Ribin, a protein encoded by a message complementary to rRNA, modulates ribosomal transcription and cell proliferation

Small RNAs from mitochondrial genome recombination sites are incorporated into T. gondii mitoribosomes

The mitochondrial genomes of apicomplexans comprise merely three protein-coding genes, alongside a set of thirty to forty genes encoding small RNAs (sRNAs), many of which exhibit homologies to rRNA from E. coli. The expression status and integration of these short RNAs into ribosomes remains unclear and direct evidence for active ribosomes within apicomplexan mitochondria is still lacking. In this study, we conducted small RNA sequencing on the apicomplexan Toxoplasma gondii to investigate the occurrence and function of mitochondrial sRNAs. To enhance the analysis of sRNA sequencing outcomes, we also re-sequenced the T. gondii mitochondrial genome using an improved organelle enrichment protocol and Nanopore sequencing. It has been established previously that the T. gondii genome comprises 21 sequence blocks that undergo recombination among themselves but that their order is not entirely random. The enhanced coverage of the mitochondrial genome allowed us to characterize block combinations at increased resolution. Employing this refined genome for sRNA mapping, we find that many small RNAs originated from the junction sites between protein-coding blocks and rRNA sequence blocks. Surprisingly, such block border sRNAs were incorporated into polysomes together with canonical rRNA fragments and mRNAs. In conclusion, apicomplexan ribosomes are active within polysomes and are indeed assembled through the integration of sRNAs, including previously undetected sRNAs with merged mRNA-rRNA sequences. Our findings lead to the hypothesis that T. gondii's block-based genome organization enables the dual utilization of mitochondrial sequences as both messenger RNAs and ribosomal RNAs, potentially establishing a link between the regulation of rRNA and mRNA expression.

Protein-coding tRNA sequences?

Transfer RNAs (tRNAs) are ancient molecules likely predating the translation machinery. These extremely conserved RNA molecules transfer amino acids to the ribosome for the synthesis of proteins encoded by mRNAs, but canonical tRNAs are not protein-coding RNAs. Surprisely, when virtually translated, I observed that peptides derived from tRNA sequences match thousands of protein entries in databases. The analysis of these sequences indicates that the vast majority of these tRNA-derived proteins are annotated as small hypothetical peptides, likely arising from sequencing, prediction and/or annotation errors. But life often surpasses fiction. Importantly, tRNA-encoded amino acid domains were also found embedded in large functional proteins. Phylogenetic analysis of representative tRNA-derived protein domains may provide new insights into the origin, plasticity, and evolution of protein-coding genes.

Rapid and accurate identification of ribosomal RNA sequences via deep learning

Advances in transcriptomic and translatomic techniques enable in-depth studies of RNA activity profiles and RNA-based regulatory mechanisms. Ribosomal RNA (rRNA) sequences are highly abundant among cellular RNA, but if the target sequences do not include polyadenylation, these cannot be easily removed in library preparation, requiring their post-hoc removal with computational techniques to accelerate and improve downstream analyses. Here, we describe RiboDetector, a novel software based on a Bi-directional Long Short-Term Memory (BiLSTM) neural network, which rapidly and accurately identifies rRNA reads from transcriptomic, metagenomic, metatranscriptomic, noncoding RNA, and ribosome profiling sequence data. Compared with state-of-the-art approaches, RiboDetector produced at least six times fewer misclassifications on the benchmark datasets. Importantly, the few false positives of RiboDetector were not enriched in certain Gene Ontology (GO) terms, suggesting a low bias for downstream functional profiling. RiboDetector also demonstrated a remarkable generalizability for detecting novel rRNA sequences that are divergent from the training data with sequence identities of <90%. On a personal computer, RiboDetector processed 40M reads in less than 6 min, which was ∼50 times faster in GPU mode and ∼15 times in CPU mode than other methods. RiboDetector is available under a GPL v3.0 license at https://github.com/hzi-bifo/RiboDetector.

