Scaling of cellular proteome with ploidy

Abstract Ploidy changes are frequent in nature and contribute to evolution, functional specialization and tumorigenesis. Analysis of model organisms of different ploidies revealed that increased ploidy leads to an increase in cell and nuclear volume, reduced proliferation, metabolic changes, lower fitness, and increased genomic instability, but the underlying mechanisms remain poorly understood. To investigate how the gene expression changes with cellular ploidy, we analyzed isogenic series of budding yeasts from 1N to 4N. We show that mRNA and protein abundance scales allometrically with ploidy, with tetraploid cells showing only threefold increase in proteins compared to haploids. This ploidy-specific scaling occurs via decreased rRNA and ribosomal protein abundance and reduced translation. We demonstrate that the Tor1 activity is reduced with increasing ploidy, which leads to rRNA gene repression via a novel Tor1-Sch9-Tup1 signaling pathway. mTORC1 and S6K activity are also reduced in human tetraploid cells and the concomitant increase of the Tup1 homolog Tle1 downregulates the rDNA transcription. Our results revealed a novel conserved mTORC1-S6K-Tup1/Tle1 pathway that ensures proteome remodeling in response to increased ploidy.

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Scaling of cellular proteome with ploidy

10.1101/2021.05.06.442919 ◽

2021 ◽

Author(s):

Galal Yahya ◽

Paul Menges ◽

Devi Anggraini Ngandiri ◽

Daniel Schulz ◽

Andreas Wallek ◽

...

Keyword(s):

Gene Repression ◽

Model Organisms ◽

Rrna Gene ◽

Functional Specialization ◽

Protein Abundance ◽

Concomitant Increase ◽

Rdna Transcription ◽

Threefold Increase ◽

Ploidy Changes ◽

Underlying Mechanisms

Ploidy changes are frequent in nature and contribute to evolution, functional specialization and tumorigenesis (1,2). Analysis of model organisms of different ploidies revealed that increased ploidy leads to an increase in cell and nuclear volume, reduced proliferation (2-4), metabolic changes (5), lower fitness (6,7), and increased genomic instability (8,9), but the underlying mechanisms remain poorly understood. To investigate how the gene expression changes with cellular ploidy, we analyzed isogenic series of budding yeasts from 1N to 4N. We show that mRNA and protein abundance scales allometrically with ploidy, with tetraploid cells showing only threefold increase in proteins compared to haploids. This ploidy-specific scaling occurs via decreased rRNA and ribosomal protein abundance and reduced translation. We demonstrate that the Tor1 activity is reduced with increasing ploidy, which leads to rRNA gene repression via a novel Tor1-Sch9-Tup1 signaling pathway. mTORC1 and S6K activity are also reduced in human tetraploid cells and the concomitant increase of the Tup1 homolog Tle1 downregulates the rDNA transcription. Our results revealed a novel conserved mTORC1-S6K-Tup1/Tle1 pathway that ensures proteome remodeling in response to increased ploidy.

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Gut Microbiome and Metabolome Profiles Associated with High-Fat Diet in Mice

Metabolites ◽

10.3390/metabo11080482 ◽

2021 ◽

Vol 11 (8) ◽

pp. 482

Author(s):

