scholarly journals Dataset-specific thresholds significantly improve detection of low transcribed regulatory genes in polysome profiling experiments

2020 ◽  
Author(s):  
Igor V. Deyneko ◽  
Orkhan N. Mustafaev ◽  
Alexander А. Tyurin ◽  
Ksenya V. Zhukova ◽  
Irina V. Goldenkova-Pavlova
Keyword(s):  
Great Influence ◽  
Background Level ◽  
Regulatory Proteins ◽  
Rna Seq ◽  
Biological Noise ◽  
Polysome Profiling ◽  
Higher Power ◽  
Genes Encoding ◽  
Supplementary Material ◽  
Modelling Approach

AbstractMotivationPolysome profiling is novel, and yet has proved to be an effective approach to detect mRNAs with differential ribosomal load and explore the regulatory mechanisms driving efficient translation. Genes encoding regulatory proteins, having a great influence of the organism, usually reveal moderate to low transcriptional levels, compared, for example, to genes of house-keeping machinery. This complicates the reliable detection of such genes in the presence of technical and/or biological noise.ResultsIn this work we investigate how cleaning of polysome profiling data on Arabidopsis thaliana influences the ability to detect genes with low level of total mRNA, but with a highly differential ribosomal load, i.e. genes translationally active. Suggested data modelling approach to identify a background level of mRNA counts individually for each dataset, shows higher power in detection of low transcribed genes, compared to the use of thresholds for the minimal required mRNA counts or the use of raw data. The significant increase in detected number of regulation–related genes was demonstrated. The described approach is applicable to a wide variety of RNA-seq data. All identified and classified mRNAs with high and low translation status are made available in supplementary material.

scholarly journals The assembled and annotated genome of the pigeon louse Columbicola columbae, a model ectoparasite

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
James G Baldwin-Brown ◽  
Scott M Villa ◽  
Anna I Vickrey ◽  
Kevin P Johnson ◽  
Sarah E Bush ◽  
...  
Keyword(s):  
Low Cost ◽  
Single Copy ◽  
Odorant Receptors ◽  
Rna Seq ◽  
Pediculus Humanus ◽  
Final Assembly ◽  
Oxford Nanopore ◽  
Genes Encoding ◽  
Host Parasite ◽  
G Protein Coupled

Abstract The pigeon louse Columbicola columbae is a longstanding and important model for studies of ectoparasitism and host-parasite coevolution. However, a deeper understanding of its evolution and capacity for rapid adaptation is limited by a lack of genomic resources. Here, we present a high-quality draft assembly of the C. columbae genome, produced using a combination of Oxford Nanopore, Illumina, and Hi-C technologies. The final assembly is 208 Mb in length, with 12 chromosome-size scaffolds representing 98.1% of the assembly. For gene model prediction, we used a novel clustering method (wavy_choose) for Oxford Nanopore RNA-seq reads to feed into the MAKER annotation pipeline. High recovery of conserved single-copy orthologs (BUSCOs) suggests that our assembly and annotation are both highly complete and highly accurate. Consistent with the results of the only other assembled louse genome, Pediculus humanus, we find that C. columbae has a relatively low density of repetitive elements, the majority of which are DNA transposons. Also similar to P. humanus, we find a reduced number of genes encoding opsins, G protein-coupled receptors, odorant receptors, insulin signaling pathway components, and detoxification proteins in the C. columbae genome, relative to other insects. We propose that such losses might characterize the genomes of obligate, permanent ectoparasites with predictable habitats, limited foraging complexity, and simple dietary regimes. The sequencing and analysis for this genome were relatively low cost, and took advantage of a new clustering technique for Oxford Nanopore RNAseq reads that will be useful to future genome projects.

scholarly journals Analysis of saponins detoxification genes in Ilyonectria mors-panacis G3B inducing root rot of Panax notoginseng by RNA-Seq

2021 ◽  
Author(s):  
Guohong Zeng ◽  
Jin Li ◽  
Yuxiu Ma ◽  
Qian Pu ◽  
Tian Xiao ◽  
...  
Keyword(s):  
Root Rot ◽  
Molecular Mechanisms ◽  
Management Strategies ◽  
Panax Notoginseng ◽  
Glycoside Hydrolases ◽  
Rna Seq ◽  
Host Interaction ◽  
Excellent Starting Point ◽  
Starting Point ◽  
Genes Encoding

