The BRENDA enzyme information system–From a database to an expert system

Schomburg, Ida; Jeske, Lisa; Ulbrich, Markus; Placzek, Sandra; Chang, Antje; Schomburg, Dietmar

doi:10.1016/j.jbiotec.2017.04.020

Cited by 183 publications

(123 citation statements)

References 78 publications

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“…The growth temperature dataset was validated by investigating the correlation between the growth temperature of each organism and the temperature optima of enzymes from that organism. For this validation all experimentally determined enzyme temperature optima were extracted from the BRENDA enzyme database (Schomburg et al 2017) , https://www.brenda-enzymes.org). The resulting data contained experimentally determined temperature optima for 31,826 enzymes, sourced from 3,421 organisms.…”

Section: Growth Temperatures Correlate Strongly With Mean Enzyme Optimamentioning

confidence: 99%

Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures

Engqvist

2018

Preprint

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Interpreting genomic data to identify temperature adaptations is challenging due to limited accessibility of growth temperature data. In this work I mine public culture collection websites to obtain growth temperature data for 21,498 organisms. Leveraging this unique dataset I identify 319 enzyme activities that either increase or decrease in abundance with temperature. This is a striking result showing that up to 9% of enzyme activities may represent metabolic changes important for adapting to growth at differing temperatures in microbes. Eight metabolic pathways were statistically enriched for these enzyme activities, further highlighting specific areas of metabolism that may be particularly important for such adaptations. Furthermore, I establish a correlation between 33 domains of unknown function (DUFs) with growth temperature in microbes, four of which (DUF438, DUF1524, DUF1957 and DUF3458_C) were significant in both archaea and bacteria. These DUFs may represent novel, as yet undiscovered, functions relating to temperature adaptation.

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Section: Growth Temperatures Correlate Strongly With Mean Enzyme Optimamentioning

confidence: 99%

Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures

Engqvist

2018

Preprint

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“… This open‐source peptide‐centric tool allows to predict in silico the proteases involved in naturally occurring peptide generation. Proteasix integrates information from MEROPS, BRENDA, and UniProtKB. Proteases retrieved from Proteasix analysis are listed in Table S1, Supporting Information.…”

Section: Introductionmentioning

confidence: 99%

Reviewing Mechanistic Peptidomics in Body Fluids Focusing on Proteases

et al. 2018

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The comprehension of how protease networks sculpt proteomes might help to disclose the functional annotation of the peptidome in health and disease. Envisioning to add new insights on the protease networks involved in the regulation of body fluid peptidomes, the authors apply Proteasix software to predict the proteases involved in the generation of the naturally occurring peptides present in six of the most studied human body fluids. Peptidome data is collected from the databases and from experimental studies. The analysis highlights 132 putative proteases from four families with the predominance of serine proteases and metalloproteases. From these, 49 proteases seem to be common to all fluids and are mostly associated to extracellular matrix organization as well as protein/peptide hormone processing. Data analysis also emphasizes: i) the similarity between plasma and CSF protease profiles; ii) that saliva and tears share proteases involved in the generation of peptides with antimicrobial activity; iii) that urine is the body fluid with the highest number of unique putative proteases, precluding an easy tracing of proteolytic events in this case. Taken together, the analysis emphasizes the intricate modus operandi of proteases, challenged by the interconnected pathways and amplification cascades in which they are involved.

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“…The BRENDA database (Schomburg et al, 2017;Jeske et al, 2019) does not list specific mannonate kinases, nor does it list mannonate as a known substrate for gluconate kinases. Indeed, Supplementary Figure S3.…”

Section: Discussionmentioning

confidence: 99%

A Novel D-Galacturonate Fermentation Pathway in Lactobacillus suebicus Links Initial Reactions of the Galacturonate-Isomerase Route With the Phosphoketolase Pathway

et al. 2020

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D-galacturonate, a key constituent of pectin, is a ubiquitous monomer in plant biomass. Anaerobic, fermentative conversion of D-galacturonate is therefore relevant in natural environments as well as in microbial processes for microbial conversion of pectincontaining agricultural residues. In currently known microorganisms that anaerobically ferment D-galacturonate, its catabolism occurs via the galacturonate-isomerase pathway. Redox-cofactor balancing in this pathway strongly constrains the possible range of products generated from anaerobic D-galacturonate fermentation, resulting in acetate as the predominant organic fermentation product. To explore metabolic diversity of microbial D-galacturonate fermentation, anaerobic enrichment cultures were performed at pH 4. Anaerobic batch and chemostat cultures of a dominant Lactobacillus suebicus strain isolated from these enrichment cultures produced near-equimolar amounts of lactate and acetate from D-galacturonate. A combination of whole-genome sequence analysis, quantitative proteomics, enzyme activity assays in cell extracts, and in vitro product identification demonstrated that D-galacturonate metabolism in L. suebicus occurs via a novel pathway. In this pathway, mannonate generated by the initial reactions of the canonical isomerase pathway is converted to 6-phosphogluconate by two novel biochemical reactions, catalyzed by a mannonate kinase and a 6-phosphomannonate 2-epimerase. Further catabolism of 6-phosphogluconate then proceeds via known reactions of the phosphoketolase pathway. In contrast to the classical isomerase pathway for D-galacturonate catabolism, the novel pathway enables redox-cofactor-neutral conversion of D-galacturonate to ribulose-5-phosphate. While further research is required to identify the structural genes encoding the key enzymes for the novel pathway, its redox-cofactor coupling is highly interesting for metabolic engineering of microbial cell factories for conversion of pectin-containing feedstocks into added-value fermentation products such as ethanol or lactate. This study illustrates the potential of microbial enrichment cultivation to identify novel pathways for the conversion of environmentally and industrially relevant compounds.

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The BRENDA enzyme information system–From a database to an expert system

Cited by 183 publications

References 78 publications

Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures

Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures

Reviewing Mechanistic Peptidomics in Body Fluids Focusing on Proteases

A Novel D-Galacturonate Fermentation Pathway in Lactobacillus suebicus Links Initial Reactions of the Galacturonate-Isomerase Route With the Phosphoketolase Pathway

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