Jae-Kwon Jo ◽

Seung-Ho Seo ◽

Seong-Eun Park ◽

Hyun-Woo Kim ◽

Eun-Ju Kim ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

High Fat Diet ◽

Amplicon Sequencing ◽

Gas Chromatography Mass Spectrometry ◽

Control Group ◽

Rrna Gene ◽

High Fat ◽

Underlying Mechanisms ◽

Insight Into

Obesity can be caused by microbes producing metabolites; it is thus important to determine the correlation between gut microbes and metabolites. This study aimed to identify gut microbiota-metabolomic signatures that change with a high-fat diet and understand the underlying mechanisms. To investigate the profiles of the gut microbiota and metabolites that changed after a 60% fat diet for 8 weeks, 16S rRNA gene amplicon sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomic analyses were performed. Mice belonging to the HFD group showed a significant decrease in the relative abundance of Bacteroidetes but an increase in the relative abundance of Firmicutes compared to the control group. The relative abundance of Firmicutes, such as Lactococcus, Blautia, Lachnoclostridium, Oscillibacter, Ruminiclostridium, Harryflintia, Lactobacillus, Oscillospira, and Erysipelatoclostridium, was significantly higher in the HFD group than in the control group. The increased relative abundance of Firmicutes in the HFD group was positively correlated with fecal ribose, hypoxanthine, fructose, glycolic acid, ornithine, serum inositol, tyrosine, and glycine. Metabolic pathways affected by a high fat diet on serum were involved in aminoacyl-tRNA biosynthesis, glycine, serine and threonine metabolism, cysteine and methionine metabolism, glyoxylate and dicarboxylate metabolism, and phenylalanine, tyrosine, and trypto-phan biosynthesis. This study provides insight into the dysbiosis of gut microbiota and metabolites altered by HFD and may help to understand the mechanisms underlying obesity mediated by gut microbiota.

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Calcium Signaling in Vertebrate Development and Its Role in Disease

International Journal of Molecular Sciences ◽

10.3390/ijms19113390 ◽

2018 ◽

Vol 19 (11) ◽

pp. 3390 ◽

Cited By ~ 8

Author(s):

Sudip Paudel ◽

Regan Sindelar ◽

Margaret Saha

Keyword(s):

Calcium Signaling ◽

Critical Role ◽

Molecular Techniques ◽

Model Organisms ◽

Vertebrate Development ◽

Developmental Defects ◽

Calcium Activity ◽

Human Genes ◽

Underlying Mechanisms

Accumulating evidence over the past three decades suggests that altered calcium signaling during development may be a major driving force for adult pathophysiological events. Well over a hundred human genes encode proteins that are specifically dedicated to calcium homeostasis and calcium signaling, and the majority of these are expressed during embryonic development. Recent advances in molecular techniques have identified impaired calcium signaling during development due to either mutations or dysregulation of these proteins. This impaired signaling has been implicated in various human diseases ranging from cardiac malformations to epilepsy. Although the molecular basis of these and other diseases have been well studied in adult systems, the potential developmental origins of such diseases are less well characterized. In this review, we will discuss the recent evidence that examines different patterns of calcium activity during early development, as well as potential medical conditions associated with its dysregulation. Studies performed using various model organisms, including zebrafish, Xenopus, and mouse, have underscored the critical role of calcium activity in infertility, abortive pregnancy, developmental defects, and a range of diseases which manifest later in life. Understanding the underlying mechanisms by which calcium regulates these diverse developmental processes remains a challenge; however, this knowledge will potentially enable calcium signaling to be used as a therapeutic target in regenerative and personalized medicine.

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Dichotomous Impact of Myc on rRNA Gene Activation and Silencing in B Cell Lymphomagenesis

Cancers ◽

10.3390/cancers12103009 ◽

2020 ◽

Vol 12 (10) ◽

pp. 3009

Author(s):

Gaurav Joshi ◽

Alexander Otto Eberhardt ◽

Lisa Lange ◽

René Winkler ◽

Steve Hoffmann ◽

...

Keyword(s):

B Cell ◽

Gene Activation ◽

Cpg Methylation ◽

Rrna Genes ◽

Rrna Gene ◽

Rdna Transcription ◽

Highly Active ◽

Pol I ◽

Polymerase I ◽

Transcriptional Output

A major transcriptional output of cells is ribosomal RNA (rRNA), synthesized by RNA polymerase I (Pol I) from multicopy rRNA genes (rDNA). Constitutive silencing of an rDNA fraction by promoter CpG methylation contributes to the stabilization of these otherwise highly active loci. In cancers driven by the oncoprotein Myc, excessive Myc directly stimulates rDNA transcription. However, it is not clear when during carcinogenesis this mechanism emerges, and how Myc-driven rDNA activation affects epigenetic silencing. Here, we have used the Eµ-Myc mouse model to investigate rDNA transcription and epigenetic regulation in Myc-driven B cell lymphomagenesis. We have developed a refined cytometric strategy to isolate B cells from the tumor initiation, promotion, and progression phases, and found a substantial increase of both Myc and rRNA gene expression only in established lymphoma. Surprisingly, promoter CpG methylation and the machinery for rDNA silencing were also strongly up-regulated in the tumor progression state. The data indicate a dichotomous role of oncogenic Myc in rDNA regulation, boosting transcription as well as reinforcing repression of silent repeats, which may provide a novel angle on perturbing Myc function in cancer cells.

