How Do Shipworms Eat Wood? Screening Shipworm Gill Symbiont Genomes for Lignin-Modifying Enzymes

Abstract

Shipworms are ecologically and economically important mollusks that feed on woody plant material (lignocellulosic biomass) in marine environments. Digestion occurs in a specialized cecum, reported to be virtually sterile and lacking resident gut microbiota. Wood-degrading CAZymes are produced both endogenously and by gill endosymbiotic bacteria, with extracellular enzymes from the latter being transported to the gut. Previous research has predominantly focused on how these animals process the cellulose component of woody plant material, neglecting the breakdown of lignin – a tough, aromatic polymer which blocks access to the holocellulose components of wood. Enzymatic or non-enzymatic modification and depolymerization of lignin has been shown to be required in other wood-degrading biological systems as a precursor to cellulose deconstruction. We investigated the genomes of five shipworm gill bacterial symbionts obtained from the Joint Genome Institute Integrated Microbial Genomes and Microbiomes Expert Review for the production of lignin-modifying enzymes, or ligninases. The genomes were searched for putative ligninases using the Joint Genome Institute’s Function Profile tool and blastp analyses. The resulting proteins were then modeled using SWISS-MODEL. Although each bacterial genome possessed at least four predicted ligninases, the percent identities and protein models were of low quality and were unreliable. Prior research demonstrates limited endogenous ability of shipworms to modify lignin at the chemical/molecular level. Similarly, our results reveal that shipworm bacterial gill-symbiont enzymes are unlikely to play a role in lignin modification during lignocellulose digestion in the shipworm gut. This suggests that our understanding of how these keystone organisms digest and process lignocellulose is incomplete, and further research into non-enzymatic and/or other unknown mechanisms for lignin modification is required.

Biochemical and structural characterisation of a family GH5 cellulase from endosymbiont of shipworm P. megotara

“…Until now, most cellulose-active enzymes have been isolated and characterised from wood-decaying fungi and soil bacteria [6][7][8][9]. Cellulose-degrading higher organisms may use symbiotic microbes as a source of enzymes for biomass degradation, such as the marine shipworm which is an eminent lignocellulose degrader [10][11][12], remain largely unexplored. In the present study, we analysed marine wood-digesting bivalve molluscs called shipworms, which feeds on submerged wood in the ocean.…”

“…However, later it was reported that endosymbiotic bacteria residing in a specialized region of the gill tissue have been shown to x atmospheric nitrogen [15] but also produce variety of carbohydrate active enzymes (CAZymes) that function in lignocellulose deconstruction in shipworms [16]. In addition to this, shipworms themselves also produce several endogenous CAZymes that are secreted by a specialized digestive gland that nally accumulate in cecum for lignocellulose digestion [10,11]. Because of these unique features, shipworms are an attractive target for the discovery of new CAZymes for depolymerization of lignocellulose.…”

Biochemical and structural characterisation of a family GH5 cellulase from endosymbiont of shipwormP. megotara

“…However, later it was reported that endosymbiotic bacteria residing in a specialized region of the gill tissue have been shown to fix atmospheric nitrogen [15] but also produce variety of carbohydrate active enzymes (CAZymes) that function in lignocellulose deconstruction in shipworms [16]. In addition to this, shipworms themselves also produce several endogenous CAZymes that are secreted by a specialized digestive gland that finally accumulate in cecum for lignocellulose digestion [10, 11]. Because of these unique features, shipworms are an attractive target for the discovery of new CAZymes for depolymerization of lignocellulose.…”

“…Until now, most cellulose-active enzymes have been isolated and characterised from wood-decaying fungi and soil bacteria [6][7][8][9]. Cellulosedegrading higher organisms may use symbiotic microbes as a source of enzymes for biomass degradation, such as the marine shipworm which is an eminent lignocellulose degrader [10][11][12], remain largely unexplored. In the present study, we analysed marine wood-digesting bivalve molluscs called shipworms, which feeds on submerged wood in the ocean.…”

Biochemical and structural characterisation of a family GH5 cellulase from endosymbiont of shipworm P. megotara

“…However, later it was reported that endosymbiotic bacteria residing in a specialized region of the gill tissue have been shown to fix atmospheric nitrogen [ 15 ] also produce variety of carbohydrate active enzymes (CAZymes) that function in lignocellulose digestion in cecum of shipworms [ 16 ]. In addition, shipworms produce several endogenous CAZymes secreted by a specialized digestive gland that finally accumulate in cecum for lignocellulose digestion [ 10 , 11 ]. Because of these unique features, shipworms are an attractive target for the discovery of new CAZymes for depolymerization of lignocellulose.…”