Phocaeicola plebeius

Phocaeicola plebeius, formerly Bacteroides plebeius, is a microbe found in the human gut, most often found in Japan natives.[1] The microbe is believed to have obtained the gene for degradation of porphyran via horizontal gene transfer. The porphyranase encoding gene is believed to have been derived from the microbe Zobellia galactanivorans.[2] Microbes in the gut are responsible for their production of carbohydrate active enzymes or CAZymes. CAZymes are responsible for a variety of functions involving complex carbohydrates such as synthesis, recognition, or metabolism. Moreover, CAZymes are not encoded in the human genome, highlighting the importance of microbes in digestive processes.[3] P. plebeius contains a gene known as BACPLE_01693 which encodes β-porphyranase-A.[3]

Phocaeicola plebeius
Scientific classification
Domain: Bacteria
Phylum: Bacteroidota
Class: Bacteroidia
Order: Bacteroidales
Family: Bacteroidaceae
Genus: Phocaeicola
Species:
P. plebeius
Binomial name
Phocaeicola plebeius
Kitahara M et al. (2005)

Composition of red algae Porphyra

Porphyra is a genus of red seaweed. The two main Porphyra used in Japanese dishes are P. yezoensis and P. tenera which are commonly used in sushi.[4] Porphyra spp. also known as nori in Japan contains compounds such porphyrans and agaroses that are indigestible to people lacking P. plebius.[3] Rhodophyta, the phylum of red algae, has a cell wall composed of sulfated galactans. Agarans, a main component of the cell wall is composed of alternating 3-linked β-D-galactose and 4-linked α-L-galactose.[5] Porphyran is a water-soluble agaran found in Porphyra. The porphyran backbone is composed of roughly 30% 3-linked β-D-galactose and 4-linked 3,6-anhydro-α-L-galactose. The remaining 70% is composed of 4-linked α-L-galactopyranose-6-sulfate or 3-linked β-D-galactopyranose.[6]

Function of β-Porphyranase-A

β-Porphyranase-A is a catalytic enzyme that hydrolyzes the (1→4) linkage between β-D-galactopyranose and α-L-galactopyranose-6-sulfate in porphyran.[6] Furthermore it contains a TIM barrel domain and two β-sandwich domains.[3]

Comparison of β-Porphyranase-B and β-Porphyranase-A

There is a 35% sequence similarity between β-Porphyranase-B and β-Porphyranase-A. [2] Furthermore, orthologs between Z. galactanivorans and P. plebeius 1698, a strain of P. plebeius, have a sequence similarity of 48%-69%.[2] Moreover, porphyranase genes in both Z. galactanivorans and P. plebeius are located in similar orders along their chromosome, or are syntenic.

References
  1. Kitahara M, Sakamoto M, Ike M, Sakata S, Benno Y (September 2005). "Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., isolated from human faeces". International Journal of Systematic and Evolutionary Microbiology. 55 (Pt 5): 2143–7. doi:10.1099/ijs.0.63788-0. PMID 16166722.
  2. Hehemann JH, Correc G, Barbeyron T, Helbert W, Czjzek M, Michel G (April 2010). "Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota". Nature. 464 (7290): 908–12. Bibcode:2010Natur.464..908H. doi:10.1038/nature08937. PMID 20376150. S2CID 2820027.
  3. Hehemann JH, Kelly AG, Pudlo NA, Martens EC, Boraston AB (November 2012). "Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes". Proceedings of the National Academy of Sciences of the United States of America. 109 (48): 19786–91. Bibcode:2012PNAS..10919786H. doi:10.1073/pnas.1211002109. PMC 3511707. PMID 23150581.
  4. Nisizawa K, Noda H, Kikuchi R, Watanabe T (September 1987). "The main seaweed foods in Japan". Hydrobiologia. 151 (1): 5–29. doi:10.1007/BF00046102. S2CID 39736004.
  5. Knutsen SH, Myslabodski DE, Larsen B, Usov AI (1994). "A Modified System of Nomenclature for Red Algal Galactans". Botanica Marina. 37 (2). doi:10.1515/botm.1994.37.2.163. S2CID 85192276.
  6. Correc G, Hehemann JH, Czjzek M, Helbert W (January 2011). "Structural analysis of the degradation products of porphyran digested by Zobellia galactanivorans β-porphyranase A". Carbohydrate Polymers. 83 (1): 277–283. doi:10.1016/j.carbpol.2010.07.060.
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