For the ornithine fermentation pathway, described more than 70 years ago, genetic and biochemical information are still incomplete.
We present here the experimental identification of the last four missing genes of this metabolic pathway. They encode l-ornithine racemase, (2R,4S)-2,4-diaminopentanoate dehydrogenase, and the two subunits of 2-amino-4-ketopentanoate thiolase. While described only for
the Clostridiaceae to date, this pathway is shown to be more widespread.
"This is a generally favoured pathway by anaerobes, for they can conserve energy without any redox reaction by splitting the deaminated intermediate citrulline by ornithine carbamoyl-phosphate transferase and conserve ATP by carbamate kinase. As expected, C. sticklandii contains all the genes involved in the arginine deiminase pathway as well as the ornithine oxidative and reductive pathways [29,30]. Like C. botulinum and C. sporogenes , C. sticklandii possesses an ornithine cyclodeaminase that directly produces proline from ornithine. "
[Show abstract][Hide abstract] ABSTRACT: Clostridium sticklandii belongs to a cluster of non-pathogenic proteolytic clostridia which utilize amino acids as carbon and energy sources. Isolated by T.C. Stadtman in 1954, it has been generally regarded as a "gold mine" for novel biochemical reactions and is used as a model organism for studying metabolic aspects such as the Stickland reaction, coenzyme-B12- and selenium-dependent reactions of amino acids. With the goal of revisiting its carbon, nitrogen, and energy metabolism, and comparing studies with other clostridia, its genome has been sequenced and analyzed.
C. sticklandii is one of the best biochemically studied proteolytic clostridial species. Useful additional information has been obtained from the sequencing and annotation of its genome, which is presented in this paper. Besides, experimental procedures reveal that C. sticklandii degrades amino acids in a preferential and sequential way. The organism prefers threonine, arginine, serine, cysteine, proline, and glycine, whereas glutamate, aspartate and alanine are excreted. Energy conservation is primarily obtained by substrate-level phosphorylation in fermentative pathways. The reactions catalyzed by different ferredoxin oxidoreductases and the exergonic NADH-dependent reduction of crotonyl-CoA point to a possible chemiosmotic energy conservation via the Rnf complex. C. sticklandii possesses both the F-type and V-type ATPases. The discovery of an as yet unrecognized selenoprotein in the D-proline reductase operon suggests a more detailed mechanism for NADH-dependent D-proline reduction. A rather unusual metabolic feature is the presence of genes for all the enzymes involved in two different CO2-fixation pathways: C. sticklandii harbours both the glycine synthase/glycine reductase and the Wood-Ljungdahl pathways. This unusual pathway combination has retrospectively been observed in only four other sequenced microorganisms.
Analysis of the C. sticklandii genome and additional experimental procedures have improved our understanding of anaerobic amino acid degradation. Several specific metabolic features have been detected, some of which are very unusual for anaerobic fermenting bacteria. Comparative genomics has provided the opportunity to study the lifestyle of pathogenic and non-pathogenic clostridial species as well as to elucidate the difference in metabolic features between clostridia and other anaerobes.
[Show abstract][Hide abstract] ABSTRACT: The exponential growth in the number of sequenced microorganisms versus the relative slow influx of direct biochemical characterization of microbes is limiting the utility of sequence information. High-throughput experimental approaches to functionally characterize microbial metabolism are urgently needed to leverage genome sequences for example: to understand host-microbe interactions, microbial communities, to utilize microbes for bioenergy, bioremediation, etc. Mass spectrometry based small molecule metabolite analysis is rapidly becoming a method of choice to meet these needs and enables multiple paths to discovering and validating the functional assignments. Approaches range from the targeted in vitro screening of small sets of metabolic transformations to define enzymatic activities to global metabolic profiling (metabolomics) to define metabolic pathways and gain insights into microbial responses to environmental and genetic perturbations. The combination of metabolite profiling with genome-scale models of metabolism and other -omic approaches provides opportunities to expand our understanding of microbial metabolic networks, stress responses, and to identify genes associated with specific enzymatic and regulatory activities.
Current opinion in microbiology 09/2009; 12(5):547-52. DOI:10.1016/j.mib.2009.07.004 · 5.90 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The persulfide sulfur formed on an active site cysteine residue of pyridoxal 5'-phosphate-dependent cysteine desulfurases is subsequently incorporated into the biosynthetic pathways of a variety of sulfur-containing cofactors and thionucleosides. In molybdenum cofactor biosynthesis, MoeB activates the C terminus of the MoaD subunit of molybdopterin (MPT) synthase to form MoaD-adenylate, which is subsequently converted to a thiocarboxylate for the generation of the dithiolene group of MPT. It has been shown that three cysteine desulfurases (CsdA, SufS, and IscS) of Escherichia coli can transfer sulfur from l-cysteine to the thiocarboxylate of MoaD in vitro. Here, we demonstrate by surface plasmon resonance analyses that IscS, but not CsdA or SufS, interacts with MoeB and MoaD. MoeB and MoaD can stimulate the IscS activity up to 1.6-fold. Analysis of the sulfuration level of MoaD isolated from strains defective in cysteine desulfurases shows a largely decreased sulfuration level of the protein in an iscS deletion strain but not in a csdA/sufS deletion strain. We also show that another iscS deletion strain of E. coli accumulates compound Z, a direct oxidation product of the immediate precursor of MPT, to the same extent as an MPT synthase-deficient strain. In contrast, analysis of the content of compound Z in DeltacsdA and DeltasufS strains revealed no such accumulation. These findings indicate that IscS is the primary physiological sulfur-donating enzyme for the generation of the thiocarboxylate of MPT synthase in MPT biosynthesis.
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