scholarly journals Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance

2019 ◽  
Author(s):  
Alison Mullis ◽  
Zhaolian Lu ◽  
Yu Zhan ◽  
Tzi-Yuan Wang ◽  
Judith Rodriguez ◽  
...  
Keyword(s):  
Concerted Evolution ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Gene Dosage ◽  
High Growth ◽  
Fungal Species ◽  
Physiological Data ◽  
Ribosomal Protein Genes ◽  
Cellular Machinery ◽  
Dosage Balance

ABSTRACTRibosomal proteins (RPs) genes encode structure components of ribosomes, the cellular machinery for protein synthesis. A single functional copy has been maintained in most of 78-80 RP families in animals due to evolutionary constraints imposed by gene dosage balance. Some fungal species have maintained duplicate copies in most RP families. How the RP genes were duplicated and maintained in these fungal species, and their functional significance remains unresolved. To address these questions, we identified all RP genes from 295 fungi and inferred the timing and nature of gene duplication for all RP families. We found that massive duplications of RP genes have independently occurred by different mechanisms in three distantly related lineages. The RP duplicates in two of them, budding yeast and Mucoromycota, were mainly created by whole genome duplication (WGD) events. However, in fission yeasts, duplicate RP genes were likely generated by retroposition, which is unexpected considering their dosage sensitivity. The sequences of most RP paralogs in each species have been homogenized by repeated gene conversion, demonstrating parallel concerted evolution, which might have facilitated the retention of their duplicates. Transcriptomic data suggest that the duplication and retention of RP genes increased RP transcription abundance. Physiological data indicate that increased ribosome biogenesis allowed these organisms to rapidly consuming sugars through fermentation while maintaining high growth rates, providing selective advantages to these species in sugar-rich environments.

scholarly journals Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance

2019 ◽  
Vol 37 (2) ◽  
pp. 455-468 ◽  
Author(s):  
Alison Mullis ◽  
Zhaolian Lu ◽  
Yu Zhan ◽  
Tzi-Yuan Wang ◽  
Judith Rodriguez ◽  
...  
Keyword(s):  
Ribosomal Protein ◽  
Concerted Evolution ◽  
Ribosome Biogenesis ◽  
Gene Dosage ◽  
High Growth ◽  
Transcript Abundance ◽  
Fungal Species ◽  
Physiological Data ◽  
Ribosomal Protein Genes ◽  
Duplication Events

Abstract Ribosomal protein (RP) genes encode structural components of ribosomes, the cellular machinery for protein synthesis. A single functional copy has been maintained in most of 78–80 RP families in animals due to evolutionary constraints imposed by gene dosage balance. Some fungal species have maintained duplicate copies in most RP families. The mechanisms by which the RP genes were duplicated and maintained and their functional significance are poorly understood. To address these questions, we identified all RP genes from 295 fungi and inferred the timing and nature of gene duplication events for all RP families. We found that massive duplications of RP genes have independently occurred by different mechanisms in three distantly related lineages: budding yeasts, fission yeasts, and Mucoromycota. The RP gene duplicates in budding yeasts and Mucoromycota were mainly created by whole genome duplication events. However, duplicate RP genes in fission yeasts were likely generated by retroposition, which is unexpected considering their dosage sensitivity. The sequences of most RP paralogs have been homogenized by repeated gene conversion in each species, demonstrating parallel concerted evolution, which might have facilitated the retention of their duplicates. Transcriptomic data suggest that the duplication and retention of RP genes increased their transcript abundance. Physiological data indicate that increased ribosome biogenesis allowed these organisms to rapidly consume sugars through fermentation while maintaining high growth rates, providing selective advantages to these species in sugar-rich environments.

scholarly journals Genome-Wide Identification, Evolution and Expression of the Complete Set of Cytoplasmic Ribosomal Protein Genes in Nile Tilapia