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Acetobacter tropicalis Is a Major Symbiont of the Olive Fruit Fly (Bactrocera oleae)

Applied and Environmental Microbiology ◽

10.1128/aem.02933-08 ◽

2009 ◽

Vol 75 (10) ◽

pp. 3281-3288 ◽

Cited By ~ 90

Author(s):

Ilias Kounatidis ◽

Elena Crotti ◽

Panagiotis Sapountzis ◽

Luciano Sacchi ◽

Aurora Rizzi ◽

...

Keyword(s):

Acetic Acid ◽

Fluorescent Protein ◽

Acetic Acid Bacteria ◽

Acetic Acid Bacterium ◽

Malpighian Tubules ◽

Bactrocera Oleae ◽

Model Organisms ◽

Rrna Gene ◽

Olive Fruit Fly ◽

Agricultural Pests

ABSTRACT Following cultivation-dependent and -independent techniques, we investigated the microbiota associated with Bactrocera oleae, one of the major agricultural pests in olive-producing countries. Bacterial 16S rRNA gene libraries and ultrastructural analyses revealed the presence of several bacterial taxa associated with this insect, among which Acetobacter tropicalis was predominant. The recent increased detection of acetic acid bacteria as symbionts of other insect model organisms, such as Anopheles stephensi (G. Favia et al., Proc. Natl. Acad. Sci. USA 104:9047-9051, 2007) or Drosophila melanogaster (C. R. Cox and M. S. Gilmore, Infect. Immun. 75:1565-1576, 2007), prompted us to investigate the association established between A. tropicalis and B. oleae. Using an A. tropicalis-specific PCR assay, the symbiont was detected in all insects tested originating from laboratory stocks or field-collected from different locations in Greece. This acetic acid bacterium was successfully established in cell-free medium, and typing analyses, carried out on a collection of isolates, revealed that different A. tropicalis strains are present in fly populations. The capability to colonize and lodge in the digestive system of both larvae and adults and in Malpighian tubules of adults was demonstrated by using a strain labeled with a green fluorescent protein.

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The Vibrio cholerae T6SS is Dispensable for Colonization but Affects Pathogenesis and the Structure of Zebrafish Intestinal Microbiome

Infection and Immunity ◽

10.1128/iai.00151-21 ◽

2021 ◽

Author(s):

Paul Breen ◽

Andrew D. Winters ◽

Kevin R. Theis ◽

Jeffrey H. Withey

Keyword(s):

Vibrio Cholerae ◽

Model Organism ◽

16S Rrna Gene Sequencing ◽

Intestinal Microbiome ◽

Model Organisms ◽

Rrna Gene ◽

Composition And Structure ◽

Aquatic Microbes ◽

Host Microbe Interactions ◽

Rrna Gene Sequencing

Zebrafish ( Danio rerio ) are an attractive model organism for a variety of scientific studies, including host-microbe interactions. The organism is particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae , an intestinal pathogen. V. cholerae must colonize the intestine of an exposed host for pathogenicity to occur. While numerous studies have explored various aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms, few, if any, have examined how a V. cholerae infection alters the resident intestinal microbiome and the role of the type six secretion system (T6SS) in that process. In this study, 16S rRNA gene sequencing was utilized to investigate how strains of V. cholerae both with and without the T6SS alter the aforementioned microbial profiles following an infection. V. cholerae infection induced significant changes in the zebrafish intestinal microbiome, and while not necessary for colonization, the T6SS was essential for inducing mucin secretion, a marker for diarrhea. Additional salient differences to the microbiome were observed based on the presence or absence of the T6SS in the V. cholerae utilized for challenging the zebrafish hosts. We conclude that V. cholerae significantly modulates the zebrafish intestinal microbiome to enable colonization and that the T6SS is important for pathogenesis induced by the examined V. cholerae strains. Furthermore, presence or absence of T6SS differentially and significantly affected the composition and structure of the intestinal microbiome, with an increased abundance of other Vibrio bacteria observed in the absence of V. cholerae T6SS.