AbstractSaponins are kinds of antifungal compounds produced by Panax notoginseng to resist invasion by pathogens. Ilyonectria mors-panacis G3B was the dominant pathogen inducing root rot of P. notoginseng, and the abilities to detoxify saponins were the key to infect P. notoginseng successfully. To research the molecular mechanisms of detoxifying saponins in I. mors-panacis G3B, we used high-throughput RNA-Seq to identify 557 and 1519 differential expression genes (DEGs) in I. mors-panacis G3B with saponins treatments for 4H (Hours) and 12H (Hours) compared with no saponins treatments, respectively. Among these DEGs, we found 93 genes which were simultaneously highly expressed in I. mors-panacis G3B with saponins treatments for 4H and 12H, they mainly belong to genes encoding transporters, glycoside hydrolases, oxidation–reduction enzymes, transcription factors and so on. In addition, there were 21 putative PHI (Pathogen–Host Interaction) genes out of those 93 up-regulated genes. In this report, we analyzed virulence-associated genes in I. mors-panacis G3B which may be related to detoxifying saponins to infect P. notoginseng successfully. They provided an excellent starting point for in-depth study on pathogenicity of I. mors-panacis G3B and developed appropriate root rot disease management strategies in the future.

scholarly journals A Transcriptomic Approach to the Metabolism of Tetrapyrrolic Photosensitizers in a Marine Annelid

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3924
Author(s):  
Maria Leonor Santos ◽  
Mariaelena D’Ambrosio ◽  
Ana P. Rodrigo ◽  
A. Jorge Parola ◽  
Pedro M. Costa
Keyword(s):  
Metabolic Pathways ◽  
Molecular Networks ◽  
Bile Pigments ◽  
Rna Seq ◽  
The Past ◽  
Wide Range ◽  
Genes Encoding ◽  
Organ Specific ◽  
Bright Green ◽  
Green Coloration

The past decade has seen growing interest in marine natural pigments for biotechnological applications. One of the most abundant classes of biological pigments is the tetrapyrroles, which are prized targets due their photodynamic properties; porphyrins are the best known examples of this group. Many animal porphyrinoids and other tetrapyrroles are produced through heme metabolic pathways, the best known of which are the bile pigments biliverdin and bilirubin. Eulalia is a marine Polychaeta characterized by its bright green coloration resulting from a remarkably wide range of greenish and yellowish tetrapyrroles, some of which have promising photodynamic properties. The present study combined metabolomics based on HPLC-DAD with RNA-seq transcriptomics to investigate the molecular pathways of porphyrinoid metabolism by comparing the worm’s proboscis and epidermis, which display distinct pigmentation patterns. The results showed that pigments are endogenous and seemingly heme-derived. The worm possesses homologs in both organs for genes encoding enzymes involved in heme metabolism such as ALAD, FECH, UROS, and PPOX. However, the findings also indicate that variants of the canonical enzymes of the heme biosynthesis pathway can be species- and organ-specific. These differences between molecular networks contribute to explain not only the differential pigmentation patterns between organs, but also the worm’s variety of novel endogenous tetrapyrrolic compounds.

scholarly journals Loss of Profilin3 Impairs Spermiogenesis by Affecting Acrosome Biogenesis, Autophagy, Manchette Development and Mitochondrial Organization

2021 ◽  
Vol 9 ◽  
Author(s):  
Naila Umer ◽  
Lena Arévalo ◽  
Sharang Phadke ◽  
Keerthika Lohanadan ◽  
Gregor Kirfel ◽  
...  
Keyword(s):  
Actin Polymerization ◽  
Regulatory Proteins ◽  
Autophagic Flux ◽  
Nuclear Fraction ◽  
Rna Seq ◽  
Head Shape ◽  
Male Factor ◽  
Protein Levels ◽  
Acrosome Formation ◽  
Actin Regulatory Proteins

