Biology subjects

Huber, P. W.

Publications and source records attributed to Huber, P. W..

3 recordsLinked to original sources

bioRxiv2022

Synonymous codon substitutions regulate transcription and translation of an upstream gene

Synonymous codons were originally viewed as interchangeable with no phenotypic consequences. However, over the years a substantial body of evidence has demonstrated that some synonymous substitutions can perturb a variety of gene expression and protein homeostasis mechanisms, including translational efficiency, translational fidelity and co-translational folding of the encoded protein. To date, synonymous codon-derived perturbations have largely focused on effects within a single gene. Here we show that synonymous codon substitutions made far within an E. coli plasmid-encoded protein coding sequence frequently led to significant upregulation of a neighboring, upstream gene. Notably, in four out of nine synonymously recoded sequences, significant upregulation of the upstream gene arose due to cryptic transcription of the anti-sense strand. Surprisingly, cryptic transcription of the upstream gene readily bypassed its native transcriptional repression mechanism. Even more surprisingly, translation of this upstream gene correlates closely with the subset of its mRNA transcribed from the cryptic internal promoter, rather than its total mRNA level. These results suggest that synonymous codons in bacteria may be under selection to both preserve the amino acid sequence of the encoded gene while also avoiding internal sequence elements that significantly perturb transcriptional and translational regulation of neighboring genes.

molecular biology↗

bioRxiv2020

Remnants of the Balbiani body are required for formation of RNA transport granules in Xenopus oocytes

Fragmentation of the Balbiani body in Xenopus oocytes engenders a region extending from the germinal vesicle (GV) towards the vegetal pole that is enriched in mitochondria. This area is later transversed by RNA that is being localized to the vegetal cortex. Inhibition of mitochondrial ATP synthesis prevents the perinuclear formation of these RNA transport granules that can be reversed by the nonhydrolyzable ATP analog, adenosine 5-({beta}{gamma}-imido) triphosphate. The protein composition and sensitivity of the transport granules to hexanediol indicate that they are liquid phase condensates. Mitochondria in the remnants of the Balbiani body produce a region of elevated ATP that appears to act as a hydrotrope to support the perinuclear phase transition leading to granule formation. SummaryMitochondria in the remnants of the Balbiani body produce elevated levels of ATP required for the formation of liquid phase condensates containing RNA transport granules.

molecular biology↗

bioRxiv2019

A Deficiency in SUMOylation Activity Disrupts Multiple Pathways Leading to Neural Tube and Heart Defects in Xenopus Embryos

BackgroundAdenovirus protein, Gam1, triggers the proteolytic destruction of the E1 SUMO-activating enzyme. Microinjection of an empirically determined amount of Gam1 mRNA into one-cell Xenopus embryos can reduce SUMOylation activity to undetectable, but nonlethal, levels, enabling an examination of the role of this post-translational modification during early vertebrate development. ResultsWe find that SUMOylation-deficient embryos consistently exhibit defects in neural tube and heart development. We have measured differences in gene expression between control and embryos injected with Gam1 mRNA at three developmental stages: early gastrula (immediately following the initiation of zygotic transcription), late gastrula (completion of the formation of the three primary germ layers), and early neurula (appearance of the neural plate). Although changes in gene expression are widespread and can be linked to many biological processes, three pathways, non-canonical Wnt/PCP, snail/twist, and Ets-1, are especially sensitive to the loss of SUMOylation activity and can largely account for the predominant phenotypes of Gam1 embryos. SUMOylation appears to generate different pools of a given transcription factor having different specificities with this post-translational modification involved in the regulation of more complex, as opposed to housekeeping, processes. ConclusionsWe have identified changes in gene expression that underlie the neural tube and heart phenotypes resulting from depressed SUMOylation activity. Notably, these developmental defects correspond to the two most frequently occurring congenital birth defects in humans, strongly suggesting that perturbation of SUMOylation, either globally or of a specific protein, may frequently be the origin of these pathologies.

genomics↗