Phocaeicola plebeius

Phocaeicola plebeius, formerly Bacteroides plebeius, is a microbe found in the human gut, most often found in Japan natives.[1] It is able to digest porphyran, a polysacchide from Porphyra seaweed (nori) that humans cannot digest on their own.[2] The porphyranase-encoding gene Bp1689 is believed to have been derived from the microbe Zobellia galactanivorans via horizontal gene transfer, as part of a gene cluster containing other carbohydrate-active enzymes.[3]

Phocaeicola plebeius
Scientific classification Edit this classification
Domain: Bacteria
Phylum: Bacteroidota
Class: Bacteroidia
Order: Bacteroidales
Family: Bacteroidaceae
Genus: Phocaeicola
Species:
P. plebeius
Binomial name
Phocaeicola plebeius
(Kitahara et al. 2005) García-López et al. 2020
Synonyms
  • Bacteroides plebeius Kitahara 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.[2] 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]

Horizontal gene transfer

P. plebeius is believed to have acquired a cluster of sugar-processing enzymes from Z. galactanivorans, a marine bacterium.[3] The two most important transferred genes are Bp1689 (GH16 β-porphyranase) and Bp1670 (GH16 agarase), as the enzymes they make deal with sugars found in the molecule.[3] (Other transferred genes, such as two GH86 aragases, a sulfatase, and various regulatory parts, play a role too.)[2] Specifically, Bp1689 hydrolyzes the (1→4) linkage between β-D-galactopyranose and α-L-galactopyranose-6-sulfate in porphyran. Structurally it contains a TIM barrel domain and two β-sandwich domains.[2]

A number of other genes are also transferred with Bp1789 and Bp1670. In total, 11 genes are believed to have been transferred: they do not occur in other Phocaeicola species (known as of 2010) and have sequence similarity of 48%-69% compared to orthologs in Z. galactanivorans. Moreover, transferred genes in both species are located in similar orders along their chromosome (i.e. they are syntenic). There are also genes related to the HGT in these 11.[3]

In 2012, it was reported that Bacteroides thetaiotaomicron VPI-5482 has a related set of genes in the same order, albeit specialized to a different task: degradation of α-mannan, a fungal sugar. Discovery of this more intact cluster further confirms the role of HGT.[2]

A different nomenclature of these genes use the gene family instead of chromosomal sequence numbers. In this scheme, Bp1689 is BpGH16B and Bp1670 is BpGH16A.[2]

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, 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.
  3. 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.
  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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