Marine ecosystems harbor vast microbial diversity encoding polysaccharide degrading enzymes with exceptional stability and catalytic breadth, enabling industrial bioprocesses and tailored marine oligosaccharide production. Yet progress from discovery to application is limited by low cultivability, difficulty reproducing deep sea conditions, slow growth, heterologous expression and screening bottlenecks, and pervasive database misannotation. This chapter integrates tools across the pipeline: culture dependent/independent mining (improved cultivation, culturomics, metagenomics, single cell genomics), database and AI guided prioritization; high efficiency heterologous expression in E. coli, Bacillus, yeasts, and Aspergillus; design of multi enzyme cascades via fusion, compartmentalization, and immobilization; enzyme engineering (directed, semi rational, rational, continuous in vivo evolution, ancestral sequence reconstruction); and ultra high throughput screening (FACS, droplet microfluidics). Key findings show that sequence and function driven metagenomic screens are complementary, with fosmid libraries balancing insert size and stability while outcomes hinge on hosts and assays. Host choice and module design—promoters, signal peptides, fusion partners, codon usage, CRISPR editing—markedly boost soluble yield and secretion; B. subtilis enables endotoxin free secretion, while yeasts/Aspergillus provide eukaryotic processing. Engineered cascades benefit from co localization/co immobilization but require careful stoichiometry and condition balancing. High throughput screens and machine learning predictors accelerate triage. Together, these tools provide a practical framework to speed translation into robust biocatalysts.

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Tools for Mining, Expression, and Modification of Marine Polysaccharide-Degrading Enzymes

  • Zhengming Zhu,
  • Yanxia Wang,
  • Liying Zhu,
  • Ling Jiang

摘要

Marine ecosystems harbor vast microbial diversity encoding polysaccharide degrading enzymes with exceptional stability and catalytic breadth, enabling industrial bioprocesses and tailored marine oligosaccharide production. Yet progress from discovery to application is limited by low cultivability, difficulty reproducing deep sea conditions, slow growth, heterologous expression and screening bottlenecks, and pervasive database misannotation. This chapter integrates tools across the pipeline: culture dependent/independent mining (improved cultivation, culturomics, metagenomics, single cell genomics), database and AI guided prioritization; high efficiency heterologous expression in E. coli, Bacillus, yeasts, and Aspergillus; design of multi enzyme cascades via fusion, compartmentalization, and immobilization; enzyme engineering (directed, semi rational, rational, continuous in vivo evolution, ancestral sequence reconstruction); and ultra high throughput screening (FACS, droplet microfluidics). Key findings show that sequence and function driven metagenomic screens are complementary, with fosmid libraries balancing insert size and stability while outcomes hinge on hosts and assays. Host choice and module design—promoters, signal peptides, fusion partners, codon usage, CRISPR editing—markedly boost soluble yield and secretion; B. subtilis enables endotoxin free secretion, while yeasts/Aspergillus provide eukaryotic processing. Engineered cascades benefit from co localization/co immobilization but require careful stoichiometry and condition balancing. High throughput screens and machine learning predictors accelerate triage. Together, these tools provide a practical framework to speed translation into robust biocatalysts.