A New<i>Bradyrhizobium japonicum</i>Gene Required for Free-Living Growth and Bacteroid Development Is Conserved in Other Bacteria and in Plants

Weidenhaupt, Marianne; Schmid-Appert, Monika; Thöny, Beat; Hennecke, Hauke; Fischer, Hans‐Martin

doi:10.1094/mpmi-8-0454

Cited by 6 publications

(2 citation statements)

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“…However, the HI0906 homologs in three other bacteria are not completely essential. A mutation of the HI0906 homologs (also of unknown function), cumB in P. putida (26), and orf74 in Bradyrhizobium japonicum (27) resulted in an extended lag phase in both organisms. In contrast, a mutation in the HI0906 homolog in E. coli orf178 (encoding a putative membrane protein involved in cell killing with the gef family of toxic proteins) confers no reported growth defect (28).…”

Section: Discussionmentioning

confidence: 99%

Genetic footprinting with mariner -based transposition in Pseudomonas aeruginosa

Wong

Mekalanos

2000

Proc. Natl. Acad. Sci. U.S.A.

150

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The complete DNA sequence of Pseudomonas aeruginosa provides an opportunity to apply functional genomics to a major human pathogen. A comparative genomics approach combined with genetic footprinting was used as a strategy to identify genes required for viability in P. aeruginosa. Use of a highly efficient in vivo mariner transposition system in P. aeruginosa facilitated the analysis of candidate genes of this class. We have developed a rapid and efficient allelic exchange system by using the I-SceI homing endonuclease in conjunction with in vitro mariner mutagenesis to generate mutants within targeted regions of the P. aeruginosa chromosome for genetic footprinting analyses. This technique for generating transposon insertion mutants should be widely applicable to other organisms that are not naturally transformable or may lack well developed in vivo transposition systems. We tested this system with three genes in P. aeruginosa that have putative essential homologs in Haemophilus influenzae. We show that one of three H. influenzae essential gene homologs is needed for growth in P. aeruginosa, validating the practicality of this comparative genomics strategy to identify essential genes in P. aeruginosa.transposon ͉ SCE jumping

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Section: Discussionmentioning

confidence: 99%

Genetic footprinting with mariner -based transposition in Pseudomonas aeruginosa

Wong

Mekalanos

2000

Proc. Natl. Acad. Sci. U.S.A.

150

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“…The existence oftwo new branches in the DM domain phylogenetic tree (subtrees C and B3), each containing diverse bacterial and eucaryotic sequences, suggests the involvment ofthe DM domain in fundamental cellular processes yet to be characterized. Subtree C contains a bacterial protein, 82:Bja_NFP, required for free-living growth and bacteroid development (Weidenhaupt et al, 1995). In the case of another sequence in this branch, 80:Eco_YFHC, a D->E mutation at position a in Figure 3 renders the mutant strain resistant to the cell-killing functions encoded by a specific gene family which kills cells from within by damaging the cell membrane FIG.…”

Section: Discussionmentioning

confidence: 99%

Statistical Modelling and Phylogenetic Analysis of a Deaminase Domain

Mian

Moser²,

Holley³

et al. 1998

Journal of Computational Biology

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Deamination reactions are catalyzed by a variety of enzymes including those involved in nucleoside/nucleotide metabolism and cytosine to uracil (C-->U) and adenosine to inosine (A-->I) mRNA editing. The active site of the deaminase (DM) domain in these enzymes contains a conserved histidine (or rarely cysteine), two cysteines and a glutamate proposed to act as a proton shuttle during deamination. Here, a statistical model, a hidden Markov model (HMM), of the DM domain has been created which identifies currently known DM domains and suggests new DM domains in viral, bacterial and eucaryotic proteins. However, no DM domains were identified in the currently predicted proteins from the archaeon Methanococcus jannaschii and possible causes for, and a potential means to ameliorate this situation are discussed. In some of the newly identified DM domains, the glutamate is changed to a residue that could not function as a proton shuttle and in one instance (Mus musculus spermatid protein TENR) the cysteines are also changed to lysine and serine. These may be non-competent DM domains able to bind but not act upon their substrate. Phylogenetic analysis using an HMM-generated alignment of DM domains reveals three branches with clear substructure in each branch. The results suggest DM domains that are candidates for yeast, platyhelminth, plant and mammalian C-->U and A-->I mRNA editing enzymes. Some bacterial and eucaryotic DM domains form distinct branches in the phylogenetic tree suggesting the existence of common, novel substrates.

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Cloning, Overexpression, and Purification of Cytosine Deaminase fromSaccharomyces cerevisiae

Hayden

Linsley

Wallace

et al. 1998

Protein Expression and Purification

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A NewBradyrhizobium japonicumGene Required for Free-Living Growth and Bacteroid Development Is Conserved in Other Bacteria and in Plants

Cited by 6 publications

References 0 publications

Genetic footprinting with mariner -based transposition in Pseudomonas aeruginosa

Genetic footprinting with mariner -based transposition in Pseudomonas aeruginosa

Statistical Modelling and Phylogenetic Analysis of a Deaminase Domain

Cloning, Overexpression, and Purification of Cytosine Deaminase fromSaccharomyces cerevisiae

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