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Abiotic drivers of protein abundance variation among natural populations

10.1101/2020.03.27.011676 ◽

2020 ◽

Author(s):

Joshua Niklas Ebner ◽

Danilo Ritz ◽

Stefanie von Fumetti

Keyword(s):

Environmental Change ◽

Natural Populations ◽

Field Studies ◽

Model Organisms ◽

Protein Abundance ◽

Molecular Systems ◽

Functional Roles ◽

Freshwater Spring ◽

Abundance Variation ◽

Plastic Responses

AbstractIdentifying when and where environmental change induces molecular responses in natural populations is an important goal in contemporary ecology. It can aid in identifying molecular signatures of populations experiencing stressful conditions and potentially inform if species are approaching the limits of their tolerance niches. Achieving this goal is hampered by our limited understanding of the influence of environmental variation on the molecular systems of most ecologically relevant species as the pathways underlying fitness-affecting plastic responses have primarily been studied in model organisms under controlled laboratory conditions. In this study, we establish relationships between protein abundance patterns and the abiotic environment by profiling the proteomes of 24 natural populations of the caddisfly Crunoecia irrorata. We subsequently relate these profiles to natural variations in the abiotic characteristics of their freshwater spring habitats which shows that protein abundances and networks respond to abiotic variation according to the functional roles these proteins have. We provide evidence that geographic and past and present environmental differences between sites affect protein abundances and identifications, and that baseline reaction norms are ubiquitous and can be used as information rather than noise in comparative field studies. Taking this natural variation into account is a prerequisite if we are to identify the effects environmental change has on natural populations.

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Revealing the Composition of the Eukaryotic Microbiome of Oyster Spat by CRISPR-Cas Selective Amplicon Sequencing (CCSAS)

10.21203/rs.3.rs-240715/v1 ◽

2021 ◽

Author(s):

Kevin Xu Zhong ◽

Anna Cho ◽

Christophe M. Deeg ◽

Amy M. Chan ◽

Curtis A. Suttle

Keyword(s):

18S Rrna ◽

Amplicon Sequencing ◽

18S Rrna Gene ◽

Model Organisms ◽

Rrna Gene ◽

Gene Sequences ◽

Oyster Spat ◽

Guide Rna ◽

16S Rna ◽

Eukaryotic Microbes

Abstract BackgroundThe microbiome affects the health of plants and animals, including humans, and has many biological, ecological and evolutionary consequences. Microbiome studies typically rely on sequencing ribosomal 16S RNA gene fragments, which serve as taxonomic markers for prokaryotic communities; however, for eukaryotic microbes this approach is compromised, because 18S rRNA gene sequences from microbial eukaryotes are swamped by contaminating host rRNA gene sequences. ResultsTo overcome this problem, we developed CRISPR-Cas Selective Amplicon Sequencing (CCSAS), a high-resolution and efficient approach for characterizing eukaryotic microbiomes. CCSAS uses taxon-specific single-guide RNA (sgRNA) to direct Cas9 to cut 18S rRNA gene sequences of the host, while leaving protistan and fungal sequences intact. We validated the specificity of the sgRNA on ten model organisms and an artificially constructed (mock) community of nine protistan and fungal pathogens. The results showed that >96.5% of host rRNA gene amplicons were cleaved, while 18S rRNA gene sequences from protists and fungi were unaffected. When used to assess the eukaryotic microbiome of oyster spat from a hatchery, CCSAS revealed a diverse community of eukaryotic microbes, typically with much less contamination from oyster 18S rRNA gene sequences than other methods using non-metazoan or blocking primers. However, each method revealed taxonomic groups that were not detected using the other methods, showing that a single approach is unlikely to uncover the entire eukaryotic microbiome in complex communities. To facilitate the application of CCSAS, we designed taxon-specific sgRNA for ~16,000 metazoan and plant taxa, making CCSAS widely available for characterizing eukaryotic microbiomes that have largely been neglected. ConclusionCCSAS provides a high-through-put and cost-effective approach for resolving the eukaryotic microbiome of metazoa and plants with minimal contamination from host 18S rRNA gene sequences. Keywords: Eukaryotic microbiome, 18S rRNA gene, Microeukaryote, CRISPR-Cas, Taxon-specific single-guide RNA, gRNA-target-site, CasOligo, CCSAS

