Global probabilistic annotation of metabolic networks enables enzyme discovery

Plata, Germán; Fuhrer, Tobias; Hsiao, Tzu-Lin; Sauer, Uwe; Vitkup, Dennis

doi:10.1038/nchembio.1063

Cited by 56 publications

(58 citation statements)

References 52 publications

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“…The transcription of the sps operon by late mother cell transcription factors, such as K and GerE, is consistent with the idea that the operon encodes enzymes involved in the synthesis of polysaccharides present on the outer surface of the spore (11). This idea also is supported by a bioinformatic analysis and experimental data that identify the distal four genes of the operon, spsIJKL, as being involved in the biosynthetic pathway leading to dTDP-L-rhamnose from D-glucose 1-phosphate and dTTP (12).…”

supporting

confidence: 66%

The sps Gene Products Affect the Germination, Hydrophobicity, and Protein Adsorption of Bacillus subtilis Spores

Cangiano

Širec

Panarella

et al. 2014

Appl Environ Microbiol

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The multilayered surface of the Bacillus subtilis spore is composed of proteins and glycans. While over 70 different proteins have been identified as surface components, carbohydrates associated with the spore surface have not been characterized in detail yet. Bioinformatic data suggest that the 11 products of the sps operon are involved in the synthesis of polysaccharides present on the spore surface, but an experimental validation is available only for the four distal genes of the operon. Here, we report a transcriptional analysis of the sps operon and a functional study performed by constructing and analyzing two null mutants lacking either all or only the promoter-proximal gene of the operon. Our results show that both sps mutant spores apparently have normal coat and crust but have a small germination defect and are more hydrophobic than wild-type spores. We also show that spores lacking all Sps proteins are highly adhesive and form extensive clumps. In addition, sps mutant spores have an increased efficiency in adsorbing a heterologous enzyme, suggesting that hydrophobic force is a major determinant of spore adsorption and indicating that a deep understanding of the surface properties of the spore is essential for its full development as a surface display platform.

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confidence: 66%

The sps Gene Products Affect the Germination, Hydrophobicity, and Protein Adsorption of Bacillus subtilis Spores

Cangiano

Širec

Panarella

et al. 2014

Appl Environ Microbiol

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“…Several coat and crust proteins have been identified and characterized, but little is known about the identities of the sugars present on the spore surface. It is, however, known that their presence on the spore surface modulates the relative hydrophobicity of the spore (7)(8)(9).…”

mentioning

confidence: 99%

CotG-Like Modular Proteins Are Common among Spore-Forming Bacilli

et al. 2016

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CotG is an abundant protein initially identified as an outer component of the Bacillus subtilis spore coat. It has an unusual structure characterized by several repeats of positively charged amino acids that are probably the outcome of multiple rounds of gene elongation events in an ancestral minigene. CotG is not highly conserved, and its orthologues are present in only two Bacillus and two Geobacillus species. In B. subtilis, CotG is the target of extensive phosphorylation by a still unidentified enzyme and has a role in the assembly of some outer coat proteins. We report now that most spore-forming bacilli contain a protein not homologous to CotG of B. subtilis but sharing a central "modular" region defined by a pronounced positive charge and randomly coiled tandem repeats. Conservation of the structural features in most spore-forming bacilli suggests a relevant role for the CotG-like protein family in the structure and function of the bacterial endospore. To expand our knowledge on the role of CotG, we dissected the B. subtilis protein by constructing deletion mutants that express specific regions of the protein and observed that they have different roles in the assembly of other coat proteins and in spore germination. IMPORTANCE CotG of B. subtilis is not highly conserved in the

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“…These annotations enable the exploration of metabolic potential of an organism and its cellular physiology; the creation of genomescale metabolic models, which are useful for metabolic engineering and systems analysis; and the identification of drug targets. In this issue, Plata et al 1 compose an approach that assigns annotations-with probabilities -to gene-scale metabolic networks with high precision, validating a select number of predictions experimentally.…”

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confidence: 98%