NAD Biosynthesis Evolution in Bacteria: Lateral Gene Transfer of Kynurenine Pathway in Xanthomonadales and Flavobacteriales

The biosynthesis of quinolinate, the de novo precursor of nicotinamide adenine dinucleotide (NAD), may be performed by two distinct pathways, namely, the bacterial aspartate (aspartate-to-quinolinate) and the eukaryotic kynurenine (tryptophan-to-quinolinate). Even though the separation into eukaryotic and bacterial routes is long established, recent genomic surveys have challenged this view, because certain bacterial species also carry the genes for the kynurenine pathway. In this work, both quinolinate biosynthetic pathways were investigated in the Bacteria clade and with special attention to Xanthomonadales and Bacteroidetes, from an evolutionary viewpoint. Genomic screening has revealed that a small number of bacterial species possess some of the genes for the kynurenine pathway, which is complete in the genus Xanthomonas and in the order Flavobacteriales, where the aspartate pathway is absent. The opposite pattern (presence of the aspartate pathway and absence of the kynurenine pathway) in close relatives (Xylella ssp. and the order Bacteroidales, respectively) points to the idea of a recent acquisition of the kynurenine pathway through lateral gene transfer in these bacterial groups. In fact, sequence similarity comparison and phylogenetic reconstruction both suggest that at least part of the genes of the kynurenine pathway in Xanthomonas and Flavobacteriales is shared by eukaryotes. These results reinforce the idea of the role that lateral gene transfer plays in the configuration of bacterial genomes, thereby providing alternative metabolic pathways, even with the replacement of primary and essential cell functions, as exemplified by NAD biosynthesis.

Leishmania amazonensis: Biosynthesis of polyprenols of 9 isoprene units by amastigotes

The isoprenoid metabolic pathway in protozoa of the Leishmania genus exhibits distinctive characteristics. These parasites, as well as other members of the Trypanosomatidae family, synthesize ergosterol, instead of cholesterol, as the main membrane sterol lipid. Leishmania has been shown to utilize leucine, instead of acetate as the main precursor for sterol biosynthesis. While mammalian dolichols are molecules containing 15-23 isoprene units, Leishmania amazonensis promastigotes synthesize dolichol of 11 and 12 units. In this paper, we show that the intracellular stages of L. amazonensis, amastigotes, synthesize mainly polyprenols of 9 isoprene units, instead of dolichol. (c) 2007 Elsevier Inc. All rights reserved.

Failure of conjugated linoleic acid supplementation to enhance biosynthesis of docosahexaenoic acid from α-linolenic acid in healthy human volunteers

A rate-limiting step in docosahexaenoic acid (DHA) formation from α-linolenic acid (ALA) involves peroxisomal oxidation of 24:6n-3 to DHA. The aim of the study was to determine whether conjugated linoleic acid (CLA) would enhance conversion of ALA to DHA in humans on an ALA-supplemented diet. The subjects (n=8 per group) received daily supplementation of ALA (11g) and either CLA (3.2g) or placebo for 8 weeks. At baseline, 4 and 8 weeks, blood was collected for plasma fatty acid analysis and a number of physiological measures were examined. The ALA-supplemented diet increased plasma levels of ALA and eicosapentaenoic acid (EPA). The addition of CLA to the ALA diet resulted in increased plasma levels of CLA, as well as ALA and EPA. Plasma level of DHA was not increased with either the ALA alone or ALA plus CLA supplementation. The results demonstrated that CLA was not effective in enhancing DHA levels in plasma in healthy volunteers.

Coupling between snoRNP assembly and 3' processing controls box C/D snoRNA biosynthesis in yeast

RNA polymerase II transcribes genes encoding proteins and a large number of small stable RNAs. While pre-mRNA 3'-end formation requires a machinery ensuring tight coupling between cleavage and polyadenylation, small RNAs utilize polyadenylation-independent pathways. In yeast, specific factors required for snRNA and snoRNA 3'-end formation were characterized as components of the APT complex that is associated with the core complex of the cleavage/polyadenylation machinery (core-CPF). Other essential factors were identified as independent components: Nrd1p, Nab3p and Sen1p. Here we report that mutations in the conserved box D of snoRNAs and in the snoRNP-specific factor Nop1p interfere with transcription and 3'-end formation of box C/D snoRNAs. We demonstrate that Nop1p is associated with box C/D snoRNA genes and that it interacts with APT components. These data suggest a mechanism of quality control in which efficient transcription and 3'-end formation occur only when nascent snoRNAs are successfully assembled into functional particles.

