Comparative In silico Analysis of Butyrate Production Pathways in Gut Commensals and Pathogens - PubMed (original) (raw)
Comparative In silico Analysis of Butyrate Production Pathways in Gut Commensals and Pathogens
Swadha Anand et al. Front Microbiol. 2016.
Abstract
Biosynthesis of butyrate by commensal bacteria plays a crucial role in maintenance of human gut health while dysbiosis in gut microbiome has been linked to several enteric disorders. Contrastingly, butyrate shows cytotoxic effects in patients with oral diseases like periodontal infections and oral cancer. In addition to these host associations, few syntrophic bacteria couple butyrate degradation with sulfate reduction and methane production. Thus, it becomes imperative to understand the distribution of butyrate metabolism pathways and delineate differences in substrate utilization between pathogens and commensals. The bacteria utilize four pathways for butyrate production with different initial substrates (Pyruvate, 4-aminobutyrate, Glutarate and Lysine) which follow a polyphyletic distribution. A comprehensive mining of complete/draft bacterial genomes indicated conserved juxtaposed genomic arrangement in all these pathways. This gene context information was utilized for an accurate annotation of butyrate production pathways in bacterial genomes. Interestingly, our analysis showed that inspite of a beneficial impact of butyrate in gut, not only commensals, but a few gut pathogens also possess butyrogenic pathways. The results further illustrated that all the gut commensal bacteria (Faecalibacterium, Roseburia, Butyrivibrio, and commensal species of Clostridia etc) ferment pyruvate for butyrate production. On the contrary, the butyrogenic gut pathogen Fusobacterium utilizes different amino acid metabolism pathways like those for Glutamate (4-aminobutyrate and Glutarate) and Lysine for butyrogenesis which leads to a concomitant release of harmful by-products like ammonia in the process. The findings in this study indicate that commensals and pathogens in gut have divergently evolved to produce butyrate using distinct pathways. No such evolutionary selection was observed in oral pathogens (Porphyromonas and Filifactor) which showed presence of pyruvate as well as amino acid fermenting pathways which might be because the final product butyrate is itself known to be cytotoxic in oral diseases. This differential utilization of butyrogenic pathways in gut pathogens and commensals has an enormous ecological impact taking into consideration the immense influence of butyrate on different disorders in humans. The results of this study can potentially guide bioengineering experiments to design therapeutics/probiotics by manipulation of butyrate biosynthesis gene clusters in bacteria.
Keywords: butyrate producers; butyrate production pathways; comparative genomics; genome mining; gut microbiome.
Figures
FIGURE 1
Schematic representation of four butyrate production pathways in bacteria. Pyruvate pathway: Pyruvate is converted to crotonyl CoA using three enzymes, namely, Thiolase (Thl), Hydroxybutyryl dehydrogenase (Hbd) and crotonase/enoyl-CoA hydratase (Cro). 4-aminobutyrate (4Ab) pathway: 4Ab is converted to crotonyl CoA by the action of AbfH (4-hydroxybutyrate dehydrogenase), 4Hbt (butyryl-CoA:4-hydroxybutyrate-CoA transferase) and AbfD (4-hydroxybutyryl dehydratase) which also possesses vinyl-acetyl-CoA isomerase activity. Glutarate pathway: 2-oxoglutarate conversion to Crotonyl-CoA involves 2-hydroxyglutarate dehydrogenase (L2Hgdh), glutaconate-CoA transferase (Gct) and 2-hydroxyglutaryl-CoA dehydrogenase (HgCoAd) and Glutaconyl-CoA decarboxylase (Gcd). Glutamate can be converted to 4-aminobutyrate and 2-oxoglutarate by enzymes Glutamate decarboxylase (Gdc) and Glutamate dehydrogenase (Gdh) enzymes. Lysine pathway: Lysine is metabolized to Crotonyl-CoA by lysine 2,3-aminomutase (KamA), lysine 5,6-aminomutase (Kam D,E), 3,5-diaminohexanoate dehydrogenase (Kdd), 3-keto-5-aminohexanoate cleavage enzymes (Kce) and 3-aminobutyryl-CoA ammonia lyase (Kal). Acetoacetate released in the last step can also be converted to Butyate by a few bacteria using butyryl-CoA:acetoacetate-CoA transferase (Ato) enzyme. Crotonyl-CoA, a product from each of the four pathways, is metabolized to butyryl-CoA by butyryl-CoA dehydrogenase (Bcd). Conversion of butyryl-CoA to butyrate is catalyzed by either two enzymesphosphate butyryl transferase (Ptb) and Butyrate kinase (Buk), or by butyryl-CoA:acetate CoA transferase (But).
FIGURE 2
Gene organization of the four butyrate production pathways in bacteria. The clustered genomic organization of four butyrate production pathways has been depicted. The text within the arrows shows the PFAM domain assignments corresponding to each gene in a pathway while the text above the arrow indicates the gene identifier for which PFAMs were used. Butyryl-CoA dehydrogenase (Bcd), the central enzyme in all four pathways, occurs in genomic context with the Pyruvate pathway genes and contains the dehydrogenase as well as Electron transferring α and β subunits. The final enzymes phosphate butyryl transferase (Ptb), butyrate kinase (Buk) and butyryl-CoA:acetate CoA transferase (But) occur on different locations in the bacterial genomes.
FIGURE 3
Butyrate production pathway composition in commensals vs. pathogens. (A) The figure depicts the pathway distribution in bacteria which form a part of human microbiome. The gut commensals (blue), gut pathogens (orange) and oral pathogens (green) show differential presence of butryogenic pathways. (B) Clustering of human microbiome bacteria on the basis of pathway presence.
FIGURE 4
(A) Depiction of beneficial anti-inflammatory immune response triggered by butyrate biosynthesis in commensal bacteria (shown in green). The commensal bacteria not capable of producing butyrate have been depicted in blue. (B) Pro-inflammatory immune response to ammonia released along with butyrogenesis by gut pathogens.
FIGURE 5
Distribution of butyrate production pathways in gut bacteria. The figure depicts the distribution of butyrate production pathways in gut bacteria. The commensal bacteria which produce butyrate have been depicted in green circles and connections have been shown to mark the butyrate production pathways present in each of them. The commensal bacteria which do not produce butyrate have been depicted in blue circles. The pathogenic bacteria have been depicted in red circles. The connections to corresponding butyrogenic pathways have been made to depict pathogens that produce butyrate.
References
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