Profilins (PFNs) are key regulatory proteins for the actin polymerization in cells and are encoded in mouse and humans by four Pfn genes. PFNs are involved in cell mobility, cell growth, neurogenesis, and metastasis of tumor cells. The testes-specific PFN3 is localized in the acroplaxome–manchette complex of developing spermatozoa. We demonstrate that PFN3 further localizes in the Golgi complex and proacrosomal vesicles during spermiogenesis, suggesting a role in vesicle transport for acrosome formation. Using CRISPR/Cas9 genome editing, we generated mice deficient for Pfn3. Pfn3–/– males are subfertile, displaying a type II globozoospermia. We revealed that Pfn3–/– sperm display abnormal manchette development leading to an amorphous sperm head shape. Additionally, Pfn3–/– sperm showed reduced sperm motility resulting from flagellum deformities. We show that acrosome biogenesis is impaired starting from the Golgi phase, and mature sperm seems to suffer from a cytoplasm removal defect. An RNA-seq analysis revealed an upregulation of Trim27 and downregulation of Atg2a. As a consequence, mTOR was activated and AMPK was suppressed, resulting in the inhibition of autophagy. This dysregulation of AMPK/mTOR affected the autophagic flux, which is hallmarked by LC3B accumulation and increased SQSTM1 protein levels. Autophagy is involved in proacrosomal vesicle fusion and transport to form the acrosome. We conclude that this disruption leads to the observed malformation of the acrosome. TRIM27 is associated with PFN3 as determined by co-immunoprecipitation from testis extracts. Further, actin-related protein ARPM1 was absent in the nuclear fraction of Pfn3–/– testes and sperm. This suggests that lack of PFN3 leads to destabilization of the PFN3–ARPM1 complex, resulting in the degradation of ARPM1. Interestingly, in the Pfn3–/– testes, we detected increased protein levels of essential actin regulatory proteins, cofilin-1 (CFL1), cofilin-2 (CFL2), and actin depolymerizing factor (ADF). Taken together, our results reveal the importance for PFN3 in male fertility and implicate this protein as a candidate for male factor infertility in humans.

scholarly journals Investigation of Drosophila fruitless neurons that express Dpr/DIP cell adhesion molecules

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Savannah G Brovero ◽  
Julia C Fortier ◽  
Hongru Hu ◽  
Pamela C Lovejoy ◽  
Nicole R Newell ◽  
...  
Keyword(s):  
Courtship Behavior ◽  
Cell Number ◽  
Neuronal Morphology ◽  
Immunoglobulin Superfamily ◽  
Rna Seq ◽  
Reproductive Behaviors ◽  
Behavioral Studies ◽  
Genes Encoding ◽  
Genomic Studies ◽  
Small Set

Drosophila reproductive behaviors are directed by fruitless neurons. A reanalysis of genomic studies shows that genes encoding dpr and DIP Immunoglobulin superfamily (IgSF) members are expressed in fru P1 neurons. We find that each fru P1 and dpr/DIP (fru P1 ∩ dpr/DIP) overlapping expression pattern is similar in both sexes, but there are dimorphisms in neuronal morphology and cell number. Behavioral studies of fru P1 ∩ dpr/DIP perturbation genotypes indicates that the mushroom body functions together with the lateral protocerebral complex to direct courtship behavior. A single-cell RNA-seq analysis of fru P1 neurons shows that many DIPs have high expression in a small set of neurons, whereas the dprs are often expressed in a larger set of neurons at intermediate levels, with a myriad of dpr/DIP expression combinations. Functionally, we find that perturbations of sex hierarchy genes and of DIP-ε change the sex-specific morphologies of fru P1 ∩ DIP-α neurons.

scholarly journals Dual RNA-Seq Analysis of Trichophyton rubrum and HaCat Keratinocyte Co-Culture Highlights Important Genes for Fungal-Host Interaction

Genes ◽  
2018 ◽  
Vol 9 (7) ◽  
pp. 362 ◽  
Author(s):  
Monise Petrucelli ◽  
Kamila Peronni ◽  
Pablo Sanches ◽  
Tatiana Komoto ◽  
Josie Matsuda ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Trichophyton Rubrum ◽  
Glyoxylate Cycle ◽  
Human Keratinocytes ◽  
Rna Seq ◽  
Fungal Host ◽  
Host Interaction ◽  
Genes Encoding ◽  
Hacat Keratinocyte