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Invertebrate Models of Nociception

The Oxford Handbook of the Neurobiology of Pain ◽

10.1093/oxfordhb/9780190860509.013.8 ◽

2020 ◽

pp. 60-100

Author(s):

Daniel Hesselson ◽

Denise S. Walker ◽

Joshua Neil Massingham ◽

William R. Schafer ◽

G. Gregory Neely ◽

...

Keyword(s):

Tissue Injury ◽

Emotional Experience ◽

Public Health Problem ◽

Experimental Models ◽

Model Organisms ◽

Experimental Systems ◽

Significant Public Health ◽

Noxious Stimuli ◽

Underlying Mechanisms ◽

High Level

Chronic pain is a significant public health problem, affecting 20–25% of the global population, and there is a clear need for more specific and effective therapeutics. To achieve this, a comprehensive understanding of the underlying mechanisms and molecular machinery driving pain-related diseases is required. The definition of pain as an “unpleasant sensory and emotional experience” associated with tissue injury is innately anthropomorphic, the emotional element being difficult to reconcile in nonhuman organisms. Even simple invertebrates are nevertheless capable of nociception, the neural processing of noxious stimuli. With the significant advantages of simpler nervous systems, experimental tractability, and a high level of conservation, they have a major role to play in advancing our understanding. This chapter reviews our current molecular- and circuit-level understanding of nociception in two of the most widely used invertebrate experimental models, the nematode Caenorhabditis elegans and the fly Drosophila melanogaster. In particular, it summarizes the molecules, cells, and circuits that contribute to nociception in response to diverse noxious stimuli in these model organisms and the behavioral paradigms that we can harness to study them. The chapter discusses how mechanistic insights gained from these experimental systems can improve our understanding of pain in humans.

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In vivo regulation of rRNA transcription occurs rapidly in nondividing and dividing Drosophila cells in response to a phorbol ester and serum.

Molecular and Cellular Biology ◽

10.1128/mcb.13.2.928 ◽

1993 ◽

Vol 13 (2) ◽

pp. 928-933 ◽

Cited By ~ 9

Author(s):

S M Vallett ◽

M Brudnak ◽

M Pellegrini ◽

H W Weber

Keyword(s):

Phorbol Ester ◽

Growth Regulation ◽

Rrna Genes ◽

Rrna Synthesis ◽

Rrna Gene ◽

Rdna Transcription ◽

Transcription System ◽

Pol I ◽

Drosophila Cells

The synthesis of ribosomes is an essential cellular process which requires the transcription of the rRNA genes by RNA polymerase I (Pol I). The regulation of rRNA synthesis is known to be coupled to growth regulation. In nongrowing, slowly growing, and rapidly growing Drosophila cells, exposure to the tumor-promoting phorbol ester 12-O-tetradecanoylphorbol-13-acetate (TPA) increases the synthesis of precursor and mature rRNAs. Using nuclear run-on assays, we show that TPA enhances transcription of the rRNA genes. These results suggest that TPA regulates expression of RNA genes transcribed by Pol I, irrespective of the growth state of the cells. In slowly dividing Drosophila cells, increasing the serum concentration rapidly alters the accumulation of rRNA by enhancing rDNA transcription within 1 h. Thus, TPA and serum are each able to rapidly regulate rRNA gene expression in Drosophila cells. These results indicate that the RNA Pol I transcription system can be regulated by agents which have previously been shown to effect specific genes transcribed by the RNA Pol II system.

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