Biology subjects

May, G.

Publications and source records attributed to May, G..

7 recordsLinked to original sources

bioRxiv2026

Suppression of upstream ORF translation is not a widespread mechanism of translational stimulation by yeast helicase Ded1

Ded1 is an essential DEAD-box helicase in yeast that broadly stimulates translation initiation and is critical for mRNAs with structured 5UTRs. We have evaluated the proposal that Ded1 stimulates translation primarily by preventing initiation at upstream ORFs (uORFs) associated with stable secondary structures. By Ribo-Seq analysis under experimental conditions designed to suppress artifactual 5UTR translation, we found that reduced translation of the main open-reading-frames (mORFs) in native mRNAs is generally not accompanied by increased 5UTR translation in ded1 mutant cells, and that the presence of translated uORFs in yeast mRNAs generally does not confer heightened dependence on Ded1 for efficient translation of mORFs. Results from a high-throughput reporter assay examining native 5UTRs reinforce the importance of Ded1 in initiation from structured 5 UTRs and show that impairing Ded1 has minimal effects on translational repression by uORFs. Our results demonstrate that, in cells growing vegetatively in rich medium, translational stimulation by suppression of inhibitory uORFs is restricted to a minority of Ded1 targets, and that unwinding of 5 UTR secondary structures per se is the principal mechanism for Ded1 stimulation of translation initiation.

genomics↗

bioRxiv2026

Biosynthesis of 14-membered cyclopeptide alkaloids via non-heme-iron- and 2-oxoglutarate-dependent oxidative decarboxylation

Cyclopeptide alkaloids are an expanding class of plant peptide natural products defined by a macrocyclic ether-crosslink via a tyrosine-derived phenol. Classical cyclopeptide alkaloids are characterized by strained 13-to 15-membered cyclophanes and terminal modifications such as N-methylation and C-terminal styrylamine moieties. While synthetic access to many classical cyclopeptide alkaloids has been established, no biosynthetic route has been reported. Here, we elucidate the biosynthetic pathway of a 14-membered cyclopeptide alkaloid, lotusine A, from Chinese date tree (Ziziphus jujuba) which features peptide cyclization on a ribosomal precursor peptide by a split burpitide cyclase, non-heme-iron and 2-oxoglutarate-dependent oxidative decarboxylation affording the C-terminal hydroxystyrylamine, and SAM-dependent N-terminal -N,N-dimethylation. We apply discovered Z. jujuba enzymes in combination with a clubmoss cyclopeptide alkaloid cyclase for biosynthesis and diversification of analgesic adouetine X and anxiolytic sanjoinine A by combining in planta and in vitro reactions. Our work expands the biocatalytic repertoire of non-heme-iron- and 2-oxoglutarate-dependent enzymology to oxidative peptide decarboxylation and primes scaled metabolic engineering and chemoenzymatic synthesis of 14-membered cyclopeptide alkaloids with terminal posttranslational modifications.

biochemistry↗

bioRxiv2025

Spatial and single-cell transcriptomics capture two distinct cell states in plant immunity

Unlike animals, plants are sessile organisms that must adapt to localized and fluctuating environmental stimuli, including abiotic and biotic stresses. While animals use mobile immune cells to eliminate pathogens, plants rely on localized cells in contact with the pathogen to detect and mount immune responses. Although bulk RNA sequencing (RNA-seq) has enabled the assessment of plant responses to pathogen infection at the whole transcriptome level, the spatial coordination of plant immune responses remains elusive. In this study, we performed both spatial and single-nuclei transcriptomic experiments to capture the spatial pattern of soybean plant responses to Asian soybean rust infection caused by the pathogen Phakopsora pachyrhizi. Through the analysis of both spatial and single-nuclei transcriptomics data, we identified two distinct host cell states with specific spatial localization in response to pathogen infection: the infected regions with the presence of the pathogen and the surrounding regions bordering the infected regions. Importantly, the surrounding regions exhibited higher expression of defense response-related genes than the infected regions, despite having minimal presence of the pathogen, indicating a cell non-autonomous defense response in the surrounding regions. Additionally, gene co-expression network analysis with single-cell resolution identified a key immune response-related gene module activated in the stressed cells captured in our single-nuclei RNA-seq data. This study reveals the intricate spatial coordination of plant defense responses against pathogen infection and enhances our understanding of the importance of localized cell non-autonomous defense responses in plant-pathogen interactions.

