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Protocol for condition-dependent metabolite yield prediction using the TRIMER pipeline

This protocol explains the pipeline for condition-dependent metabolite yield prediction using Transcription Regulation Integrated with MEtabolic Regulation (TRIMER). TRIMER targets metabolic engineering applications via a hybrid model integrating transcription factor (TF)-gene regulatory network (TRN) with a Bayesian network (BN) inferred from transcriptomic expression data to effectively regulate metabolic reactions. For E. coli and yeast, TRIMER achieves… [Read More]

Silencing of Dicer‐like protein 2a restores the resistance phenotype in the rice mutant, sxi4 (suppressor of Xa21‐mediated immunity 4)

The rice immune receptor XA21 confers resistance to Xanthomonas oryzae pv. oryzae (Xoo), and upon recognition of the RaxX21-sY peptide produced by Xoo, XA21 activates the plant immune response. Here we screened 21 000 mutant plants expressing XA21 to identify components involved in this response, and reported here the identification of a rice mutant, sxi4, which… [Read More]

Active anaerobic methane oxidation and sulfur disproportionation in the deep terrestrial subsurface

Microbial life is widespread in the terrestrial subsurface and present down to several kilometers depth, but the energy sources that fuel metabolism in deep oligotrophic and anoxic environments remain unclear. In the deep crystalline bedrock of the Fennoscandian Shield at Olkiluoto, Finland, opposing gradients of abiotic methane and ancient seawater-derived sulfate create a terrestrial sulfate-methane… [Read More]

Isolation and sequencing of a single copy of an introgressed chromosome from a complex genome for gene and SNP identification

Key messageThis manuscript describes the identification, isolation and sequencing of a single chromosome containing high value resistance genes from a complex polyploid where sequencing the whole genome is too costly.AbstractThe large complex genomes of many crops constrain the use of new technologies for genome-assisted selection and genetic improvement. One method to simplify a genome is… [Read More]

Soil pH influences the structure of virus communities at local and global scales

The influence of biotic and abiotic factors on viral communities across environmental gradients in soil is relatively unknown. While soil pH strongly influences microbial community structure, it is unclear whether there is a similar influence on soil viruses. In this study, prokaryotic and viral communities were characterized in soils from a long-term pH-manipulated soil gradient… [Read More]

Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland

Microbial communities are early responders to wetland degradation, and instrumental players in the reversal of this degradation. However, our understanding of soil microbial community structure and function throughout wetland development remains incomplete. We conducted a survey across cranberry farms, young retired farms, old retired farms, flooded former farms, ecologically restored former farms, and natural reference… [Read More]

pHBMT1, a BAHD-family monolignol acyltransferase, mediates lignin acylation in poplar

Poplar (Populus) lignin is naturally acylated with p-hydroxybenzoate ester moieties. However, the enzyme(s) involved in the biosynthesis of the monolignol-p-hydroxybenzoates have remained largely unknown. Here, we performed an in vitro screen of the Populus trichocarpa BAHD acyltransferase superfamily (116 genes) using a wheatgerm cell-free translation system and found five enzymes capable of producing monolignol-p-hydroxybenzoates. We… [Read More]

Soil compartments (bulk soil, litter, root and rhizosphere) as main drivers of soil protistan communities distribution in forests with different nitrogen deposition

Protists, in particular bacterivores, are essential players in the rhizosphere; thus, how their interactions with bacteria and fungi affect plant productivity and soil nutrient cycles warrants more attention. Using next-generation sequencing of the 18 S rRNA gene, we investigated the distribution of two major protistan phyla, Cercozoa and Endomyxa, across four seasons, and four soil compartments… [Read More]

A sorghum genome-wide association study (GWAS) identifies a WRKY transcription factor as a candidate gene underlying sugarcane aphid (Melanaphis sacchari) resistance

Main conclusionA WRKY transcription factor identified through forward genetics is associated with sorghum resistance to the sugarcane aphid and through heterologous expression reduces aphid populations in multiple plant species.AbstractCrop plant resistance to insect pests is based on genetically encoded traits which often display variability across diverse germplasm. In a comparatively recent event, a predominant sugarcane… [Read More]

Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea

The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from… [Read More]