Biosynthesis, localization, and macromolecular arrangement of the plasmodium falciparum translocon of exported proteins (PTEX)

To survive within its host erythrocyte, Plasmodium falciparum must export hundreds of proteins across both its parasite plasma membrane and surrounding parasitophorous vacuole membrane, most of which are likely to use a protein complex known as PTEX (Plasmodium translocon of exported proteins). PTEX is a putative protein trafficking machinery responsible for the export of hundreds of proteins across the parasitophorous vacuole membrane and into the human host cell. Five proteins are known to comprise the PTEX complex, and in this study, three of the major stoichiometric components are investigated including HSP101 (a AAA+ ATPase), a protein of no known function termed PTEX150, and the apparent membrane component EXP2. We show that these proteins are synthesized in the preceding schizont stage (PTEX150 and HSP101) or even earlier in the life cycle (EXP2), and before invasion these components reside within the dense granules of invasive merozoites. From these apical organelles, the protein complex is released into the host cell where it resides with little turnover in the parasitophorous vacuole membrane for most of the remainder of the following cell cycle. At this membrane, PTEX is arranged in a stable macromolecular complex of >1230 kDa that includes an ∼600-kDa apparently homo-oligomeric complex of EXP2 that can be separated from the remainder of the PTEX complex using non-ionic detergents. Two different biochemical methods undertaken here suggest that PTEX components associate as EXP2-PTEX150-HSP101, with EXP2 associating with the vacuolar membrane. Collectively, these data support the hypothesis that EXP2 oligomerizes and potentially forms the putative membrane-spanning pore to which the remainder of the PTEX complex is attached.

Echium oil provides no benefit over linseed oil for (n-3) long-chain PUFA biosynthesis in rainbow trout

The implementation of alternative lipid sources for use in aquaculture is of considerable interest globally. However, the possible benefit of using stearidonic acid (SDA)–rich fish oil (FO) alternatives has led to scientific confusion. Two hundred and forty rainbow trout (Oncorhynchus mykiss) were fed 1 of 4 diets (3 replicate tanks/treatment) containing either FO, linseed oil (LO), echium oil, or mixed vegetable oil (72% LO, 23% sunflower oil, and 6% canola oil) as the dietary lipid source (16.5%) for 73 d to investigate the competition and long-chain PUFA (LC-PUFA) biosynthesis between the fatty acid substrates α-linolenic acid (ALA) and SDA. SDA was more efficiently bioconverted to LC-PUFA compared with ALA. However, when the dietary lipid sources were directly compared, the increased provision of C18 PUFA within the LO diet resulted in no significant differences in (n-3) LC-PUFA content compared with fish fed the other diets. This study therefore shows that, rather than the previously speculated substrate competition, the limiting process in the apparent in vivo (n-3) LC-PUFA biosynthesis appears to be substrate availability. Rainbow trout fed the SDA- and ALA-rich dietary lipid sources subsequently had similar significant reductions in (n-3) LC-PUFA compared with fish fed the FO diet, therefore providing no additional dietary benefit on (n-3) LC-PUFA concentrations.

Microbial biosynthesis of biopolymers and applications in the biopharmaceutical, biomedical and food industries

Biopolymers can be produced through a variety of mechanisms. They can be derived from microbial systems, extracted from higher organisms such as plants, or synthesized chemically from basic biological building blocks. A wide range of emerging applications rely on all three of these production techniques. In recent years, considerable attention has been given to biopolymers produced by microbes. It is on the microbial level where the tools of genetic engineering can be most readily applied. A number of novel materials are now being developed or introduced into the market. Biopolymers are being developed for use as medical materials, packaging, cosmetics, food additives, clothing fabrics, water treatment chemicals, industrial plastics, absorbents, biosensors, and even data storage elements. This review identifies the possible commercial applications and describes the various methods of production of microbial biopolymers.

Modulating LC-PUFA biosynthesis in freshwater farmed fish

This work focused on the in vivo fatty acid metabolism of freshwater fish, towards minimising the unsustainable use of fish oil in aquaculture feed. A series of innovative nutritional approaches have been hypothesised and verified for maximising the omega-3 long chain polyunsaturated fatty acid biosynthesis capabilities of cultured fish.

Biosynthesis and expression of a disintegrin-like and metalloproteinase domain with thrombospondin-1 repeats-15

Background
ADAMTS proteoglycanases show proteolytic activity toward versican and other proteoglycans.

Results
ADAMTS15, which cleaves versican, is expressed during early cardiac development and during musculoskeletal development.

Conclusion
With unique and overlapping biological properties, ADAMTS15 is likely to have cooperative roles with other members of the ADAMTS proteoglycanase clade.

Significance
Versican cleavage has profound effects on developmental morphogenesis and regulates cancer cell behavior.

APETALA2/ETHYLENE respnse factor and basic helix-loop-helix tobacco transcription factors cooperatively mediate jasmonate-elicited nicotine biosynthesis.

