Cysteine and S-sulphocysteine biosynthesis in bacteria

Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501

Pseudomonas stutzeri A1501 is a non-fluorescent denitrifying bacteria that belongs to the gram-negative bacterial group. As a prominent strain in the fields of agriculture and bioengineering, there is still a lack of comprehensive understanding regarding its metabolic capabilities, specifically in terms of central metabolism and substrate utilization. Therefore, further exploration and extensive studies are required to gain a detailed insight into these aspects. This study reconstructed a genome-scale metabolic network model for P. stutzeri A1501 and conducted extensive curations, including correcting energy generation cycles, respiratory chains, and biomass composition. The final model, iQY1018, was successfully developed, covering more genes and reactions and having higher prediction accuracy compared with the previously published model iPB890. The substrate utilization ability of 71 carbon sources was investigated by BIOLOG experiment and was utilized to validate the model quality. The model prediction accuracy of substrate utilization for P. stutzeri A1501 reached 90 %. The model analysis revealed its new ability in central metabolism and predicted that the strain is a suitable chassis for the production of Acetyl CoA-derived products. This work provides an updated, high-quality model of P. stutzeri A1501for further research and will further enhance our understanding of the metabolic capabilities.

Pathway-Consensus Approach to Metabolic Network Reconstruction for Pseudomonas putida KT2440 by Systematic Comparison of Published Models

Over 100 genome-scale metabolic networks (GSMNs) have been published in recent years and widely used for phenotype prediction and pathway design. However, GSMNs for a specific organism reconstructed by different research groups usually produce inconsistent simulation results, which makes it difficult to use the GSMNs for precise optimal pathway design. Therefore, it is necessary to compare and identify the discrepancies among networks and build a consensus metabolic network for an organism. Here we proposed a process for systematic comparison of metabolic networks at pathway level. We compared four published GSMNs of Pseudomonas putida KT2440 and identified the discrepancies leading to inconsistent pathway calculation results. The mistakes in the models were corrected based on information from literature so that all the calculated synthesis and uptake pathways were the same. Subsequently we built a pathway-consensus model and then further updated it with the latest genome annotation information to obtain modelPpuQY1140 for P. putida KT2440, which includes 1140 genes, 1171 reactions and 1104 metabolites. We found that even small errors in a GSMN could have great impacts on the calculated optimal pathways and thus may lead to incorrect pathway design strategies. Careful investigation of the calculated pathways during the metabolic network reconstruction process is essential for building proper GSMNs for pathway design.

The complete genome sequence of the plant growth-promoting bacterium Pseudomonas sp. UW4

The plant growth-promoting bacterium (PGPB) Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs) were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated “housekeeping” genes (16S rRNA, gyrB, rpoB and rpoD) of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup.

O-Acetylserine sulfhydrylase from Methanosarcina thermophila

Cysteine is the major source of fixed sulfur for the synthesis of sulfur-containing compounds in organisms of the Bacteria and Eucarya domains. Though pathways for cysteine biosynthesis have been established for both of these domains, it is unknown how the Archaea fix sulfur or synthesize cysteine. None of the four archaeal genomes sequenced to date contain open reading frames with identities to either O-acetyl-L-serine sulfhydrylase (OASS) or homocysteine synthase, the only sulfur-fixing enzymes known in nature. We report the purification and characterization of OASS from acetate-grown Methanosarcina thermophila, a moderately thermophilic methanoarchaeon. The purified OASS contained pyridoxal 5'-phosphate and catalyzed the formation of L-cysteine and acetate from O-acetyl-L-serine and sulfide. The N-terminal amino acid sequence has high sequence similarity with other known OASS enzymes from the Eucarya and Bacteria domains. The purified OASS had a specific activity of 129 micromol of cysteine/min/mg, with a K(m) of 500 +/- 80 microM for sulfide, and exhibited positive cooperativity and substrate inhibition with O-acetyl-L-serine. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a single band at 36 kDa, and native gel filtration chromatography indicated a molecular mass of 93 kDa, suggesting that the purified OASS is either a homodimer or a homotrimer. The optimum temperature for activity was between 40 and 60 degrees C, consistent with the optimum growth temperature for M. thermophila. The results of this study provide the first evidence for a sulfur-fixing enzyme in the Archaea domain. The results also provide the first biochemical evidence for an enzyme with the potential for involvement in cysteine biosynthesis in the Archaea.

