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PubMed2025

Translation of the downstream ORF from bicistronic mRNAs by human cells: Impact of codon usage and splicing in the upstream ORF.

Biochemistry textbooks describe eukaryotic mRNAs as monocistronic. However, increasing evidence reveals the widespread presence and translation of upstream open reading frames preceding the "main" ORF. DNA and RNA viruses infecting eukaryotes often produce polycistronic mRNAs and viruses have evolved multiple ways of manipulating the host's translation machinery. Here, we introduce an experimental model to study gene expression regulation from virus-like bicistronic mRNAs in human cells. The model consists of a short upstream ORF and a reporter downstream ORF encoding a fluorescent protein. We have engineered synonymous variants of the upstream ORF to explore large parameter space, including codon usage preferences, mRNA folding features, and splicing propensity. We show that human translation machinery can translate the downstream ORF from bicistronic mRNAs, albeit reporter protein levels are thousand times lower than those from the upstream ORF. Furthermore, synonymous recoding of the upstream ORF exclusively during elongation significantly influences its own translation efficiency, reveals cryptic splice signals, and modulates the probability of downstream ORF translation. Our results are consistent with a leaky scanning mechanism facilitating downstream ORF translation from bicistronic mRNAs in human cells, offering new insights into the role of upstream ORFs in translation regulation.

Humans↗

PubMed2019

Distinct types of short open reading frames are translated in plant cells.

Genomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important biological roles, and their impact on cellular processes has long been underestimated. Here, we analyzed approximately 70,000 transcribed sORFs in the model plant Physcomitrella patens (moss). Several distinct classes of sORFs that differ in terms of their position on transcripts and the level of evolutionary conservation are present in the moss genome. Over 5000 sORFs were conserved in at least one of 10 plant species examined. Mass spectrometry analysis of proteomic and peptidomic data sets suggested that tens of sORFs located on distinct parts of mRNAs and long noncoding RNAs (lncRNAs) are translated, including conserved sORFs. Translational analysis of the sORFs and main ORFs at a single locus suggested the existence of genes that code for multiple proteins and peptides with tissue-specific expression. Functional analysis of four lncRNA-encoded peptides showed that sORFs-encoded peptides are involved in regulation of growth and differentiation in moss. Knocking out lncRNA-encoded peptides resulted in a decrease of moss growth. In contrast, the overexpression of these peptides resulted in a diverse range of phenotypic effects. Our results thus open new avenues for discovering novel, biologically active peptides in the plant kingdom.

Bryopsida↗

PubMed2026

Recent advances for the pharmaceutical production of highly attenuated poxviruses as viral vector platforms.

INTRODUCTION: Highly attenuated poxviruses serve as potent viral vectors, oncolytic agents, and therapeutic vaccines. They can accommodate and stably maintain a large genomic payload of foreign inserts. Their limited replication in human cells provides an excellent safety profile, but it concomitantly necessitates higher doses of infectious particles for full therapeutic efficacy. AREAS COVERED: We review recent advances in bioprocesses for the pharmaceutical production of poxvirus-based vectors, focusing mainly on the vaccinia virus and the Orf virus. These include upstream processing using highly permissive cell substrates, optimized feeding strategies, and a virus phenotype that facilitates downstream processing. The study explores ongoing challenges and identifies strategies to adapt the downstream process to intensified upstream processes in order to achieve an economic end-to-end production. EXPERT OPINION: For notably increased virus yields of up to 2 log after amplification, we propose to replace classic adsorption chromatography by a collective and continuous purification platform for separating the virus from process-related impurities. Filtration operations facilitate process scalability while reducing volumes, which is beneficial for a flow-through polishing to meet pharmaceutical quality attributes. Combined with artificial intelligence modeling, these advancements alleviate financial pressures on healthcare systems and accelerate the production of novel vaccine candidates for clinical use.

Humans↗

PubMed2026

Clone and characterization of a cytochrome P450 gene for drought tolerance in rice.