Transcription factors of the plant-specific apetala2/ethylene response factor (AP2/ERF) family control plant secondary metabolism, often as part of signalling cascades induced by jasmonate (JA) or other elicitors. Here, we functionally characterized the JA-inducible tobacco (Nicotiana tabacum) AP2/ERF factor ORC1, one of the members of the NIC2-locus ERFs that control nicotine biosynthesis and a close homologue of ORCA3, a transcriptional activator of alkaloid biosynthesis in Catharanthus roseus. ORC1 positively regulated the transcription of several structural genes coding for the enzymes involved in nicotine biosynthesis. Accordingly, overexpression of ORC1 was sufficient to stimulate alkaloid biosynthesis in tobacco plants and tree tobacco (Nicotiana glauca) root cultures. In contrast to ORCA3 in C. roseus, which needs only the GCC motif in the promoters of the alkaloid synthesis genes to induce their expression, ORC1 required the presence of both GCC-motif and G-box elements in the promoters of the tobacco nicotine biosynthesis genes for maximum transactivation. Correspondingly, combined application with the JA-inducible Nicotiana basic helix–loop–helix (bHLH) factors that bind the G-box element in these promoters enhanced ORC1 action. Conversely, overaccumulation of JAZ repressor proteins that block bHLH activity reduced ORC1 functionality. Finally, the activity of both ORC1 and bHLH proteins was post-translationally upregulated by a JA-modulated phosphorylation cascade, in which a specific mitogen-activated protein kinase kinase, JA-factor stimulating MAPKK1 (JAM1), was identified. This study highlights the complexity of the molecular machinery involved in the regulation of tobacco alkaloid biosynthesis and provides mechanistic insights about its transcriptional regulators.

Creatine transporter (SLC6A8) knockout mice display an increased capacity for in vitro creatine biosynthesis in skeletal muscle.

The present study aimed to investigate whether skeletal muscle from whole body creatine transporter (CrT; SLC6A8) knockout mice (CrT(-/y)) actually contained creatine (Cr) and if so, whether this Cr could result from an up regulation of muscle Cr biosynthesis. Gastrocnemius muscle from CrT(-/y) and wild type (CrT(+/y)) mice were analyzed for ATP, Cr, Cr phosphate (CrP), and total Cr (TCr) content. Muscle protein and gene expression of the enzymes responsible for Cr biosynthesis L-arginine:glycine amidotransferase (AGAT) and guanidinoacetate methyltransferase (GAMT) were also determined as were the rates of in vitro Cr biosynthesis. CrT(-/y) mice muscle contained measurable (22.3 ± 4.3 mmol.kg(-1) dry mass), but markedly reduced (P < 0.05) TCr levels compared with CrT(+/y) mice (125.0 ± 3.3 mmol.kg(-1) dry mass). AGAT gene and protein expression were higher (~3 fold; P < 0.05) in CrT(-/y) mice muscle, however GAMT gene and protein expression remained unchanged. The in vitro rate of Cr biosynthesis was elevated 1.5 fold (P < 0.05) in CrT(-/y) mice muscle. These data clearly demonstrate that in the absence of CrT protein, skeletal muscle has reduced, but not absent, levels of Cr. This presence of Cr may be at least partly due to an up regulation of muscle Cr biosynthesis as evidenced by an increased AGAT protein expression and in vitro Cr biosynthesis rates in CrT(-/y) mice. Of note, the up regulation of Cr biosynthesis in CrT(-/y) mice muscle was unable to fully restore Cr levels to that found in wild type muscle.

Dietary micronutrients and in vivo n-3 LC-PUFA biosynthesis in Atlantic salmon

Aquaculture, and in particular Atlantic salmon culture, is expected to deliver n. -3 long-chain polyunsaturated fatty acid (n. -3 LC-PUFA) rich products. Nevertheless, the availability of n. -3 LC-PUFA rich raw materials for aquafeed is dwindling, and at an ever increasing market price. Thus, there is the need to better understand the in vivo n. -3 LC-PUFA biosynthetic capabilities of cultured fish to enable the possible maximization of dietary 18:3n. -3 (ALA) bioconversion to 20:5n. -3 (EPA) and 22:6n. -3 (DHA). The cofactors and coenzymes involved in this metabolic pathway have so far received limited research attention. In this study, juvenile Atlantic salmon were fed an ALA-rich diet with no, normal, or over-fortified inclusion of those micronutrients reported to be essential cofactors (iron; zinc; magnesium) and coenzymes (riboflavin; biotin; niacin) for the fatty acid elongase and desaturase enzymes. The results showed that reduced dietary inclusion of these micronutrients impaired the normal n. -3 LC-PUFA biosynthetic capabilities of fish, whereas the over fortification did not provide any additional benefit. This study provides new knowledge on micronutrients and lipid metabolism interactions in a commercially important cultured species, and is envisaged to be a useful contribution towards developing more sustainable and commercially viable aquafeed for the future.Statement of relevance. This work is the continuation and extension of a previous study (Lewis et al., 2013, Aquaculture 412/413, 215-222) in which we explored the physiological roles and potential effects of micronutrients on fatty acid metabolism in cultured fish. The present study differed from the previous in the blend of minerals and vitamins used, the species, the fatty acid composition of the test diet, and the inclusion also of a negative control. The results are most interesting, showing that riboflavin (B2), biotin (B7), and niacin (B3), Iron (Fe), Magnesium (Mg) and Zinc (Zn) are all required for proper fatty acid bioconversion, but also that a dietary over-fortification does not translate into proportional improved bioconversion.

A defective mutant of Salmonella enterica Serovar Gallinarum in cobalamin biosynthesis is avirulent in chickens

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)