9 research outputs found
Widespread Occurrence of Secondary Lipid Biosynthesis Potential in Microbial Lineages
Bacterial production of long-chain omega-3 polyunsaturated fatty acids (PUFAs),
such as eicosapentaenoic acid (EPA, 20:5n-3) and
docosahexaenoic acid (DHA, 22:6n-3), is constrained to a narrow
subset of marine γ-proteobacteria. The genes responsible for de
novo bacterial PUFA biosynthesis, designated
pfaEABCD, encode large, multi-domain protein complexes akin
to type I iterative fatty acid and polyketide synthases, herein referred to as
“Pfa synthases”. In addition to the archetypal Pfa synthase gene
products from marine bacteria, we have identified homologous type I FAS/PKS gene
clusters in diverse microbial lineages spanning 45 genera representing 10 phyla,
presumed to be involved in long-chain fatty acid biosynthesis. In total, 20
distinct types of gene clusters were identified. Collectively, we propose the
designation of “secondary lipids” to describe these
biosynthetic pathways and products, a proposition consistent with the
“secondary metabolite” vernacular. Phylogenomic analysis reveals a
high degree of functional conservation within distinct biosynthetic pathways.
Incongruence between secondary lipid synthase functional clades and taxonomic
group membership combined with the lack of orthologous gene clusters in closely
related strains suggests horizontal gene transfer has contributed to the
dissemination of specialized lipid biosynthetic activities across disparate
microbial lineages
Genomic Analysis of the Hydrocarbon-Producing, Cellulolytic, Endophytic Fungus Ascocoryne sarcoides
The microbial conversion of solid cellulosic biomass to liquid biofuels may provide a renewable energy source for transportation fuels. Endophytes represent a promising group of organisms, as they are a mostly untapped reservoir of metabolic diversity. They are often able to degrade cellulose, and they can produce an extraordinary diversity of metabolites. The filamentous fungal endophyte Ascocoryne sarcoides was shown to produce potential-biofuel metabolites when grown on a cellulose-based medium; however, the genetic pathways needed for this production are unknown and the lack of genetic tools makes traditional reverse genetics difficult. We present the genomic characterization of A. sarcoides and use transcriptomic and metabolomic data to describe the genes involved in cellulose degradation and to provide hypotheses for the biofuel production pathways. In total, almost 80 biosynthetic clusters were identified, including several previously found only in plants. Additionally, many transcriptionally active regions outside of genes showed condition-specific expression, offering more evidence for the role of long non-coding RNA in gene regulation. This is one of the highest quality fungal genomes and, to our knowledge, the only thoroughly annotated and transcriptionally profiled fungal endophyte genome currently available. The analyses and datasets contribute to the study of cellulose degradation and biofuel production and provide the genomic foundation for the study of a model endophyte system