BACKGROUND: Drought is a major abiotic stress limiting rice production worldwide. Identifying genes that enhance drought tolerance is essential for breeding resilient varieties. RESULTS: In this study, we report the map-based cloning and functional characterization of DT1, a novel cytochrome P450 gene conferring drought tolerance in rice. Using near isogenic lines (NILs) derived from a cross between Xiang743 and Katy, we delimited DT1 into a 115 kb interval on chromosome 3, where contains 18 open read frames (ORFs). Quantitative real-time polymerase chain reaction (qRT-PCR) analysis identified Os03g55250 as the candidate gene. Clustered regularly interspaced short palindromic repeats-associated nuclease 9 (CRISPR/Cas9) knockout mutants of Os03g55250 exhibited increased drought sensitivity, while overexpression lines showed enhanced drought tolerance, confirming that Os03g55250 was the target gene and positively regulates drought resistance. DT1 was mainly expressed in stems, leaves, and leaf sheaths, and the DT1 protein localized in the endoplasmic reticulum. Haplotype analysis identified Hap1 as a favorable allele in japonica rice. CONCLUSIONS: Our findings provide a promising genetic resource for breeding drought-resistant rice varieties and offers new insights into the role of P450 genes in abiotic stress adaptation.

Oryza↗

PubMed2026

Cucurbit Leaf Crumple Virus: An Important Pathogen of Cucurbit and Snap Bean Crops.

TAXONOMY: Cucurbit leaf crumple virus (CuLCrV); Begomovirus cucurbitae; Geminiviridae; Geplafuvirales. GEOGRAPHICAL DISTRIBUTION: The presence of CuLCrV is exclusively limited to North America, mainly Mexico and the United States. PHYSICAL PROPERTIES: CuLCrV is a bipartite begomovirus comprising two circular single-stranded DNA molecules (DNA-A and DNA-B), encapsidated within geminate icosahedral particles. GENOME AND ORGANIZATION: CuLCrV possesses a bipartite genome of DNA-A (2632 nucleotides) and DNA-B (2600 nucleotides). DNA-A contains five open reading frames (ORFs): AV1 (coat protein), AC1 (replication-associated protein), AC2 (transcriptional activator protein), AC3 (replication enhancer protein) and AC4. DNA-B contains two ORFs: BV1 (nuclear shuttle protein) and BC1 (movement protein). TRANSMISSION: CuLCrV is transmitted by the sweetpotato whitefly, Bemisia tabaci, in a persistent, circulative and non-propagative manner. HOSTS: CuLCrV primarily infects crop members of the Cucurbitaceae and snap bean (Phaseolus vulgaris, Fabaceae). Multiple weed species belonging to Brassicaceae, Convolvulaceae, Cucurbitaceae and Verbenaceae act as persistent virus reservoir hosts. SYMPTOMS: Symptom expression varies with host and infection timing. In cucurbits, infection induces leaf crumpling, thickening and downward curling of leaves, with green streaks and distortion of fruits. In snap bean, symptoms include leaf distortion, chlorosis and malformed pods. CONTROL: No commercial cultivars with resistance to CuLCrV are available for cucurbit crops, although some resistance has been reported in snap bean cultivars. Therefore, management relies primarily on integrated disease management.

Plant Diseases↗

PubMed1978

Correlation between phosphorylated H1 histones and satellite DNAs in Drosophila virilis.

Drosophila virilis DNA contains satellites I, II, and III. D. novamexicana DNA contains satellite I. D. virilis H1 histone contains subfractions a, b, c, d, and e; D. novamexicana H1 contains subfractions a, b, and c. Therefore, satellites II and III might be correlated with H1d and H1e. To test the validity of this correlation, the H1 histones of polytene nuclei, which contain less than 1% satellite DNA, were analyzed. Polytene nuclei of D. virilis contain substantially decreased levels of H1c and H1e and marginally decreased levels of H1d. Polytene nuclei of D. novamexicana contain decreased levels of H1c.H1c is correlated with satellite I (common to D. virilis and D. novamexicana); H1e is correlated with satellites II and III; H1d is not correlated with any satellite DNA, because its level is virtually unchanged in polytene cells lacking detectable amounts of satellite DNA. Alkaline phosphatase digestion of the H1 histones reveals that H1c is the phosphorylated form of H1b and H1e is the phosphorylated form of H1d. Therefore, the under-replication of satellite DNAs is correlated with the decreased phosphorylation of H1 histones. In vitro, D. virilis H1 histones preferentially bind D. virilis DNAs in the progression III greater than II greater than I greater than main band, whereas D. virilis core histones do not preferentially bind any D. virilis DNA. As an extension of these results, we suggest that phosphorylated H1 histones bind D. virilis satellite DNAs in vivo and are involved in the compaction of heterochromatin.

Alkaline Phosphatase↗