ArticleMetabolic engineering communications2020
Genomic and proteomic biases inform metabolic engineering strategies for anaerobic fungi.
Article in Metabolic engineering communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed, 28 citations in OpenAlex.
- Full ribosomal operon sequencing of anaerobic gut fungi (phylumIMA fungus · 2026Article
- Anaerobic fungi: effective warriors in lignocellulosic biomass degradation and fermentation.FEMS microbiology ecology · 2025Review
- The anaerobic fungus Neocallimastix californiae shifts metabolism and produces melanin in response to lignin-derived aromatic compounds.Biotechnology for biofuels and bioproducts · 2025Article
- Genomic and transcriptomic characterization of carbohydrate-active enzymes in the anaerobic fungus Neocallimastix cameroonii var. constans.G3 (Bethesda, Md.) · 2025Article
- A Genetic Engineering Toolbox for the Lignocellulolytic Anaerobic Gut FungusACS synthetic biology · 2023Article
- Lignin deconstruction by anaerobic fungi.Nature microbiology · 2023Article
- Enzyme Discovery in Anaerobic Fungi (Neocallimastigomycetes) Enables Lignocellulosic Biorefinery Innovation.Microbiology and molecular biology reviews : MMBR · 2022Review
- In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi.Journal of fungi (Basel, Switzerland) · 2022Article
- Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates.Biotechnology for biofuels · 2021Article
- Anaerobic Fungal Mevalonate Pathway Genomic Biases Lead to Heterologous Toxicity Underpredicted by Codon Adaptation Indices.Microorganisms · 2021Article
- Article
- Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes.Annual review of biomedical engineering · 2021Review
- Article
- The Anaerobic Fungi: Challenges and Opportunities for Industrial Lignocellulosic Biofuel Production.Microorganisms · 2021Review
- Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus.mSystems · 2021Article
- A Genomic Catalog of Stress Response Genes in Anaerobic Fungi for Applications in Bioproduction.Frontiers in fungal biology · 2021Article
- Grand Challenges in Fungal Biotechnology.Frontiers in fungal biology · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Anaerobic fungi (Neocallimastigomycota) are emerging non-model hosts for biotechnology due to their wealth of biomass-degrading enzymes, yet tools to engineer these fungi have not yet been established. Here, we show that the anaerobic gut fungi have the most GC depleted genomes among 443 sequenced organisms in the fungal kingdom, which has ramifications for heterologous expression of genes as well as for emerging CRISPR-based genome engineering approaches. Comparative genomic analyses suggest that anaerobic fungi may contain cellular machinery to aid in sexual reproduction, yet a complete mating pathway was not identified. Predicted proteomes of the anaerobic fungi also contain an unusually large fraction of proteins with homopolymeric amino acid runs consisting of five or more identical consecutive amino acids. In particular, threonine runs are especially enriched in anaerobic fungal carbohydrate active enzymes (CAZymes) and this, together with a high abundance of predicted N-glycosylation motifs, suggests that gut fungal CAZymes are heavily glycosylated, which may impact heterologous production of these biotechnologically useful enzymes. Finally, we present a codon optimization strategy to aid in the development of genetic engineering tools tailored to these early-branching anaerobic fungi.
Indexed as
Identifiers
What Socratic holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.