The Evolution of Biochemical Syntheses — Retrospect and Prospect

Horowitz, N. H.

doi:10.1016/b978-1-4832-2734-4.50009-7

Cited by 85 publications

(52 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Enzymes catalyzing related reactions have, in many cases, been shown to exhibit substantial sequence similarity, suggesting that they arose from a common ancestor. Gene duplication has, for example, been proposed as a mechanism for the evolution of biosynthetic pathways (22). Consistent with this proposal, the enzymes catalyzing the sequential reactions in the biosynthesis of methionine in E. coli exhibit a high degree of sequence similarity (2).…”

supporting

confidence: 50%

Nucleotide sequence of aceK, the gene encoding isocitrate dehydrogenase kinase/phosphatase

et al. 1988

View full text Add to dashboard Cite

In Escherichia coli, the phosphorylation and dephosphorylation of isocitrate dehydrogenase (IDH) are catalyzed by a bifunctional protein kinase/phosphatase. We have determined the nucleotide sequence of aceK, the gene encoding IDH kinase/phosphatase. This gene consists of a single open reading frame of 1,734 base pairs preceded by a Shine-Dalgarno ribosome-binding site. Examination of the deduced aminQ acid sequence of IDH kinase/phosphatase revealed sequences which are similar to the consensus sequence for ATP-binding sites. This protein did not, however, exhibit the extensive sequence homologies which are typical of other protein kinases. Multiple copies of the REP family of repetitive extragenic elements were found within the intergenic region between aceA (encoding isocitrate lyase) and aceK. These elements have the potential for combining to form an exceptionally stable stem-loop structure (AG = -54 kcal/mol [ca. -226 kJ/moll) in the miRNA. This structure, which masks the ribosome-binding site and start codon for aceK, may contribute to the downshift in expression observed between aceA and aceK. Another potential stem-loop structure (AG = -29 kcal/mol [ca. 121 kJ/mol]), unrelated to the REP sequences, was found within aceK.For Escherichia coli, adaptation to growth on acetate requires the induction of the enzymes of the glyoxylate bypass, isocitrate lyase and malate synthase (26,27). This pathway allows the net synthesis of cellular constituents from acetate because it bypasses the CO2-producing steps of the Krebs cycle. Once induced, this pathway is regulated, at least in part, through the phosphorylation of isocitrate dehydrogenase (IDH), the Krebs cycle enzyme which competes with isocitrate lyase (3,17,18,21,54). This phosphorylation site has been identified as serine 113 (5, 51). During growth on acetate, ca. 70% of the IDH is maintained in the inactive, phosphorylated form (4, 30, 31), forcing isocitrate through the glyoxylate bypass (32, 41). Mutant strains which fail to express IDH kinase/phosphatase are usually unable to grow on acetate, indicating that the phosphorylation of IDH is essential for growth on this carbon source (31).The phosphorylation and dephosphorylation of IDH are catalyzed by a bifunctional enzyme, IDH kinase/phosphatase. This protein is expressed from a single gene, aceK (28), and yields a single band on sodium dodecyl sulfate electrophoresis (28, 29). These observatioihs support the proposal that IDH kinase and IDH phosphatase reside on the same polypeptide. The physical association of opposing regulatory activities is not unique to IDH kinase/phosphatase. Other bifunctional regulatory proteins have been identified in mammals (14), plants (6), and microorganisms (7,16,42).In addition to regulation mediated by the phosphorylation of IDH, the glyoxylate bypass is regulated at the level of gene expression. Using genetic techniques, Maloy and Nunn demonstrated that the genes which encode isocitrate lyase (aceA) and malate synthase (aceB) are expressed from the same operon and that a...

show abstract

supporting

confidence: 50%

Nucleotide sequence of aceK, the gene encoding isocitrate dehydrogenase kinase/phosphatase

et al. 1988

View full text Add to dashboard Cite

show abstract

“…These differences were also reflected in the lack of homology between the two structural genes. It might be expected that these two enzymes, catalyzing dehydrogenation reactions on structurally related substrates as sequential reactions in a pathway, would be ideal candidates for having evolved by tandem duplication from a common ancestral gene (13). This may still be a possibility, but if so, the two copies must have subsequently diverged widely.…”

Section: Discussionmentioning

confidence: 99%

Gene organization of the first catabolic operon of TOL plasmid pWW53: production of indigo by the xylA gene product

