Dual diaminopimelate biosynthesis pathways in Bacteroides fragilis and Clostridium thermocellum

Hudson, André O.; Klartag, Ayelet; Gilvarg, Charles; Dobson, Renwick C. J.; Marques, Felipe Garbelini; Leustek, Thomas

doi:10.1016/j.bbapap.2011.04.019

Cited by 18 publications

(31 citation statements)

References 33 publications

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“…Thus, we had started the screening of stable meso -DAPDH by detection of the enzyme activity in many strains of thermophiles stocked as type cultures and isolated from soils and composts, and found the activity in an aerobically well-grown thermophile from a compost. Just recently, meso -DAPDH in a thermophilic bacterium, Clostridium thermocellum was found and the enzymological properties were reported with emphasizing to show the presence of meso -DAPDH pathway in as well as a succinyl and acetyl-DAP pathway (Hudson et al, 2011). In the present study, the thermophile of meso -DAPDH producer isolated from compost was identified to be Ureibacillus thermosphaericus strain A1.…”

Section: Introductionmentioning

confidence: 99%

Highly stable meso-diaminopimelate dehydrogenase from an Ureibacillus thermosphaericus strain A1 isolated from a Japanese compost: purification, characterization and sequencing

et al. 2011

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We screened various thermophiles for meso-diaminopimelate dehydrogenase (meso-DAPDH, EC 1.4.1.16), which catalyzes the NAD(P)-dependent oxidative deamination of meso-diaminopimelate, and found the enzyme in a thermophilic bacterium isolated from compost in Japan. The bacterium grew well aerobically at around 55°C and was identified as Ureibacillus thermosphaericus strain A1. We purified the enzyme about 47-fold to homogeneity from crude cell extract using five successive purification steps. The molecular mass of the purified protein was about 80 kDa, and the molecule consists of a homodimer with the subunit molecular mass of about 40 kDa. The optimum pH and temperature for the catalytic activity of the enzyme are about 10.5 and 65°C, respectively. The enzyme is highly selective for meso-diaminopimelate as the electron donor, and NADP but not NAD can serve as the electron acceptor. The Km values for meso-diaminopimelate and NADP at 50°C and pH 10.5 are 1.6 mM and 0.13 mM, respectively. The nucleotide sequence of this meso-DAPDH gene encodes a 326-amino acid peptide. When the gene was cloned and overexpressed in Escherichia coli Rosetta (DE3), the specific activity in the crude extract of the recombinant cells was about 18.0-fold higher than in the extract from U. thermosphaericus strain A1. This made more rapid and simpler purification of the enzyme possible.

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Section: Introductionmentioning

confidence: 99%

Highly stable meso-diaminopimelate dehydrogenase from an Ureibacillus thermosphaericus strain A1 isolated from a Japanese compost: purification, characterization and sequencing

et al. 2011

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“…DapC sequences were chosen as out group and used to root the tree. DapL with the prefix “EP” have been experimentally validated in previous studies (Hudson et al, 2006, 2008, 2011; McCoy et al, 2006; Nachar et al, 2012). …”

Section: The Distribution Of Dapl In the Domain Bacteriamentioning

confidence: 87%

“…In addition, in the majority of bacteria that contain dapL, the DapL pathway is the sole route toward DAP/lys synthesis (Hudson et al, 2008; Nachar et al, 2012). The only exceptions that have been experimentally confirmed are in the genomes of Bacterioides fragilis and Clostridium thermocellum , which were found to contain both the Ddh and DapL pathways (Hudson et al, 2011). A search of the bacterial proteomes using the protein signature IPR010190, which is a signature of Ddh, revealed that C. trachomatis , L. interrogans , and Treponema sp.…”

Section: Dapl As a Target For Narrow-spectrum Antibacterial Developmentmentioning

confidence: 99%

L,L-diaminopimelate aminotransferase (DapL): a putative target for the development of narrow-spectrum antibacterial compounds

et al. 2014

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Despite the urgent need for sustained development of novel antibacterial compounds to combat the drastic rise in antibiotic resistant and emerging bacterial infections, only a few clinically relevant antibacterial drugs have been recently developed. One of the bottlenecks impeding the development of novel antibacterial compounds is the identification of new enzymatic targets. The nutritionally essential amino acid anabolic pathways, for example lysine biosynthesis, provide an opportunity to explore the development of antibacterial compounds, since human genomes do not possess the genes necessary to synthesize these amino acids de novo. The diaminopimelate (DAP)/lysine (lys) anabolic pathways are attractive targets for antibacterial development since the penultimate lys precursor meso-DAP (m-DAP) is a cross-linking amino acid in the peptidoglycan (PG) cell wall of most Gram-negative bacteria and lys plays a similar role in the PG of most Gram-positive bacteria, in addition to its role as one of the 20 proteogenic amino acids. The L,L-diaminopimelate aminotransferase (DapL) pathway was recently identified as a novel variant of the DAP/lys anabolic pathways. The DapL pathway has been identified in the pathogenic bacteria belonging to the genus; Chlamydia, Leptospira, and Treponema. The dapL gene has been identified in the genomes of 381 or approximately 13% of the 2771 bacteria that have been sequenced, annotated and reposited in the NCBI database, as of May 23, 2014. The narrow distribution of the DapL pathway in the bacterial domain provides an opportunity for the development and or discovery of narrow spectrum antibacterial compounds.

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“…These include Bacillus sphaericus, Brevibacterium sp., C. glutamicum and Proteus vulgaris (Misono et al, 1979). Characterised DAPDH enzymes are comprised of approximately 320 residues and share greater than 27% sequence identity (Ishino et al, 1987;Hudson et al, 2011b). Kinetic studies of DAPDH from C. glutamicum has yielded K M values for NADPH, L-2-amino-6-ketopimelate and ammonia of 0.13 mM, 0.28 mM and 36 mM, respectively (Misono et al, 1986).…”

Section: Inhibition Of Dapementioning

confidence: 99%

“…For example, C. glutamicium (Schrumpf et al, 1991) can synthesise lysine by either the dehydrogenase or succinylase pathway, whilst Bacillus macerans (Hudson et al, 2011b) can employ enzymes of the dehydrogenase or acetylase pathways.…”

Section: Inhibition Of Dapementioning

confidence: 99%

Enzymology of Bacterial Lysine Biosynthesis

Dogovski¹,

Atkinson²,

Dommaraju³

et al. 2012

Biochemistry

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Dual diaminopimelate biosynthesis pathways in Bacteroides fragilis and Clostridium thermocellum

Cited by 18 publications

References 33 publications

Highly stable meso-diaminopimelate dehydrogenase from an Ureibacillus thermosphaericus strain A1 isolated from a Japanese compost: purification, characterization and sequencing

Highly stable meso-diaminopimelate dehydrogenase from an Ureibacillus thermosphaericus strain A1 isolated from a Japanese compost: purification, characterization and sequencing

L,L-diaminopimelate aminotransferase (DapL): a putative target for the development of narrow-spectrum antibacterial compounds

Enzymology of Bacterial Lysine Biosynthesis

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