Integrative transcriptomics, proteomics, and metabolomics data analysis exploring the injury mechanism of ricin on human lung epithelial cells

Ricin (RT) is a plant toxin belonging to the family of type II ribosome-inactivating protein with high bioterrorism potential. Aerosol RT exposure is the most lethal route, but its mechanism of injury needs further investigation. In the present study, we performed a comprehensive transcriptomics, proteomics and metabolomics analysis on the potential mechanism of injury caused by RT on human lung epithelial cells. In total, 5872 genes, 187 proteins, and 143 metabolites were shown to be significantly changed in human lung epithelial cells after RT treatment. Molecular function, pathway, and network analyses, the genes and proteins regulated in RT-treated cells were mainly attributed to fatty acid metabolism, arginine and proline metabolism and ubiquitin-mediated proteolysis pathway. Furthermore, a comprehensive analysis of transcripts, proteins, and metabolites was performed. The results revealed the correlated genes, proteins, and metabolic pathways regulated in metabolic pathways, amino acid metabolism, transcription and energy metabolism. These genes, proteins, and metabolites involved in these dis-regulated pathways may provide a more targeted and credible direction to study the mechanism of RT injury on human lung epithelial cells. This study provides large-scale omics data that can be used to develop a new strategy for the prevention, rapid diagnosis, and treatment of RT poisoning, especially of RT aerosol.

The Ribosome as a Missing Link in Prebiotic Evolution III: Over-Representation of tRNA- and rRNA-Like Sequences and Plieofunctionality of Ribosome-Related Molecules Argues for the Evolution of Primitive Genomes from Ribosomal RNA Modules

We propose that ribosomal RNA (rRNA) formed the basis of the first cellular genomes, and provide evidence from a review of relevant literature and proteonomic tests. We have proposed previously that the ribosome may represent the vestige of the first self-replicating entity in which rRNAs also functioned as genes that were transcribed into functional messenger RNAs (mRNAs) encoding ribosomal proteins. rRNAs also encoded polymerases to replicate itself and a full complement of the transfer RNAs (tRNAs) required to translate its genes. We explore here a further prediction of our “ribosome-first” theory: the ribosomal genome provided the basis for the first cellular genomes. Modern genomes should therefore contain an unexpectedly large percentage of tRNA- and rRNA-like modules derived from both sense and antisense reading frames, and these should encode non-ribosomal proteins, as well as ribosomal ones with key cell functions. Ribosomal proteins should also have been co-opted by cellular evolution to play extra-ribosomal functions. We review existing literature supporting these predictions. We provide additional, new data demonstrating that rRNA-like sequences occur at significantly higher frequencies than predicted on the basis of mRNA duplications or randomized RNA sequences. These data support our “ribosome-first” theory of cellular evolution.

Regulating ehrlich and demethiolation pathways for alcohols production by the expression of ubiquitin-protein ligase gene HUWE1

Ehrlich and demethiolation pathways as two competing branches converted amino acid into alcohols. Controlling both pathways offers considerable potential for industrial applications including alcohols overproduction, flavor-quality control and developing new flavors. While how to regulate ehrlich and demethiolation pathways is still not applicable. Taking the conversion of methionine into methionol and methanethiol for example, we constructed two suppression subtractive cDNA libraries of Clonostachys rosea by using suppression subtractive hybridization (SSH) technology for screening regulators controlling the conversion. E3 ubiquitin-protein ligase gene HUWE1 screened from forward SSH library was validated to be related with the biosynthesis of end products. Overexpressing HUWE1 in C. rosea and S. cerevisiae significantly increased the biosynthesis of methanethiol and its derivatives in demethiolation pathway, while suppressed the biosynthesis of methional and methionol in ehrlich pathway. These results attained the directional regulation of both pathways by overexpressing HUWE1. Thus, HUWE1 has potential to be a key target for controlling and enhancing alcohols production by metabolic engineering.

The nucleolus: a raft adrift in the nuclear sea or the keystone in nuclear structure?

The nucleolus is a prominent nuclear structure that is the site of ribosomal RNA (rRNA) transcription, and hence ribosome biogenesis. Cellular demand for ribosomes, and hence rRNA, is tightly linked to cell growth and the rRNA makes up the majority of all the RNA within a cell. To fulfill the cellular demand for rRNA, the ribosomal RNA (rDNA) genes are amplified to high copy number and transcribed at very high rates. As such, understanding the rDNA has profound consequences for our comprehension of genome and transcriptional organization in cells. In this review, we address the question of whether the nucleolus is a raft adrift the sea of nuclear DNA, or actively contributes to genome organization. We present evidence supporting the idea that the nucleolus, and the rDNA contained therein, play more roles in the biology of the cell than simply ribosome biogenesis. We propose that the nucleolus and the rDNA are central factors in the spatial organization of the genome, and that rapid alterations in nucleolar structure in response to changing conditions manifest themselves in altered genomic structures that have functional consequences. Finally, we discuss some predictions that result from the nucleolus having a central role in nuclear organization.

Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies

In the course of analyzing 9,522,746 pyrosequencing reads from 23 stations in the Southwestern Pacific and equatorial Atlantic oceans, it came to our attention that misannotations of rRNA as proteins is now so widespread that false positive matching of rRNA pyrosequencing reads to the National Center for Biotechnology Information (NCBI) non-redundant protein database approaches 90%. One conserved portion of 23S rRNA was consistently misannotated often enough to prompt curators at Pfam to create a spurious protein family. Detailed examination of the annotation history of each seed sequence in the spurious Pfam protein family (PF10695, 'Cw-hydrolase') uncovered issues in the standard operating procedures and quality assurance programs of major sequencing centers, and other issues relating to the curation practices of those managing public databases such as GenBank and SwissProt. We offer recommendations for all these issues, and recommend as well that workers in the field of metatranscriptomics take extra care to avoid including false positive matches in their datasets.

Improved insights into the transcriptomes of the human hookworm Necator americanus--fundamental and biotechnological implications

Hookworms of humans are blood-feeding parasitic nematodes of major socio-economic significance in a wide range of countries. They cause a neglected tropical disease (NTD) called "hookworm disease" (=necatoriasis and/or ancylostomiasis). Necator americanus is the most widely distributed hookworm of humans and is a leading cause of iron deficiency anaemia, which can cause physical and mental retardation and deaths in children as well as adverse maternal-foetal outcomes. Currently, there is a significant focus on the development of new approaches for the prevention and control of hookworms in humans. Technological advances are underpinning the discovery of drug and vaccine targets through insights into the molecular biology and genomics of these parasites and their relationship with the human host. In spite of the widespread socio-economic impacts of human necatoriasis, molecular datasets for N. americanus are scant, limiting progress in molecular research. The present article explores all currently available EST datasets for adult and larval stages of N. americanus using a semi-automated bioinformatic pipeline. In the current repertoire of molecules now available, some have been or are being considered as candidate vaccines against N. americanus. Among others, the most abundant sets of molecules relate to the pathogenesis-related protein (PRP) superfamily, comprising various members, such as the Ancylostoma-secreted or activation-associated proteins (ASPs) and the kunitz-type proteins, both of which are inferred to play key roles in the interplay between N. americanus and the human host. Understanding the molecular biology of these and other novel molecules discovered could have important implications for finding new ways of disrupting the pathways that they are involved in, and should facilitate the identification of new drug and vaccine targets. Also, the bioinformatic prediction of the essentiality of genes and gene products as well as molecular network connectivity of nematode-specific genes, together with sequencing by 454 technology, are likely to assist in the genomic discovery efforts in the very near future, to also underpin fundamental, molecular research of hookworms.

Expression of the rDNA-encoded mitochondrial protein Tar1p is stringently controlled and responds differentially to mitochondrial respiratory demand and dysfunction

The novel yeast protein Tar1p is encoded on the anti-sense strand of the multi-copy nuclear 25S rRNA gene, localizes to mitochondria, and partially suppresses the mitochondrial RNA polymerase mutant, rpo41-R129D. However, the function of Tar1p in mitochondria and how its expression is regulated are currently unknown. Here we report that Tar1p is subject to glucose repression and is up-regulated during post-diauxic shift in glucose medium and in glycerol medium, conditions requiring elevated mitochondrial respiration. However, Tar1p expression is down-regulated in response to mitochondrial dysfunction caused by the rpo41-R129D mutation or in strains lacking respiration. Furthermore, in contrast to the previously reported beneficial effects of moderate over-expression of Tar1p in the rpo41-R129D strain, higher-level over-expression exacerbates the ROS-derived phenotypes of this mutant, including decreased respiration and life span. Finally, two-hybrid screening and in vitro-binding studies revealed a physical interaction between Tar1p and Coq5p, an enzyme involved in synthesizing the mitochondrial electron carrier and antioxidant, coenzyme Q. We propose that Tar1p expression is induced under respiratory conditions to maintain oxidative phosphorylation capacity, but that its levels in mitochondria are typically low and stringently controlled. Furthermore, we speculate that Tar1p is down-regulated when respiration is defective to prevent deleterious ROS-dependent consequences of mitochondrial dysfunction.