2020 ◽  
Vol 21 (4) ◽  
pp. 1230
Author(s):  
Gangqiao Kuang ◽  
Wenjing Tao ◽  
Shuqing Zheng ◽  
Xiaoshuang Wang ◽  
Deshou Wang
Keyword(s):  
Ribosomal Proteins ◽  
Nile Tilapia ◽  
Ribosome Biogenesis ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Ribosomal Protein Genes ◽  
Expression Levels ◽  
Sexually Dimorphic Expression ◽  
Complete Set ◽  
Almost All

Ribosomal proteins (RPs) are indispensable in ribosome biogenesis and protein synthesis, and play a crucial role in diverse developmental processes. In the present study, we carried out a comprehensive analysis of RPs in chordates and examined the expression profiles of the complete set of 92 cytoplasmic RP genes in Nile tilapia. The RP genes were randomly distributed throughout the tilapia genome. Phylogenetic and syntenic analyses revealed the existence of duplicated RP genes from 2R (RPL3, RPL7, RPL22 and RPS27) and 3R (RPL5, RPL19, RPL22, RPL41, RPLP2, RPS17, RPS19 and RPS27) in tilapia and even more from 4R in common carp and Atlantic salmon. The RP genes were found to be expressed in all tissues examined, but their expression levels differed among different tissues. Gonadal transcriptome analysis revealed that almost all RP genes were highly expressed, and their expression levels were highly variable between ovaries and testes at different developmental stages in tilapia. No sex- and stage-specific RP genes were found. Eleven RP genes displayed sexually dimorphic expression with nine higher in XY gonad and two higher in XX gonad at all stages examined, which were proved to be phenotypic sex dependent. Quantitative real-time PCR and immunohistochemistry ofRPL5b and RPL24 were performed to validate the transcriptome data. The genomic resources and expression data obtained in this study will contribute to a better understanding of RPs evolution and functions in chordates.

scholarly journals The High-resolution Timeline of Expression of Ribosomal Protein Genes in Yeast

2017 ◽  
Author(s):  
Xueling Li ◽  
Gang Chen ◽  
Bernard Fongang ◽  
Dirar Homouz ◽  
Maga Rowicka ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Resolution ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Center Of Mass ◽  
Regulatory Elements ◽  
Ribosomal Protein Genes ◽  
Translational Initiation ◽  
Expression Of Genes ◽  
Expression Time

AbstractThe yeast ribosome is a complex molecular machine built from four rRNAs and over 70 r-proteins. Ribosome biogenesis involves ordered incorporation of ribosomal proteins, accompanied by and association and dissociation of other proteins specific to different stages of the process. By model-based analysis of temporal profiles of gene expression in a metabolically regulated system, we obtained an accurate, high-resolution estimation of the time of expression of genes coding for proteins involved in ribosome biogenesis. The ribosomal proteins are expressed in a sequence that spans approximately 25-minutes under metabolically regulated conditions. The genes coding for proteins incorporated into the mature ribosome are expressed significantly later than those that are not incorporated, but are otherwise involved in ribosome biogenesis, localization and assembly, rRNA processing and translational initiation. The relative expression time of proteins localized within specified neighborhood is significantly correlated with the distance to the centroid of the mature ribosome: protein localized closer to the center of mass of the entire complex tend to be expressed earlier than the protein localized further from the center. The timeline of gene expression also agrees with the known dependencies between recruitment of specific proteins into the mature ribosome. These findings are consistent in two independent experiments. We have further identified regulatory elements correlated with the time of regulation, including a possible dependence of expression time on the position of the RAP1 binding site within the 5’UTR.

scholarly journals Human Ribosomal Proteins RPeL27, RPeL43, and RPeL41 Are Upregulated in Nasopharyngeal Carcinoma Cell Lines

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Edmund Ui-Hang Sim ◽  
Stella Li-Li Chan ◽  
Kher-Lee Ng ◽  
Choon-Weng Lee ◽  
Kumaran Narayanan
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Ribosomal Protein ◽  
Cell Lines ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Expression Patterns ◽  
Transcript Level ◽  
Ribosomal Protein Genes ◽  
Significant Differential Expression ◽  
Protein Levels