Thiosulfate, polythionates and elemental sulfur assimilation and reduction in the bacterial world

Among sulfur compounds, thiosulfate and polythionates are present at least transiently in many environments. These compounds have a similar chemical structure and their metabolism appears closely related. They are commonly used as energy sources for photoautotrophic or chemolithotrophic microorganisms, but their assimilation has been seldom studied and their importance in bacterial physiology is not well understood. Almost all bacterial strains are able to cleave these compounds since they possess thiosulfate sulfur transferase, thiosulfate reductase or S-sulfocysteine synthase activities. However, the role of these enzymes in the assimilation of thiosulfate or polythionates has not always been clearly established. Elemental sulfur is, on the contrary, very common in the environment. It is an energy source for sulfur-reducing eubacteria and archaebacteria and many sulfur-oxidizing archaebacteria. A phenomenon still not well understood is the 'excessive assimilatory sulfur metabolism' as observed in methanogens which perform a sulfur reduction which exceeds their anabolic needs without any apparent benefit. In heterotrophs, assimilation of elemental sulfur is seldom described and it is uncertain whether this process actually has a physiological significance. Thus, reduction of thiosulfate and elemental sulfur is a common but incompletely understood feature among bacteria. These activities could give bacteria a selective advantage, but further investigations are needed to clarify this possibility. Presence of thiosulfate, polythionates and sulfur reductase activities does not imply obligatorily that these activities play a role in thiosulfate, polythionates or sulfur assimilation as these compounds could be merely intermediates in bacterial metabolism. The possibility also exists that the assimilation of these sulfur compounds is just a side effect of an enzymatic activity with a completely different function. As long as these questions remain unanswered, our understanding of sulfur and thiosulfate metabolism will remain incomplete.

Sulfate and thiosulfate transport in Escherichia coli K-12: nucleotide sequence and expression of the cysTWAM gene cluster

The nucleotide sequence of the sulfate and thiosulfate transport gene cluster has been determined and located 3' to the gene (cysP) encoding the thiosulfate-binding protein. Four open reading frames, designated cysT, cysW, cysA, and cysM, have been identified. Similarities in primary structure were observed between (i) the deduced amino acid sequences of CysT and CysW with membrane-bound components of other binding protein-dependent transport systems, (ii) that of the CysA sequence with the "conserved" component of such systems, and (iii) that of the CysM sequence with O-acetylserine sulfhydrylase A (cysK gene product) and the beta-subunit of tryptophan synthase (coded by trpB). Expression of the four genes was analyzed in the T7 promoter-polymerase system.

Metabolism of sulfur-containing amino acids in the dermatophyte Microsporum gypseum. II. Acidic amino acid derivatives

The dermatophyte Microsporum gypseum was cultivated on a glucose-arginine medium supplemented with five strongly acidic derivatives of cysteine (L-cysteine sulfinic acid, L-cysteic acid, L-serine-O-sulfate and taurine at a concentration of 5 mmol/l, and L-S-sulfocysteine at a concentration of 2.5 mmol/l). The addition of these substances did not stimulate the growth as compared with the control containing 0.5 mmol/l cystine. Cysteine sulfinic acid and cysteic acid showed rather inhibitory effects. A strong inhibition of the growth was caused by the presence of serine sulfate. During the growth, all substances investigated were gradually consumed and utilized not only as a source of sulfur but of nitrogen and carbon as well. Cysteine sulfinic acid and S-sulfocysteine were utilized most rapidly. Cysteic acid was also rapidly utilized but after a certain adaptation. Taurine was utilized slowly and serine sulfate very slowly. Excess sulfur contained in the substances used was excreted into the medium in the form of sulfate. Sulfate excretion was most rapid with cysteine sulfinic acid and slowest with taurine. With cysteine sulfinic acid, S-sulfocysteine and cysteic acid, small amounts of sulfite were found in the medium. The results obtained are in accordance with the presumption that cysteine sulfinic acid (but not cysteic acid and taurine) is an intermediate of cysteine catabolism in dermatophytes.