Hepatoma-derived growth factor, a new trophic factor for motor neurons, is up-regulated in the spinal cord of PQBP-1 transgenic mice before onset of degeneration

Hepatoma-derived growth factor (HDGF) is a nuclear protein homologous to the high-mobility group B1 family of proteins. It is known to be released from cells and to act as a trophic factor for dividing cells. In this study HDGF was increased in spinal motor neurons of a mouse model of motor neuron degeneration, polyglutamine-tract-binding protein-1 (PQBP-1) transgenic mice, before onset of degeneration. HDGF promoted neurite extension and survival of spinal motor neurons in primary culture. HDGF repressed cell death of motor neurons after facial nerve section in newborn rats in vivo. We also found a significant increase in p53 in spinal motor neurons of the transgenic mice. p53 bound to a sequence in the upstream of the HDGF gene in a gel mobility shift assay, and promoted gene expression through the cis-element in chloramphenicol acetyl transfer (CAT) assay. Finally, we found that HDGF was increased in CSF of PQBP-1 transgenic mice. Collectively, our results show that HDGF is a novel trophic factor for motor neurons and suggest that it might play a protective role against motor neuron degeneration in PQBP-1 transgenic mice.

Polyglutamine tract-binding protein-1 dysfunction induces cell death of neurons through mitochondrial stress

Polyglutamine tract-binding protein-1 (PQBP-1) is a nuclear protein that interacts and colocalizes with mutant polyglutamine proteins. We previously reported that PQBP-1 transgenic mice show a late-onset motor neuron disease-like phenotype and cell death of motor neurons analogous to human neurodegeneration. To investigate the molecular mechanisms underlying the motor neuron death, we performed microarray analyses using the anterior horn tissues of the spinal cord and compared gene expression profiles between pre-symptomatic transgenic and age-matched control mice. Surprisingly, half of the spots changed more than 1.5-fold turned out to be genes transcribed from the mitochondrial genome. Northern and western analyses confirmed up-regulation of representative mitochondrial genes, cytochrome c oxidase (COX) subunit 1 and 2. Immunohistochemistry revealed that COX1 and COX2 proteins are increased in spinal motor neurons. Electron microscopic analyses revealed morphological abnormalities of mitochondria in the motor neurons. PQBP-1 overexpression in primary neurons by adenovirus vector induced abnormalities of mitochondrial membrane potential from day 5, while cytochrome c release and caspase 3 activation were observed on day 9. An increase of cell death by PQBP-1 was also confirmed on day 9. Collectively, these results indicate that dysfunction of PQBP-1 induces mitochondrial stress, a key molecular pathomechanism that is shared among human neurodegenerative disorders.

The inhibition of tumor growth by triplex-forming oligonucleotides

We have previously shown that oligonucleotides designed to bind in triplex fashion to a specific p53 binding site homology inhibit the proliferation of colon cancer cells in vitro. The present study was designed to extend these observations in an in vivo model. HCT 116 human colon carcinoma cells were injected subcutaneously into Ncr nude mice and tumors formed at one to two weeks. Tumors were injected daily for 14 days with either triplex forming oligonucleotide (Hoog 1), a scrambled Hoog 1 oligonucleotide (Hoog3) as control, or vehicle. Tumor size was measured twice weekly. Active triplex forming oligonucleotide (Hoog1) reduced tumor size in comparison to either control oligonucleotide (Hoog3) or vehicle. Tumor sizes in the three groups were significantly different (P < 0.001). Student Newman Keuls test shows statistically significant differences between the experimental group and each of the control and vehicle groups (P < 0.05). A triplex forming oligonucleotide directed at a p53 consensus binding site reduces tumor growth suggesting a novel method of tumor inhibition.

A novel mitochondrial protein, Tar1p, is encoded on the antisense strand of the nuclear 25S rDNA

In eukaryotes, it is widely assumed that genes coding for proteins and structural RNAs do not overlap. Using a transposon-tagging strategy to globally analyze the Saccharomyces cerevisiae genome for expressed genes, we identified multiple insertions in an open reading frame that is contained fully within and transcribed antisense to the 25S rRNA gene in the nuclear rDNA repeat region on Chromosome XII. Expression of this gene, TAR1 (Transcript Antisense to Ribosomal RNA), can be detected at the RNA and protein levels, and the primary sequence of the corresponding 124-amino-acid protein is conserved in several yeast species. Tar1p was found to localize to mitochondria, and overexpression of the protein suppresses the respiration-deficient petite phenotype of a point mutation in mitochondrial RNA polymerase that affects mitochondrial gene expression and mtDNA stability. These findings indicate that coding information for protein and structural RNAs can overlap, raising issues regarding the coevolution of such complex genes, and also suggest that rDNA transcription and mitochondrial function are coordinately regulated in eukaryotic cells.