Transcriptome-Guided Identification of Carbohydrate Active Enzymes (CAZy) from the Christmas Island Red Crab, Gecarcoidea natalis and a Vote for the Inclusion of Transcriptome-Derived Crustacean CAZys in Comparative Studies

Mar Biotechnol (NY). 2018 Oct;20(5):654-665. doi: 10.1007/s10126-018-9836-2. Epub 2018 Jul 11.

Abstract

The Christmas Island red crab, Gecarcoidea natalis, is an herbivorous land crab that consumes mostly fallen leaf litter. In order to subsist, G. natalis would need to have developed specialised digestive enzymes capable of supplying significant amounts of metabolisable sugars from this diet. To gain insights into the carbohydrate metabolism of G. natalis, a transcriptome assembly was performed, with a specific focus on identifying transcripts coding for carbohydrate active enzyme (CAZy) using in silico approaches. Transcriptome sequencing of the midgut gland identified 70 CAZy-coding transcripts with varying expression values. At least three newly discovered putative GH9 endo-β-1,4-glucanase ("classic cellulase") transcripts were highly expressed in the midgut gland in addition to the previously characterised GH9 and GH16 (β-1,3-glucanase) transcripts, and underscoring the utility of whole transcriptome in uncovering new CAZy-coding transcripts. A highly expressed transcript coding for GH5_10 previously missed by conventional screening of cellulase activity was inferred to be a novel endo-β-1,4-mannase in G. natalis with in silico support from homology modelling and amino acid alignment with other functionally validated GH5_10 proteins. Maximum likelihood tree reconstruction of the GH5_10 proteins demonstrates the phylogenetic affiliation of the G. natalis GH5_10 transcript to that of other decapods, supporting endogenous expression. Surprisingly, crustacean-derived GH5_10 transcripts were near absent in the current CAZy database and yet mining of the transcriptome shotgun assembly (TSA) recovered more than 100 crustacean GH5_10s in addition to several other biotechnological relevant CAZys, underscoring the unappreciated potential of the TSA database as a valuable resource for crustacean CAZys.

Keywords: Cellulase; Crustacean; Endo-β-1,4-mannase; GH5_10; Hemicellulase; Transcriptome.

Publication types

  • Comparative Study

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Arthropod Proteins / chemistry
  • Arthropod Proteins / classification
  • Arthropod Proteins / genetics*
  • Arthropod Proteins / metabolism
  • Brachyura / classification
  • Brachyura / enzymology
  • Brachyura / genetics*
  • Carbohydrate Metabolism / genetics*
  • Cellulase / chemistry
  • Cellulase / classification
  • Cellulase / genetics*
  • Cellulase / metabolism
  • Databases, Genetic
  • Diet
  • Gene Expression
  • Gene Ontology
  • Isoenzymes / chemistry
  • Isoenzymes / classification
  • Isoenzymes / genetics
  • Isoenzymes / metabolism
  • Models, Molecular
  • Molecular Sequence Annotation
  • Phylogeny
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Sequence Alignment
  • Structural Homology, Protein
  • Transcriptome*

Substances

  • Arthropod Proteins
  • Isoenzymes
  • RNA, Messenger
  • Cellulase