The dermatophyte Trichophyton rubrum is the major fungal pathogen of skin, hair, and nails that uses keratinized substrates as the primary nutrients during infection. Few strategies are available that permit a better understanding of the molecular mechanisms involved in the interaction of T. rubrum with the host because of the limitations of models mimicking this interaction. Dual RNA-seq is a powerful tool to unravel this complex interaction since it enables simultaneous evaluation of the transcriptome of two organisms. Using this technology in an in vitro model of co-culture, this study evaluated the transcriptional profile of genes involved in fungus-host interactions in 24 h. Our data demonstrated the induction of glyoxylate cycle genes, ERG6 and TERG_00916, which encodes a carboxylic acid transporter that may improve the assimilation of nutrients and fungal survival in the host. Furthermore, genes encoding keratinolytic proteases were also induced. In human keratinocytes (HaCat) cells, the SLC11A1, RNASE7, and CSF2 genes were induced and the products of these genes are known to have antimicrobial activity. In addition, the FLG and KRT1 genes involved in the epithelial barrier integrity were inhibited. This analysis showed the modulation of important genes involved in T. rubrum–host interaction, which could represent potential antifungal targets for the treatment of dermatophytoses.

scholarly journals Transcriptome of peanut kernel and shell reveals the mechanism of calcium on peanut pod development

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sha Yang ◽  
Jianguo Wang ◽  
Zhaohui Tang ◽  
Feng Guo ◽  
Ye Zhang ◽  
...  
Keyword(s):  
Early Stage ◽  
Central Element ◽  
Abnormal Development ◽  
Transcriptional Level ◽  
Peanut Kernel ◽  
Rna Seq ◽  
Embryo Abortion ◽  
Genes Encoding ◽  
Pod Development ◽  
The Relationship

Abstract Calcium is not only a nutrient necessary for plant growth but also a ubiquitous central element of different signaling pathways. Ca2+ deficiency in soil may cause embryo abortion, which can eventually lead to abnormal development of peanut pods during the harvest season. To further study the mechanisms by which Ca2+ affects the shells and kernels of peanuts, transcriptome sequencing was used to explore the genes differentially expressed in shells and kernels during the early stage of peanut pod development between Ca2+ sufficient and deficient treatments. In this study, 38,894 expressed genes were detected. RNA-seq based gene expression profiling showed a large number of genes at the transcriptional level that changed significantly in shells and kernels between the Ca2+ sufficient and deficient treatments, respectively. Genes encoding key proteins involved in Ca2+ signal transduction, hormones, development, ion transport, and nutrition absorption changed significantly. Meanwhile, in the early stage of pod development, calcium first promoted nutrient absorption and development of shells, which has less effect on the formation of seed kernels. These results provide useful information for understanding the relationship between Ca2+ absorption and pod development.

scholarly journals Petal abscission in fragrant roses is associated with large scale differential regulation of the abscission zone transcriptome

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Priya Singh ◽  
Neeraj Bharti ◽  
Amar Pal Singh ◽  
Siddharth Kaushal Tripathi ◽  
Saurabh Prakash Pandey ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Large Scale ◽  
Scale Up ◽  
Differential Regulation ◽  
Regulatory Proteins ◽  
Comparative Transcriptome ◽  
Ethylene Sensitivity ◽  
Core Set ◽  
Genes Encoding ◽  
Rosa Bourboniana

Abstract Flowers of fragrant roses such as Rosa bourboniana are ethylene-sensitive and undergo rapid petal abscission while hybrid roses show reduced ethylene sensitivity and delayed abscission. To understand the molecular mechanism underlying these differences, a comparative transcriptome of petal abscission zones (AZ) of 0 h and 8 h ethylene-treated flowers from R. bourboniana was performed. Differential regulation of 3700 genes (1518 up, 2182 down) representing 8.5% of the AZ transcriptome was observed between 0 and 8 h ethylene-treated R. bourboniana petal AZ. Abscission was associated with large scale up-regulation of the ethylene pathway but prominent suppression of the JA, auxin and light-regulated pathways. Regulatory genes encoding kinases/phosphatases/F-box proteins and transcription factors formed the major group undergoing differential regulation besides genes for transporters, wall modification, defense and phenylpropanoid pathways. Further comparisons with ethylene-treated petals of R. bourboniana and 8 h ethylene-treated AZ (R. hybrida) identified a core set of 255 genes uniquely regulated by ethylene in R. bourboniana AZ. Almost 23% of these encoded regulatory proteins largely conserved with Arabidopsis AZ components. Most of these were up-regulated while an entire set of photosystem genes was prominently down-regulated. The studies provide important information on regulation of petal abscission in roses.

