA, Deinococcus radiodurans; TREPA, Treponema pallidum; BACSU, Bacillus subunittilis; RICPR, Rickettsia prowazekii; CAUCR, Caulobacter crescentus; CORGL, Corynebacterium glutamicum; HELPY, Helicobacter pylori; YERPE, Yersinia pestis; SALTY, Salmonella typhimurium; COXBU, Coxiella burnetii; RHILE, Rhizobium leguminosarum; RHIET, Rhizobium etli; AGRRA, Agrobacterium rhizogenes; ARGTU, Agrobacterium tumefaciens; RHISP, Rhizobium sp.; PSEFL, Pseudomonas fluorescens; BACAN, Bacillus anthracis; CLOST, Clostridium sticklandii; HALSP, Halobacterium sp.; RHOER, Rhodococcus erythropolis; MYCPN, Mycoplasma pneumoniae; MYCGE, Mycoplasma genitalium; LACLA, Lactococcus lactis; SYNSP, Synechococcus sp.; CHLTR, Chlamydia trachomatis; CHLPS, Chlamydia psittaci; CHLPN, Chlamydia pneumoniae




Table S1. Identification of Vibrio cholerae El Tor N16961 genes.

Gene identification numbers that correspond to those in Fig. 1 are listed here with the prefix VC (chrI) or VCA (chrII) indicates the chromosome location followed by the commom name assigned to each protein. Each gene identified is listed in its functional role category, adopted from 1.


Amino acid biosynthesis

Aromatic amino acid family

VC0297 3-dehydroquinate dehydratase (aroQ)

VC2628 3-dehydroquinate synthase (aroB)

VC1732 3-phosphoshikimate 1-carboxyvinyltransferase (aroA)

VC1172 anthranilate phosphoribosyltransferase (trpD)

VC1174 anthranilate synthase component I (trpE)

VC1173 anthranilate synthase component II (trpG)

VC0705 chorismate mutase/prephenate dehydratase (pheA)

VC0696 chorismate mutase/prephenate dehydrogenase (tyrA)

VC2116 chorismate synthase (aroC)

VC1171 indole-3-glycerol P synthase/phosphoribosylanthranilate isomerase (trpC/F)

VCA1036 phospho-2-dehydro-3-deoxyheptonate aldolase, phe-sensitive (aroG)

VC1507 phospho-2-dehydro-3-deoxyheptonate aldolase, trp-sensitive (aroH)

VC0695 phospho-2-dehydro-3-deoxyheptonate aldolase, tyr-sensitive (aroF)

VC0056 shikimate 5-dehydrogenase (aroE)

VC2629 shikimate kinase (aroK)

VC1169 tryptophan synthase, alpha subunitunit (trpA)

VC1170 tryptophan synthase, beta subunitunit (trpB)

Aspartate family

VC2329 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase, (dapD)

VC2685 5,10-methylenetetrahydrofolate reductase (metF)

VC0390 5-methyltetrahydrofolate--homocysteine methyltransferase (metH)

VC1704 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (metE)

VC0991 asparagine synthase B, glutamine-hydrolyzing (asnB)

VC1293 aspartate aminotransferase (aspC)

VC1977 aspartate aminotransferase, putative

VC2036 aspartate-semialdehyde dehydrogenase (asd)

VC2107 aspartate-semialdehyde dehydrogenase, putative

VC2364 aspartokinase I/homoserine dehydrogenase, threonine-sensitive (thrA)

VC2684 aspartokinase II/homoserine dehydrogenase, methionine-sensitive (metL)

VC0391 aspartokinase III, lysine-sensitive (lysC)

VC0547 aspartokinase, alpha and beta subunitunits

VCA0822 aspartokinase, putative

VC1671 cystathionine beta-lyase (metC)

VC2683 cystathionine gamma-synthase (metB)

VC0125 diaminopimelate decarboxylase (lysA)

VC0126 diaminopimelate epimerase (dapF)

VC2391 dihydrodipicolinate reductase (dapB)

VC2157 dihydrodipicolinate synthase (dapA)

VC2363 homoserine kinase (thrB)

VC1611 homoserine O-succinyltransferase (metA)

VC2152 succinyl-diaminopimelate desuccinylase (dapE)

VC2362 threonine synthase (thrC)

Glutamate family

VC2643 acetylglutamate kinase (argB)

VC2618 acetylornithine aminotransferase (argD)

VC2645 acetylornithine deacetylase (argE)

VC2641 argininosuccinate lyase (argH)

VC2642 argininosuccinate synthase (argG)

VC2273 gamma-glutamyl P reductase (proA)

VC2274 glutamate 5-kinase (proB)

VC2376 glutamate synthase, large subunit (gltB)

VC2373 glutamate synthase, large subunit (gltB)

VC2377 glutamate synthase, small subunit (gltD)

VC2374 glutamate synthase, small subunit (gltD)

VC2746 glutamate--ammonia ligase (glnA)

VC2438 glutamate-ammonia-ligase adenylyltransferase (glnE)

VC2644 N-acetyl-gamma-glutamyl-phosphate reductase (argC)

VC2316 N-acetylglutamate synthase (argA)

VC2239 nitrogen reg protein P-II (glnB)

VC2508 ornithine carbamoyltransferase (argF)

VC2262 protein-P-II uridylyltransferase (glnD)

VC0460 pyrroline-5-carboxylate reductase (proC)

Pyruvate family

VC2490 2-isopropylmalate synthase (leuA)

VC2492 3-isopropylmalate dehydratase, large subunit (leuC)

