Proteomic investigation of amino acid catabolism in the indigenous gut anaerobe <b><i>Fusobacterium varium</i></b>

Potrykus, Joanna; White, Robert L.; Bearne, Stephen L.

doi:10.1002/pmic.200700437

Cited by 57 publications

(63 citation statements)

References 79 publications

(130 reference statements)

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“…Throughout moult the little penguin microbiota was associated with potentially Butyrate producing microbes ( Fusobacteria and Clostridia ) [22], [23], known gastrointestinal commensals and known human and veterinary pathogens [24], [25] such as Campylobacteriaceae which has also been associated with disease in penguins [26]. Whilst the king penguin microbiota is dominated by microbes that are associated with butyrate production, chitin degradation, a novel probiotic ( Psychrobacter ) and known gut commensals [22], [23], [27]. Known pathogens such as Campylobacter , Escherichia coli , and Helicobacter also dominate the microbiota during early moult [23].…”

Section: Discussionmentioning

confidence: 99%

“…Whilst the king penguin microbiota is dominated by microbes that are associated with butyrate production, chitin degradation, a novel probiotic ( Psychrobacter ) and known gut commensals [22], [23], [27]. Known pathogens such as Campylobacter , Escherichia coli , and Helicobacter also dominate the microbiota during early moult [23]. By late moult, the microbiota is dominated by Fusobacteria, which is a known butyrate producer.…”

Section: Discussionmentioning

confidence: 99%

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Influence of Fasting during Moult on the Faecal Microbiota of Penguins

et al. 2014

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Many seabirds including penguins are adapted to long periods of fasting, particularly during parts of the reproductive cycle and during moult. However, the influence of fasting on the gastrointestinal (GI) microbiota has not been investigated in seabirds. Therefore, the present study aimed to examine the microbial composition and diversity of the GI microbiota of fasting little (Eudyptula minor) and king penguins (Aptenodytes patagonicus) penguins during early and late moult. The results from this study indicated that there was little change in the abundance of the major phyla during moult, except for a significant increase in the level of Proteobacteria in king penguins. In king penguins the abundance of Fusobacteria increases from 1.73% during early moult to 33.6% by late moult, whilst the abundance of Proteobacteria (35.7% to 17.2%) and Bacteroidetes (19.5% to 11%) decrease from early to late moult. In little penguins, a decrease in the abundances of Firmicutes (44% to 29%) and an increase in the abundance of Bacteroidetes (11% to 20%) were observed from early to late moult respectively. The results from this study indicate that the microbial composition of both king and little penguins alters during fasting. However, it appears that the microbial composition of king penguins is more affected by fasting than little penguins with the length of fast the most probable cause for this difference.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Influence of Fasting during Moult on the Faecal Microbiota of Penguins

et al. 2014

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“…However, it is possible that YbeY affects the cellular translation machinery indirectly. For instance, depletion of nucleotides (7), starvation for an amino acid (15), and even a specific defect in cotranslational protein targeting of integral inner membrane proteins (6) can all lead to an apparent general translational defect.…”

Section: Resultsmentioning

confidence: 99%

The Heat Shock Protein YbeY Is Required for Optimal Activity of the 30S Ribosomal Subunit