Evidence that thiosulfate assimilation by Salmonella typhimurium is catalyzed by cysteine synthase B

Mutants carrying defects in cysteine synthase A or B or both were isolated from Salmonella typhimurium LT2. Parent strains were able to grow on minimal media containing sulfate, sulfite, sulfide, or thiosulfate as sulfur sources. Mutants lacking cysteine synthase B were unable to grow on thiosulfate, whereas mutants lacking cysteine synthase A grew on the four inorganic sulfur sources described above with little difference in their growth rates. Mutants lacking both cysteine synthases failed to grow on media containing any of the inorganic sulfur sources tested. Purification of cysteine synthase B resulted in the copurification of S-sulfocysteine synthase. In addition, the two activities were also cotransduced. These activities appear to be associated with the cysM gene, and this is able to be cotransducted with the cysK gene at a high frequency. From these results, it may be concluded that thiosulfate is assimilated via S-sulfocysteine exclusively with the aid of S-sulfocysteine synthase.

O-Acetylserine sulfhydrylase and S-sulfocysteine synthase activities of Rhodospirillum tenue

O-Acetylserine sulfhydrylase in cell-free extracts of Rhodospirillum tenue was markedly repressed after growth in the presence of sulfide or thiosulfate, whereas S-sulfocysteine synthase activity remained almost unchanged. Purification on DE52 cellulose resulted in the separation of two proteins: Protein I with a molecular weight of 57000 had O-acetylserine sulfhydrylase activity only, while protein II with a molecular weight of 46000 had S-sulfocysteine synthase activity in addition. The activity of protein II with O-acetylserine plus sulfide was about 1.5 of that with O-acetylserine plus thiosulfate. Protein I from sulfate-grown cells possessed 74% of the total O-acetylserine sulfhydrylase, protein II 26%. Growth with sulfide repressed only the synthesis of protein I, which after separation showed only 19% of the measurable O-acetylserine sulfhydrylase, whereas protein II now possessed 81%. Regulatory and kinetic phenomena of the two activities were studied. In addition to the phototrophic bacteria studied earlier, also Rhodomicrobium vannielii, Rhodopseudomonas acidophila, Rhodocyclus purpureus and Thiocystis violacea were found to contain O-acetylserine sulfhydrylase activities; the latter two species contained S-sulfocysteine synthase activities in addition.

Organic sulphur sources for the growth of the dermatophyte Microsporum gypseum

The suitability of 30 organic compounds (of them 19 sulphur-containing amino acids) at a concentration of 1 mM as sulphur sources for the growth of the dermatophyte Microsporum gypseum was investigated. The dry mass of the mycelium after an 11-d growth served as a measure of utilizability. Of sulphur amino acid cystine, cysteine, reduced and oxidized glutathione, cysteic and cysteinesulphinic acids, S-sulphocysteine, lanthionine, taurine and serine sulphate were the best sources. Methionine and methionine-sulphone were utilized slightly less effectively. Other compounds were medium to poor sources and only S-carboxymethylcysteine was not utilized at all. All organic compounds that are not of amino acid type were poor sulphate sources or were utilized at all. Sodium dodecyl sulphate inhibited germination and growth completely.

Cysteine and S-sulfocysteine biosynthesis in phototrophic bacteria

Forteen species (17 strains) of phototrophic bacteria as well as one strain of Thiobacillus denitrificans were tested for cysteine synthase and S-sulfocysteine synthase. All strains contain cysteine sythase active with O-acetylserine; only the Chromatiaceae, two species of the Rhodospirillaceae and T. denitrificans contain S-sulfocysteine synthase. In six species repression by different sulfur compounds in the medium was studied. In Chromatium vinosum, cysteine synthase was found to be constitutive, while in the Rhodospirillaceae tested the enzyme is repressed by sulfide. Thiosulfate had a derepressive effect in Rhodopseudomonas globiformis but strongly repressed cysteine synthase in R. sulfidophila and R. palustris. Cysteine had only moderate effects with the species tested.