Keil¹,

Saint²,

Williams³

1987

J Bacteriol

View full text Add to dashboard Cite

The entire operon coding for the enzymes responsible for conversion of toluenes to benzoates has been cloned from TOL plasmid pWW53 and the position of the genes accurately located. The coding region was 7.4 kilobase pairs (kbp) long, and the gene order was operator-promoter region (OPl)-a small open reading frame-xylC (1.6 kbp)-xyLA (2.9 kbp)-xylB (1.8 kbp). Within the coding region there was considerable homology with the isofunctional region of the archetypal TOL plasmid pWWO. A central region of 2.9 kbp complemented an xylA (for xylene oxygenase) mutant of Pseudomonas putida mt-2 and was also capable of conferring the ability to convert indole to indigo on strains of Escherichia coli and P. putida. This reaction has been reported previously only for dioxygenases involved in aromatic catabolism but not for monooxygenases. It is proposed that the region encodes xylene oxygenase activity capable of direct monohydroxylation of indole to 3-hydroxyindole (oxindole), which then spontaneously dimerizes to form indigo.In soil isolates of Pseudomonas spp. the ability to catabolize toluene and substituted toluenes via benzoate and substituted benzoates (20, 29) appears to be almost always plasmid encoded (27), but the plasmids themselves differ considerably in properties and structure (5,28).Horizontal transfer on plasmid vectors through different members of the soil microbial population undoubtedly imposes selection pressures on catabolic genes different from those which are chromosomally located. One way of monitoring and assessing these differences is to compare the structure and organization of catabolic genes on isofunctional plasmids isolated from different geographical locations.The archetypal TOL plasmid pWWO (117 kilobase pairs [kbp]) was found in Pseudomonas putida mt-2 (23, 27), a strain originally isolated in Japan in the 1950s. The majority of molecular biological studies on the catabolic structural genes of the toluene-xylene pathway have been performed on pWW0 or its derivatives (7,10,11,15,16,21). More recently, we isolated P. putida MT53 in North Wales and initiated studies on its TOL plasmid, the 105-kbp plasmid pWW53, and its RP4 cointegrate, pWW53-4 (18). The DNA of its second operon (xylDLEGF. . ,), coding for the enzymes converting benzoic acids to central metabolites, has the same gene order as the corresponding operon on pWWO, and its restriction map shows a number of common sites. This paper reports parallel studies on the first operon of the pathway (xylCAB) responsible for the conversion of toluenes to benzoates. MATERIALS AND METHODSBacterial strains and media. The Escherichia coli and P. putida strains used or constructed in this study are listed in been described elsewhere (19,29). To maintain recombinant plasmids in E. coli, streptomycin sulfate, kanamycin, ampicillin, and tetracycline were added to final concentrations of 15, 15, 25, and 7.5 p.g/ml, respectively, when appropriate. In Pseudomonas hosts, streptomycin and kanamycin were added at 150 and 50 ,ug/ml, respectively.Enzyme assays...

show abstract

“…This result was unexpected, as D. radiodurans does not carry another typical lysZ homologue ; hence, it was suggested that DR1420 was not essential for lysine biosynthesis in D. radiodurans. In general, enzymes that show strict substrate specificity are believed to originate from an ancestor that had a broad substrate specificity (Horowitz, 1965 ;Jensen, 1976 ;Parsot et al, 1987 ;Roy, 1999). This is certainly the case for enzymes involved in amino-acid biosynthesis.…”

Section: Resultsmentioning

confidence: 99%

Disruption analysis of DR1420 and/or DR1758 in the extremely radioresistant bacterium Deinococcus radiodurans

Nishida

Narumi

2002

Microbiology

View full text Add to dashboard Cite

The extremely radioresistant bacterium Deinococcus radiodurans encodes two genes that are homologous to those involved in bacterial lysine biosynthesis. In lysine biosynthesis, these genes are involved in the aminoadipate pathway and the diaminopimelate (DAP) pathway. DR1420 is homologous to lysZ, which is essential for bacterial lysine biosynthesis via the aminoadipate pathway, and DR1758 is homologous to lysA, which is essential for lysine biosynthesis via the DAP pathway. In this study, DR1420 and/or DR1758 were disrupted. Each disruptant of DR1420 and DR1758, and of DR1420 or DR1758 grew in a minimal medium, as did the wild-type. These results show that D. radiodurans performs lysine biosynthesis in a unique way.

show abstract

The Evolution of Biochemical Syntheses — Retrospect and Prospect

Cited by 85 publications

References 27 publications

Nucleotide sequence of aceK, the gene encoding isocitrate dehydrogenase kinase/phosphatase

Nucleotide sequence of aceK, the gene encoding isocitrate dehydrogenase kinase/phosphatase

Gene organization of the first catabolic operon of TOL plasmid pWW53: production of indigo by the xylA gene product

Disruption analysis of DR1420 and/or DR1758 in the extremely radioresistant bacterium Deinococcus radiodurans

Contact Info

Product

Resources

About