Apart from their canonical role in ribosome biogenesis, there is increasing evidence of ribosomal protein genes’ involvement in various cancers. A previous study by us revealed significant differential expression of three ribosomal protein genes (RPeL27, RPeL41, and RPeL43) between cell lines derived from tumor and normal nasopharyngeal epithelium. However, the results therein were based on a semiquantitative assay, thus preliminary in nature. Herein, we provide findings of a deeper analysis of these three genes in the context to nasopharyngeal carcinoma (NPC) tumorigenesis. Their expression patterns were analyzed in a more quantitative manner at transcript level. Their protein expression levels were also investigated. We showed results that are contrary to previous report. Rather than downregulation, these genes were significantly overexpressed in NPC cell lines compared to normal control at both transcript and protein levels. Nevertheless, their association with NPC has been established. Immunoprecipitation pulldown assays indicate the plausible interaction of either RPeL27 or RPeL43 with POTEE/TUBA1A and ACTB/ACTBL2 complexes. In addition, RPeL43 is shown to bind with MRAS and EIF2S1 proteins in a NPC cell line (HK1). Our findings support RPeL27, RPeL41, and RPeL43 as potential markers of NPC and provide insights into the interaction targets of RPeL27 and RPeL43 proteins.

scholarly journals Transcriptional control of ribosome biogenesis in yeast: links to growth and stress signals

2021 ◽  
Author(s):  
David Shore ◽  
Sevil Zencir ◽  
Benjamin Albert
Keyword(s):  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Transcriptional Control ◽  
Yeast Cells ◽  
Ribosomal Protein Genes ◽  
Recent Developments ◽  
Pioneer Transcription Factor ◽  
Stress Signals ◽  
Transcriptional Output ◽  
Major Recent Development

Ribosome biogenesis requires prodigious transcriptional output in rapidly growing yeast cells and is highly regulated in response to both growth and stress signals. This minireview focuses on recent developments in our understanding of this regulatory process, with an emphasis on the 138 ribosomal protein genes (RPGs) themselves and a group of >200 ribosome biogenesis (RiBi) genes whose products contribute to assembly but are not part of the ribosome. Expression of most RPGs depends upon Rap1, a pioneer transcription factor (TF) required for the binding of a pair of RPG-specific TFs called Fhl1 and Ifh1. RPG expression is correlated with Ifh1 promoter binding, whereas Rap1 and Fhl1 remain promoter-associated upon stress-induced down regulation. A TF called Sfp1 has also been implicated in RPG regulation, though recent work reveals that its primary function is in activation of RiBi and other growth-related genes. Sfp1 plays an important regulatory role at a small number of RPGs where Rap1–Fhl1–Ifh1 action is subsidiary or non-existent. In addition, nearly half of all RPGs are bound by Hmo1, which either stabilizes or re-configures Fhl1–Ifh1 binding. Recent studies identified the proline rotamase Fpr1, known primarily for its role in rapamycin-mediated inhibition of the TORC1 kinase, as an additional TF at RPG promoters. Fpr1 also affects Fhl1–Ifh1 binding, either independently or in cooperation with Hmo1. Finally, a major recent development was the discovery of a protein homeostasis mechanism driven by unassembled ribosomal proteins, referred to as the Ribosome Assembly Stress Response (RASTR), that controls RPG transcription through the reversible condensation of Ifh1.

scholarly journals The roles of ribosomal proteins in nasopharyngeal cancer: culprits, sentinels or both

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Edmund Ui-Hang Sim ◽  
Choon-Weng Lee ◽  
Kumaran Narayanan
Keyword(s):  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Protein Biosynthesis ◽  
Physiological Activity ◽  
Nasopharyngeal Cancer ◽  
Protein Translation ◽  
Cellular Protein ◽  
Cellular Growth ◽  
Ribosomal Protein Genes ◽  
Relationship Of

