Biology subjects

Fu, D.

Publications and source records attributed to Fu, D..

4 recordsLinked to original sources

bioRxiv2018

Microbial coexistence through chemical-mediated interactions

Many microbial functions happen within communities of interacting species. Explaining how species with intrinsically disparate fitness can coexist is important for applications such as manipulating host-associated microbiota or engineering industrial communities. Previous coexistence studies have often neglected interaction mechanisms. Here, we formulate and experimentally constrain a model in which chemical mediators of microbial interactions (e.g. metabolites or waste-products) are explicitly incorporated. We construct many instances of coexistence by simulating community assembly through enrichment and ask how species interactions can explain coexistence. We show that growth-facilitating influences between members are favored in assembled communities. Among negative influences, self-restraint, such as production of self-inhibiting waste, contributes to coexistence, whereas inhibition of other species disrupts coexistence. Coexistence is also favored when interactions are mediated by depletable chemicals that get consumed or degraded, rather than by reusable chemicals that are unaffected by recipients. Our model creates null predictions for coexistence driven by chemical-mediated interactions.

ecology↗

bioRxiv2018

Formation of tRNA wobble inosine in humans is perturbed by a millennia-old mutation linked to intellectual disability

The formation of inosine at the wobble position of eukaryotic tRNAs is an essential modification catalyzed by the ADAT2/ADAT3 complex. In humans, a valine to methionine mutation (V144M) in ADAT3 that originated [~]1,600 years ago is the most common cause of autosomal-recessive intellectual disability (ID) in Arabia. Here, we show that ADAT3-V144M exhibits perturbations in subcellular localization and has increased propensity to form aggregates associated with cytoplasmic chaperonins. While ADAT2 co-expression can suppress the aggregation of ADAT3-V144M, the ADAT2/3 complexes assembled with ADAT3-V144M exhibit defects in adenosine deaminase activity. Moreover, extracts from cell lines derived from ID-affected individuals expressing only ADAT3-V144M display a reduction in tRNA deaminase activity. Notably, we find that the same cell lines from ID-affected individuals exhibit decreased wobble inosine in certain tRNAs. These results identify a role for ADAT2-dependent localization and folding of ADAT3 in wobble inosine modification that is crucial for the developing human brain.

molecular biology↗

bioRxiv2018

Anamorphic development and extended parental care in a 520 million-year-old stem-group euarthropod from China

Extended parental care (XPC) is a complex reproductive strategy in which progenitors actively look after their offspring up to - or beyond - the first juvenile stage in order to maximize their fitness. Although the euarthropod fossil record has produced several examples of brood-care, the appearance of XPC within this phylum remains poorly constrained given the scarcity of developmental data for Palaeozoic stem-group representatives that would link juvenile and adult forms in an ontogenetic sequence. Here, we describe the post-embryonic growth of Fuxianhuia protensa from the early Cambrian Chengjiang Lagerstatte, and show parental care in this stem-group euarthropod. We recognize fifteen distinct ontogenetic stages based on the number and shape of the trunk tergites, and their allocation between the morphologically distinct thorax and abdomen. Our data demonstrate anamorphic post-embryonic development in F. protensa, in which tergites were sequentially added from a posterior growth zone. A life assemblage consisting of a sexually mature F. protensa adult alongside four ontogenetically coeval juveniles, constitutes the oldest occurrence of XPC in the panarthropod fossil record. These findings provide the most phylogenetically basal evidence of anamorphosis in the evolutionary history of total-group Euarthropoda, and reveal a complex post-embryonic reproductive ecology for its early representatives.

paleontology↗

bioRxiv2018

Monitoring the 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification in eukaryotic tRNAs via the gamma-toxin endonuclease

The post-transcriptional modification of tRNA at the wobble position is a universal process occurring in all domains of life. In eukaryotes, the wobble uridine of particular tRNAs is transformed to the 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification which is critical for proper mRNA decoding and protein translation. However, current methods to detect mcm5s2U are technically challenging and/or require specialized instrumental expertise. Here, we show that gamma-toxin endonuclease from the yeast Kluyveromyces lactis can be used as a probe for assaying mcm5s2U status in the tRNA of diverse eukaryotic organisms ranging from protozoans to mammalian cells. The assay couples the mcm5s2U-dependent cleavage of tRNA by gamma-toxin with standard molecular biology techniques such as Northern blot analysis or quantitative PCR to monitor mcm5s2U levels in multiple tRNA isoacceptors. The results gained from the gamma-toxin assay reveals the evolutionary conservation of the mcm5s2U modification across eukaryotic species. Moreover, we have employed the gamma-toxin assay to verify uncharacterized eukaryotic Trm9 and Trm112 homologs that catalyze the formation of mcm5s2U. These findings demonstrate the use of gamma-toxin as a detection method to monitor mcm5s2U status in diverse eukaryotic cell types for cellular, genetic and biochemical studies.

molecular biology↗