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Genomics and Proteomics

DNA Sequence Duplication in Rhodobacter sphaeroides 2.4.1: Evidence of an Ancient Partnership between Chromosomes I and II

Madhusudan Choudhary, Yun-Xin Fu, Chris Mackenzie, Samuel Kaplan
Madhusudan Choudhary
1Department of Microbiology and Molecular Genetics
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Yun-Xin Fu
2Computational Genomic Section, Human Genetics Center, The University of Texas Health Science Center, Houston, Texas 77030
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Chris Mackenzie
1Department of Microbiology and Molecular Genetics
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Samuel Kaplan
1Department of Microbiology and Molecular Genetics
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  • For correspondence: Samuel.Kaplan@uth.tmc.edu
DOI: 10.1128/JB.186.7.2019-2027.2004
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  • FIG. 1.
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    FIG. 1.

    Schematic representation of chromosomal duplications within and between CI and CII. CI and CII are depicted as horizontal bars from left (5′ DNA end) to right (3′ DNA end). Connecting vertical lines represent the locations on the chromosome(s) where the sequence matches perfectly. Genes involved in flagellum biosynthesis (fl-), electron transport (nuo), chemotaxis (che), and carbon assimilation (cbb) are duplicated as gene clusters, and they are indicated by different colors.

  • FIG. 2.
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    FIG. 2.

    Frequency distribution of the number of intra- and interchromosomal DNA sequence duplications. The two panels have different scales for the x and y axes.

  • FIG. 3.
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    FIG. 3.

    Phylogenetic relationships of duplicated gene paralogues of R. sphaeroides and the orthologous sequences from closely related species or genera. As examples, consensus phylogenetic trees representing four gene pairs, rdxA/rdxB, hemA/hemT, pucB1/pucB2, and flhB1/flhB2, and their orthologous sequences are shown. The relationships reflect the two types of topology (type A and type B), and the strength of branching support is indicated by the bootstrap values at the nodes. Scale bars represent genetic distances.

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  • TABLE 1.

    DNA exact duplication in R. sphaeroides 2.4.1

    ChromosomeNo. of nucleotidesNo. of duplicated nucleotides (%)
    CICII
    CI3,188,63139,056 (1.22)54,967 (1.33)
    CII943,02254,967 (1.33)17,726 (1.88)
    Total4,131,653111,749 (2.70)
  • TABLE 2.

    Frequency distribution of sequence duplications for CI and CII of R. sphaeroides 2.4.1

    Length of duplication (nucleotides)No. of duplications
    CI-CICII-CIICI-CIITotal
    20-253461121,0821,540
    26-505301703171,017
    51-1001304483257
    101-2002491346
    201-50030811
    501-1,0001124
    >1,0000145
    Total1,0343371,5092,880
  • TABLE 3.

    Large duplicated regions of CI and CII

    Duplicated regionCoordinates on chromosomeLength (kb)
    CIA1 (rrnA)0-53505.35
    CIB1222609-25370031.1
    CIB2737289-76273425.45
    CIIA2 (rrnC)0-53505.35
    CIIA3 (rrnB)33674-390225.35
    CIIB1645366-67396628.6
    CIIB2922523-891191 reverse34.8
  • TABLE 4.