AbstractRibosomal protein genes encode products that are essential for cellular protein biosynthesis and are major components of ribosomes. Canonically, they are involved in the complex system of ribosome biogenesis pivotal to the catalysis of protein translation. Amid this tightly organised process, some ribosomal proteins have unique spatial and temporal physiological activity giving rise to their extra-ribosomal functions. Many of these extra-ribosomal roles pertain to cellular growth and differentiation, thus implicating the involvement of some ribosomal proteins in organogenesis. Consequently, dysregulated functions of these ribosomal proteins could be linked to oncogenesis or neoplastic transformation of human cells. Their suspected roles in carcinogenesis have been reported but not specifically explained for malignancy of the nasopharynx. This is despite the fact that literature since one and half decade ago have documented the association of ribosomal proteins to nasopharyngeal cancer. In this review, we explain the association and contribution of dysregulated expression among a subset of ribosomal proteins to nasopharyngeal oncogenesis. The relationship of these ribosomal proteins with the cancer are explained. We provide information to indicate that the dysfunctional extra-ribosomal activities of specific ribosomal proteins are tightly involved with the molecular pathogenesis of nasopharyngeal cancer albeit mechanisms yet to be precisely defined. The complete knowledge of this will impact future applications in the effective management of nasopharyngeal cancer.

scholarly journals Control of ribosomal protein synthesis by the Microprocessor complex

2021 ◽  
Vol 14 (671) ◽  
pp. eabd2639
Author(s):  
Xuan Jiang ◽  
Amit Prabhakar ◽  
Stephanie M. Van der Voorn ◽  
Prajakta Ghatpande ◽  
Barbara Celona ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Ribosomal Protein ◽  
Nuclear Export ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Cellular Growth ◽  
Ribosomal Protein Genes ◽  
Erythroid Progenitors ◽  
Microprocessor Complex ◽  
Ribosomal Protein Synthesis

Ribosome biogenesis in eukaryotes requires the coordinated production and assembly of 80 ribosomal proteins and four ribosomal RNAs (rRNAs), and its rate must be synchronized with cellular growth. Here, we showed that the Microprocessor complex, which mediates the first step of microRNA processing, potentiated the transcription of ribosomal protein genes by eliminating DNA/RNA hybrids known as R-loops. Nutrient deprivation triggered the nuclear export of Drosha, a key component of the Microprocessor complex, and its subsequent degradation by the E3 ubiquitin ligase Nedd4, thereby reducing ribosomal protein production and protein synthesis. In mouse erythroid progenitors, conditional deletion of Drosha led to the reduced production of ribosomal proteins, translational inhibition of the mRNA encoding the erythroid transcription factor Gata1, and impaired erythropoiesis. This phenotype mirrored the clinical presentation of human “ribosomopathies.” Thus, the Microprocessor complex plays a pivotal role in synchronizing protein synthesis capacity with cellular growth rate and is a potential drug target for anemias caused by ribosomal insufficiency.

Ribosomal Proteins Are Overexpressed in Hyperdiploid Multiple Myeloma.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2495-2495
Author(s):  
Niels Weinhold ◽  
John DeVos ◽  
Dirk Hose ◽  
Jean-Francois Rossi ◽  
Benner Axel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Cross Validation ◽  
Gene Dosage ◽  
Misclassification Rate ◽  
Ribosomal Protein Genes ◽  
Training Set ◽  
Global Test