Oxidant stress responses in influenza virus pneumonia: gene expression and transcription factor activation

1996 ◽  
Vol 271 (3) ◽  
pp. L383-L391 ◽  
Author(s):  
A. M. Choi ◽  
K. Knobil ◽  
S. L. Otterbein ◽  
D. A. Eastman ◽  
D. B. Jacoby
Keyword(s):  
Influenza Virus ◽  
Viral Infection ◽  
Heme Oxygenase ◽  
Stress Responses ◽  
Oxidant Stress ◽  
Regulatory Proteins ◽  
Heme Oxygenase 1 ◽  
Nf Kappa B ◽  
Transcriptional Regulatory ◽  
Genes Encoding

The pathogenesis of influenza virus infections of the lungs is in part mediated by oxidative stress. Such infections might therefore be expected to induce expression of stress-response genes and genes encoding antioxidant enzymes and to activate transcriptional regulatory proteins. Mice (C57B1/6 and C3H/HeJ) were infected intranasally with influenza virus A/PR/8/34 (H1N1). Expression of the genes encoding the antioxidant enzymes manganese superoxide dismutase (Mn- SOD), indoleamine-2, 3-dioxygenase (IDO), heme oxygenase-1, and glutathione peroxidase were increased in the lungs of virus-infected animals. Cu/ZnSOD and catalase mRNA were not induced by viral infection. Activation of the transcriptional regulatory proteins AP-1, C/EBP, and NF-kappa B (which are known to be affected by oxidant stress) was demonstrated by electrophoretic mobility shift assay after viral infection. In the case of MnSOD, despite increased gene expression enzyme activity was not increased. In contrast, for heme oxygenase-1 both mRNA and activity were increased. C3H/ HeJ and C57B1/6 mice, which are known to have different responses to other types of oxidant stress, also differed in their responses to viral infection. Induction of heme oxygenase-1 expression was greater in C57B1/6 mice than in C3H/ HeJ mice, although inhibiting this enzyme did not alter virus-induced mortality. In contrast, IDO was more strongly induced in C3H/HeJ mice. Activation of NF-kappa B was much more marked in C57B1/6 mice than in C3H/HeJ mice. Although virus replication and inflammatory responses were equivalent in the two strains, lung injury (as measured by wet-to-dry wt ratios) and mortality were greater in C3H/HeJ mice than in C57B1/6 mice, a difference that may be related to differing oxidant stress responses. Thus influenza pneumonia causes an oxidant stress response in the lungs, the nature of which is determined in part by the genetic background of the host.

scholarly journals The Evolution, Gene Expression Profile, and Secretion of Digestive Peptidases in Lepidoptera Species

Catalysts ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 217
Author(s):  
Lucas R. Lima ◽  
Renata O. Dias ◽  
Felipe Jun Fuzita ◽  
Clélia Ferreira ◽  
Walter R. Terra ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profile ◽  
Catalytic Triad ◽  
Rna Seq ◽  
Anterior Portion ◽  
Gene Family Expansion ◽  
Genes Encoding ◽  
Peptidase Inhibitor ◽  
Family Expansion ◽  
Midgut Lumen

Serine peptidases (SPs) are responsible for most primary protein digestion in Lepidoptera species. An expansion of the number of genes encoding trypsin and chymotrypsin enzymes and the ability to upregulate the expression of some of these genes in response to peptidase inhibitor (PI) ingestion have been associated with the adaptation of Noctuidae moths to herbivory. To investigate whether these gene family expansion events are common to other Lepidoptera groups, we searched for all genes encoding putative trypsin and chymotrypsin enzymes in 23 publicly available genomes from this taxon. Phylogenetic analysis showed that several gene family expansion events may have occurred in the taxon’s evolutionary history and that these events gave rise to a very diverse group of enzymes, including proteins lacking the canonical SP catalytic triad. The expression profile of these enzymes along the midgut and the secretion mechanisms by which these enzymes enter the luminal content were also analyzed in Spodoptera frugiperda larvae using RNA-seq and proteomics. These results support the proposal of a midgut countercurrent flux responsible for the direction of these proteins to the anterior portion of the midgut and show that these enzymes reach the midgut lumen via both exocytosis and microapocrine secretion mechanisms.

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