plant biology↗

bioRxiv2024

Deciphering the cis-regulatory landscape of natural yeast Transcript Leaders

Protein synthesis is a vital process that is highly regulated at the initiation step of translation. Eukaryotic 5 transcript leaders (TLs) contain a variety of cis-regulatory features that influence translation and mRNA stability. However, the relative influences of these features in natural TLs are poorly characterized. To address this, we used massively parallel reporter assays (MPRAs) to quantify RNA levels, ribosome loading, and protein levels from 11,027 natural yeast TLs in vivo and systematically compared the relative impacts of their sequence features on gene expression. We found that yeast TLs influence gene expression over two orders of magnitude. While a leaky scanning model using Kozak contexts and uAUGs explained half of the variance in expression across transcript leaders, the addition of other features explained [~]70% of gene expression variation. Our analyses detected key cis-acting sequence features, quantified their effects in vivo, and compared their roles to motifs reported from an in vitro study of ribosome recruitment. In addition, our work quantitated the effects of alternative transcription start site usage on gene expression in yeast. Thus, our study provides new quantitative insights into the roles of TL cis-acting sequences in regulating gene expression.

genomics↗

bioRxiv2023

The International Weed Genomics Consortium: Community Resources for Weed Genomics Research

The International Weed Genomics Consortium is a collaborative group of researchers focused on developing genomic resources for the study of weedy plants. Weeds are attractive systems for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Our goal is to use genomic information to develop sustainable and effective weed control methods and to provide insights about biotic and abiotic stress tolerance to assist crop breeding. Here, we outline resources under development by the consortium and highlight areas of research that will be impacted by these enabling resources.

genomics↗

bioRxiv2018

Defensive symbiosis and the evolution of virulence

Although environments rife with enemies should cause selection for defensive traits, such enemy-rich environments should also select for greater virulence in co-occurring symbionts, yet many defensive symbionts cause little to no damage while protecting their hosts from enemies. Thus, co-infection of a defensive symbiont and a parasite is predicted to select both for increased virulence in co-infecting symbionts and for increased defense in the protective symbiont. Why then do we observe defensive mutualists that protect hosts while causing little damage? To address this question, we build a symbiont-centered model that incorporates the evolution of two independent traits: defense and virulence. Virulence is modeled as a continuous trait spanning mutualism (negative virulence) and parasitism (virulence) and thus accounts for the entire range of direct effects that symbionts have on host mortality. Defense is modeled as a continuous trait that ameliorates the costs to the host associated with co-infection with a deleterious parasite. We obtain the counterintuitive result that the evolution of increased defense in one symbiont largely leads to the evolution of lower virulence in both symbionts and may even facilitate pathogens evolving to mutualism. However, results are context-dependent and when defensive traits are costly, the evolution of greater defense may also lead to higher virulence.

evolutionary biology↗

bioRxiv2018

A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping

The advent of long-read sequencing technologies has greatly facilitated assemblies of large eukaryotic genomes. In this paper, Oxford Nanopore sequences generated on a MinION sequencer were combined with BioNano Genomics Direct Label and Stain (DLS) optical maps to generate a chromosome-scale de novo assembly of the repeat-rich Sorghum bicolor Tx430 genome. The final hybrid assembly consists of 29 scaffolds, encompassing in most cases entire chromosome arms. It has a scaffold N50 value of 33.28Mbps and covers >90% of Sorghum bicolor expected genome length. A sequence accuracy of 99.67% was obtained in unique regions after aligning contigs against Illumina Tx430 data. Alignments showed that 99.4% of the 34,211 public gene models are present in the assembly, including 94.2% mapping end-to-end. Comparisons of the DLS optical maps against the public Sorghum Bicolor v3.0.1 BTx623 genome assembly suggest the presence of substantial genomic rearrangements whose origin remains to be determined.

genomics↗