Abstract Multiple myeloma (MM) is proposed to consist of two main pathogenetic groups. While hyperdiploidy (HD) is characterized by multiple trisomies of odd-numbered chromosomes (i.e. 3, 5, 9, 11, 15, and 19), non-hyperdiploid MM (NHD) show frequently one of the several recurrent IgH-translocations. The aim was to compare HD versus NHD by gene expression profiling (GEP). CD138-positive multiple myeloma cells from 74 newly diagnosed MM patients (42 GEP training group (TG), 32 GEP validation group (VG)) were purified by autoMACS-sorting. Sorted cells were analyzed by interphase-FISH with probes specific for 6q21, 8p21, 9q34, 11q23, 13q14, 15q22, 17p13, 19q13 and translocations t(4;14) and t(11;14). HD and NHD were defined by using a copy number score (CS), which was calculated by subtracting the number of probes indicating losses from the number of probes detecting additional copies (CS >0: HD; CS ≤0: NHD). GEP was performed with Affymetrix DNA-microarrays. Nearest shrunken centroid classification (NSCC) was used to discriminate the different groups, using GCRMA-normalized gene expression values. The prediction error was estimated by means of nested cross-validation using 10 repetitions of 10-fold cross-validation within the training set and separately calculated by use of the NSCC classifier of the training set to predict the validation set. Goeman’s global test was used to check the influence of ribosomal protein expression between HD and NHD. In the TG, both HD and NHD were found in 21 patients. The VG comprised 13 patients with NHD and 19 patients with HD. NSCC resulted in a predictor for HD versus NHD of 81 probe sets with a cross-validated misclassification rate of 14.2% for the TG and 26.5% for the VG. Three of the top ten genes were ribosomal proteins, overexpressed in patients with HD. Goeman’s global test further showed that ribosomal proteins are overexpressed in HD (TG: p<0.001; VG: p=0.03). Interestingly, ribosomal protein genes located on even-numbered chromosomes were also overexpressed. In conclusion, overexpression of ribosomal proteins independent of their location on odd- or even-numbered chromosomes indicates more than just a gene dosage effect and therefore a pathogenetic role of the upregulation of the ribosomal machinery in HD.

scholarly journals The Host Gene for Intronic U17 Small Nucleolar RNAs in Mammals Has No Protein-Coding Potential and Is a Member of the 5′-Terminal Oligopyrimidine Gene Family

1998 ◽  
Vol 18 (8) ◽  
pp. 4509-4518 ◽  
Author(s):  
Pawel Pelczar ◽  
Witold Filipowicz
Keyword(s):  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Transcription Unit ◽  
Host Gene ◽  
Small Nucleolar Rnas ◽  
Ribosomal Protein Genes ◽  
Protein Coding ◽  
Genes Encoding ◽  
Terminal Oligopyrimidine ◽  
Nucleolar Rnas

ABSTRACT Intron-encoded U17a and U17b RNAs are members of the H/ACA-box class of small nucleolar RNAs (snoRNAs) participating in rRNA processing and modification. We have investigated the organization and expression of the U17 locus in human cells and found that intronic U17a and U17b sequences are transcribed as part of the three-exon transcription unit, named U17HG, positioned approximately 9 kb upstream of the RCC1 locus. Comparison of the human and mouse U17HG genes has revealed that snoRNA-encoding intron sequences but not exon sequences are conserved between the two species and that neither human nor mouse spliced U17HGpoly(A)+ RNAs have the potential to code for proteins. Analyses of polysome profiles and effects of translation inhibitors on the abundance of U17HG RNA in HeLa cells indicated that despite its cytoplasmic localization, little if any U17HGRNA is associated with polysomes. This distinguishes U17HGRNA from another non-protein-coding snoRNA host gene product,UHG RNA, described previously (K. T. Tycowski, M. D. Shu, and J. A. Steitz, Nature 379:464–466, 1996). Determination of the 5′ terminus of the U17HG RNA revealed that transcription of the U17HG gene starts with a C residue followed by a polypyrimidine tract, making this gene a member of the 5′-terminal oligopyrimidine (5′TOP) family, which includes genes encoding ribosomal proteins and some translation factors. Interestingly, other known snoRNA host genes, including theUHG gene (Tycowski et al., op. cit.), have features of the 5′TOP genes. Similar characteristics of the transcription start site regions in snoRNA host and ribosomal protein genes raise the possibility that expression of components of ribosome biogenesis and translational machineries is coregulated.

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