2010

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The highly conserved bacterial ybeY gene is a heat shock gene whose function is not fully understood. Previously, we showed that the YbeY protein is involved in protein synthesis, as Escherichia coli mutants with ybeY deleted exhibit severe translational defects in vivo. Here we show that the in vitro activity of the translation machinery of ybeY deletion mutants is significantly lower than that of the wild type. We also show that the lower efficiency of the translation machinery is due to impaired 30S small ribosomal subunits.Many heat shock proteins are chaperones and proteases that constitute the protein quality control system (4,5,13,18). Recent studies demonstrated that beyond protein quality control, the heat shock response includes proteins implemented in the translation machinery (16,17), such as FtsJ (2, 3) and Hsp15 (11).FtsJ catalyzes methylation of U2552 in 23S rRNA (3). This modification occurs during the final steps of 50S biogenesis and is important for the structural stability of the 50S subunit (2). ftsJ deletion mutants accumulate ribosomal subunits at the expense of polysomes (2). Consequently, crude ribosome extracts prepared from ftsJ deletion mutants are far less active than wild-type preparations (3). Hsp15 recognizes and binds with high affinity to the aberrant state of the 50S subunit in complex with peptidyl tRNA positioned at the A site (10), which is more frequent at high temperatures (10). It has been proposed that Hsp15 participates in releasing the bound peptide and thereby helps recycle the 50S subunit (8, 10). Thus, heat shock proteins play a significant role both in the biogenesis of ribosomes and in the translation process.YbeY is a 17-kDa heat shock protein, highly conserved among bacteria, that belongs to the UPF0054 family of metaldependent hydrolases, suggesting that it may have a potential hydrolytic function (14,21). In Aquifex aeolicus, analysis of YbeY structure homology showed similarity to eukaryotic extracellular proteinases such as collagenase and gelatinase. However, in vitro experiments could not detect collagenase, gelatinase, or other hydrolase activity in YbeY (14).Recently, we showed that ybeY deletion mutants exhibit severe translational defects manifested by a very low level of polysomes and accumulation of free ribosomes and ribosomal subunits, indicating that most ribosomes in the cell are not engaged in translation. This translational defect intensifies at elevated temperatures (42°C) and results in growth arrest (17).Here we present in vitro studies indicating that the activity of the translation machinery prepared from ybeY deletion mutants is lower than in the wild type. In addition, we show that this lower activity stems specifically from a defective 30S ribosomal subunit. MATERIALS AND METHODSPurification of ribosomes and S100 subunits. Ribosomes and S100 subunits were prepared essentially as described previously (1). Cultures of Escherichia coli MG1655 and its ⌬ybeY derivative were grown in LB broth (Difco) medium at 37°C to an optical density at 60...

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“…Indeed, among proteins that best characterized microbiota from mice fed the HF diet, we noted the presence of enzymes metabolizing amino acids (aminotransferases and proteases) that were not detected in CARB mice. We thus propose that shifts in the metabolism of amino acids such as histidine (ammonia-lyase, glutamate formimidoyltransferase, urocanate hydratase) and alanine (alanine and glutamate dehydrogenase) as well as arginine and proline coupled with the use of glutamate as a source of pyruvate for energy production (acetylornithine aminotransferase, glutamate dehydrogenase, (R)-2-hydroxyglutaryl-CoA dehydratase, urease) represent the most prominent metabolic adaptations of the microbial ecosystem to the HF diet (Potrykus et al, 2008). This may corroborate (i) the higher protein to carbohydrate ratio in the HF vs CARB diet (ca.…”

Section: Discussionmentioning

confidence: 99%

High-fat diet alters gut microbiota physiology in mice

Daniel¹,

Gholami²,

Berry³

et al. 2013

The ISME Journal

589

386

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The intestinal microbiota is known to regulate host energy homeostasis and can be influenced by highcalorie diets. However, changes affecting the ecosystem at the functional level are still not well characterized. We measured shifts in cecal bacterial communities in mice fed a carbohydrate or high-fat (HF) diet for 12 weeks at the level of the following: (i) diversity and taxa distribution by high-throughput 16S ribosomal RNA gene sequencing; (ii) bulk and single-cell chemical composition by Fourier-transform infrared-(FT-IR) and Raman micro-spectroscopy and (iii) metaproteome and metabolome via highresolution mass spectrometry. High-fat diet caused shifts in the diversity of dominant gut bacteria and altered the proportion of Ruminococcaceae (decrease) and Rikenellaceae (increase). FT-IR spectroscopy revealed that the impact of the diet on cecal chemical fingerprints is greater than the impact of microbiota composition. Diet-driven changes in biochemical fingerprints of members of the Bacteroidales and Lachnospiraceae were also observed at the level of single cells, indicating that there were distinct differences in cellular composition of dominant phylotypes under different diets. Metaproteome and metabolome analyses based on the occurrence of 1760 bacterial proteins and 86 annotated metabolites revealed distinct HF diet-specific profiles. Alteration of hormonal and anti-microbial networks, bile acid and bilirubin metabolism and shifts towards amino acid and simple sugars metabolism were observed. We conclude that a HF diet markedly affects the gut bacterial ecosystem at the functional level.

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Proteomic investigation of amino acid catabolism in the indigenous gut anaerobe Fusobacterium varium

Cited by 57 publications

References 79 publications

Influence of Fasting during Moult on the Faecal Microbiota of Penguins

Influence of Fasting during Moult on the Faecal Microbiota of Penguins

The Heat Shock Protein YbeY Is Required for Optimal Activity of the 30S Ribosomal Subunit

High-fat diet alters gut microbiota physiology in mice

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