VC2493 3-isopropylmalate dehydratase, small subunit (leuD)

VC2491 3-isopropylmalate dehydrogenase (leuB)

VC1590 acetolactate synthase (ilvK)

VC0031 acetolactate synthase II, large subunit (ilvG)

VC0030 acetolactate synthase II, small subunit (ilvM)

VC2483 acetolactate synthase III, large subunit (ilvI)

VC2482 acetolactate synthase III, small subunit (ilvH)

VC0029 branched-chain amino acid amiotransferase (ilvE)

VC0028 dihydroxy-acid dehydratase (ilvD)

VC0162 ketol-acid reductoisomerase (ilvC)

VC0027 threonine dehydratase (ilvA)

VC0019 valine--pyruvate aminotransferase (avtA)

Serine family

VC0968 cysteine synthase A (cysK)

VC0537 cysteine synthase B (cysM)

VC1061 cysteine synthase/cystathionine beta-synthase family protein

VC2481 D-3-phosphoglycerate dehydrogenase (serA)

VC1159 phosphoserine aminotransferase (serC)

VC2345 phosphoserine phosphatase (serB)

VC2649 serine acetyltransferase (cysE)

VC0941 serine hydroxymethyltransferase (glyA)

VCA0278 serine hydroxymethyltransferase (glyA)

Histidine family

VC1136 amidotransferase HisH (hisH)

VC1132 ATP phosphoribosyltransferase (hisG)

VC1133 histidinol dehydrogenase (hisD)

VC1134 histidinol-phosphate aminotransferase (hisC)

VC1135 imidazoleglycerol-phosphate dehydratase/histidinol-phosphatase (hisB)

VC1138 imidazoleglycerol-phosphate synthase, cyclase subunit (hisF)

VC1139 phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphohydrolase (hisI)

VC1137 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA)

Other

VCA0513 amino acid biosynthesis aminotransferase




Purines, pyrimidines, nucleosides, and nucleotides

2'-Deoxyribonucleotide metabolism

VCA0511 anaerobic ribonucleoside-triphosphate reductase (nrdD)

VCA0512 anaerobic ribonucleoside-triphosphate reductase activating protein (nrdG)

VC1256 ribonucleoside-diphosphate reductase, alpha subunit (nrdA)

VC1255 ribonucleoside-diphosphate reductase, beta subunit (nrdB)

VC0675 thymidylate synthase (thyA)

Nucleotide and nucleoside interconversions

VCA0545 5`-nucleotidase, putative

VC0986 adenylate kinase (adk)

VC1916 cytidylate kinase (cmk)

VC1979 deoxyguanosinetriphosphate triphosphohydrolase (dgt)

VCA0197 GMP reductase (guaC)

VC2708 guanylate kinase (gmk)

VC1129 inosine-guanosine kinase (gsk)

VCA0801 inosine-guanosine kinase (gsk)

VC0756 nucleoside diphosphate kinase (ndk)

VC1167 thymidine kinase (tdk)

VC2016 thymidylate kinase (tmk)

VC1038 uridine kinase (udk)

VC2258 uridylate kinase (pyrH)

Purine ribonucleotide biosynthesis

VC1126 adenylosuccinate lyase (purB)

VC2602 adenylosuccinate synthase (purA)

VC1004 amidophosphoribosyltransferase (purF)

VC1992 formyltetrahydrofolate deformylase (purU)

VC0768 GMP synthase (guaA)

VC0767 inosine-5`-monophosphate dehydrogenase (guaB)

VC0275 phosphoribosylamine--glycine ligase (purD)

VC0051 phosphoribosylaminoimidazole carboxylase, ATPase subunit (purK)

VC0052 phosphoribosylaminoimidazole carboxylase, catalytic subunit (purE)

VC1190 phosphoribosylaminoimidazole-succinocarboxamide synthase, putative

VC0276 phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase (purH)

VC2226 phosphoribosylformylglycinamidine cyclo-ligase (purM)

VC0869 phosphoribosylformylglycinamidine synthase (purL)

VC2227 phosphoribosylglycinamide formyltransferase (purN)

VC1228 phosphoribosylglycinamide formyltransferase 2 (purT)

VC2183 ribose-phosphate pyrophosphokinase (prsA)

Pyrimidine ribonucleotide biosynthesis

VC2510 aspartate carbamoyltransferase, catalytic subunit (pyrB)

VC2511 aspartate carbamoyltransferase, reg subunit (pyrI)

VC2389 carbamoyl-phosphate synthase, large subunit (carB)

VC2390 carbamoyl-phosphate synthase, small subunit (carA)

VC2448 CTP synthase (pyrG)

VCA0925 dihydroorotase (pyrC)

VC1491 dihydroorotate dehydrogenase (pyrD)

VC0211 orotate phosphoribosyltransferase (pyrE)

VC1911 orotidine 5`-phosphate decarboxylase (pyrF)

Salvage of nucleosides and nucleotides

VC1053 adenine phosphoribosyltransferase (apt)

VC1231 cytidine deaminase (cdd)

VC0585 hypoxanthine phosphoribosyltransferase (hpt)

VC2225 uracil phosphoribosyltransferase, (upp)

VC2277 xanthine-guanine phosphoribosyltransferase (gpt)

Sugar-nucleotide biosynthesis and conversions

VC2174 UDP-sugar hydrolase, (ushA)

VC0395 UTP--glucose-1-phosphate uridylyltransferase (galU)

Other

VC2562 2`,3`-cyclic-nucleotide 2`-phosphodiesterase (cpdB)
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