    Similarity analysis of gene paralogues and orthologues

    Duplicated gene(s)No. of copies in R. sphaeroidesFunction% IdentityaClose matchTreec
    Organism% IdentitybTypeBootstrap value
    CI-CI
        pucB1/pucB22Light entrapment100 Rhodovulum sulfidophilum 80B94
        pucA1/pucA22Light entrapment58 R. sulfidophilum 54A55
        dxsI/dxsII2Isoprenoid synthesis66 Rhodobacter capsulatus 75A100
        flgG2Flagellum biosynthesis42 Caulobacter crescentus 47A82
        flgI2Flagellum biosynthesis42 C. crescentus 50A43
        flhA2Flagellum biosynthesis32 C. crescentus 32A100
        fliI2Flagellum biosynthesis36 C. crescentus 44A76
        fliP2Flagellum biosynthesis39 Sinorhizobium meliloti 40A57
        fliQ2Flagellum biosynthesis47 S. meliloti 40B62
        fliR2Flagellum biosynthesis33 S. meliloti 27A42
        fliN2Flagellum biosynthesis35 C. crescentus 37A79
        fliF2Flagellum biosynthesis30 C. crescentus 30B73
        flhB2Flagellum biosynthesis33 C. crescentus 32B98
        flgH2Flagellum biosynthesis30 C. crescentus 42A100
        flgF2Flagellum biosynthesis33 C. crescentus 42B57
        flgE2Flagellum biosynthesis25 S. meliloti 29A90
        flgC2Flagellum biosynthesis28 Bradyrhizobium japonicum 39A100
        flgB2Flagellum biosynthesis31 Pseudomonas aeruginosa 46B57
        nuoA2Electron transport protein36 R. capsulatus 85A85
        nuoB2Electron transport protein53 R. capsulatus 88A80
        nuoD2Electron transport protein42 R. capsulatus 83A98
        nuoF2Electron transport protein38 R. capsulatus 88A99
        nuoH2Electron transport protein42 R. capsulatus 82A100
        nuoI2Electron transport protein43 R. capsulatus 88A96
        nuoL2Electron transport protein30 R. capsulatus 33A98
        fnrL2Anaerobic regulator33 R. capsulatus 77A41
        rpoN2Sigma factor41 R. capsulatus 50A100
        hemN/Z4Coproporphyrinogen III oxidase24 S. meliloti 43B54
        cheA4Chemotaxis histidine kinase35 C. crescentus 47A99
        cheB2MCPd-glutamate methylesterase41 C. crescentus 45A70
        cheR3MCP-glutamate methyltransferase33 C. crescentus 48A100
        cheW4Chemotaxis protein33 C. crescentus 48A100
    CI-CII
        rdxA/rdxB2Electron transport protein67 R. capsulatus 67A97
        qoxA2Electron transport protein45 S. meliloti 48A62
        qor2Electron transport protein31 R. capsulatus 54A100
        cbbGI/cbbGII2Carbon assimilation84 Paraccocus denitrificans 84B77
        hemA/hemT2ALAe synthase (tetrapyrrole biosynthesis)54 R. capsulatus 76A100
        cbbTI/cbbTII2Carbon assimilation58 R. capsulatus 66A100
        cbbAI/cbbAII2Carbon assimilation78 R. capsulatus 89A78
        cbbFI/cbbFII2Carbon assimilation67 R. capsulatus 69A99
        cbbPI/cbbPII2Carbon assimilation86 R. capsulatus 86B71
        cbbMI/cbbMII2Carbon assimilation31 R. capsulatus 94A100
        groEL3HSP6040 R. capsulatus 70A100
        groES2HSP1035 R. capsulatus 84A99
    • ↵ a Amino acid identity for duplicate pair.

    • ↵ b Amino acid identity with orthologue.

    • ↵ c Phylogenetic relationship.

    • ↵ d MCP, membrane-spanning chemoreceptor proteins.

    • ↵ e ALA, 5-aminolevulinic acid.

Additional Files

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  • HTML Page - index.htslp

    Files in this Data Supplement:

    • Fig. S1 - Phylogenetic relationships analyzed using pairs of duplicated alleles and their othologous DNA sequences from several species and genera closely relaled to R. sphaeroides. (Word document)
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DNA Sequence Duplication in Rhodobacter sphaeroides 2.4.1: Evidence of an Ancient Partnership between Chromosomes I and II
Madhusudan Choudhary, Yun-Xin Fu, Chris Mackenzie, Samuel Kaplan
Journal of Bacteriology Mar 2004, 186 (7) 2019-2027; DOI: 10.1128/JB.186.7.2019-2027.2004

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DNA Sequence Duplication in Rhodobacter sphaeroides 2.4.1: Evidence of an Ancient Partnership between Chromosomes I and II
Madhusudan Choudhary, Yun-Xin Fu, Chris Mackenzie, Samuel Kaplan
Journal of Bacteriology Mar 2004, 186 (7) 2019-2027; DOI: 10.1128/JB.186.7.2019-2027.2004
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    • ABSTRACT
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KEYWORDS

Bacterial Proteins
Chromosomes, Bacterial
Evolution, Molecular
gene duplication
Rhodobacter sphaeroides

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