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Sanpedro-Luna JA, Vega-Alvarado L, Vázquez-Cruz C, Sánchez-Alonso P. Global Gene Expression of Post-Senescent Telomerase-Negative ter1Δ Strain of Ustilago maydis. J Fungi (Basel) 2023; 9:896. [PMID: 37755003 PMCID: PMC10532341 DOI: 10.3390/jof9090896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 09/28/2023] Open
Abstract
We analyzed the global expression patterns of telomerase-negative mutants from haploid cells of Ustilago maydis to identify the gene network required for cell survival in the absence of telomerase. Mutations in either of the telomerase core subunits (trt1 and ter1) of the dimorphic fungus U. maydis cause deficiencies in teliospore formation. We report the global transcriptome analysis of two ter1Δ survivor strains of U. maydis, revealing the deregulation of telomerase-deleted responses (TDR) genes, such as DNA-damage response, stress response, cell cycle, subtelomeric, and proximal telomere genes. Other differentially expressed genes (DEGs) found in the ter1Δ survivor strains were related to pathogenic lifestyle factors, plant-pathogen crosstalk, iron uptake, meiosis, and melanin synthesis. The two ter1Δ survivors were phenotypically comparable, yet DEGs were identified when comparing these strains. Our findings suggest that teliospore formation in U. maydis is controlled by key pathogenic lifestyle and meiosis genes.
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Affiliation(s)
- Juan Antonio Sanpedro-Luna
- Posgrado en Microbiología, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico;
| | - Leticia Vega-Alvarado
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico;
| | - Candelario Vázquez-Cruz
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico;
| | - Patricia Sánchez-Alonso
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico;
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The long non-coding RNA landscape of Candida yeast pathogens. Nat Commun 2021; 12:7317. [PMID: 34916523 PMCID: PMC8677757 DOI: 10.1038/s41467-021-27635-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/30/2021] [Indexed: 12/29/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) constitute a poorly studied class of transcripts with emerging roles in key cellular processes. Despite efforts to characterize lncRNAs across a wide range of species, these molecules remain largely unexplored in most eukaryotic microbes, including yeast pathogens of the Candida clade. Here, we analyze thousands of publicly available sequencing datasets to infer and characterize the lncRNA repertoires of five major Candida pathogens: Candida albicans, Candida tropicalis, Candida parapsilosis, Candida auris and Candida glabrata. Our results indicate that genomes of these species encode hundreds of lncRNAs that show levels of evolutionary constraint intermediate between those of intergenic genomic regions and protein-coding genes. Despite their low sequence conservation across the studied species, some lncRNAs are syntenic and are enriched in shared sequence motifs. We find co-expression of lncRNAs with certain protein-coding transcripts, hinting at potential functional associations. Finally, we identify lncRNAs that are differentially expressed during infection of human epithelial cells for four of the studied species. Our comprehensive bioinformatic analyses of Candida lncRNAs pave the way for future functional characterization of these transcripts. Long non-coding RNAs (lncRNAs) play roles in key cellular processes, but remain largely unexplored in fungal pathogens such as Candida. Here, Hovhannisyan and Gabaldón analyze thousands of sequencing datasets to infer and characterize the lncRNA repertoires of five Candida species, paving the way for their future functional characterization.
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Xu Z, Teixeira MT. The many types of heterogeneity in replicative senescence. Yeast 2019; 36:637-648. [PMID: 31306505 PMCID: PMC6900063 DOI: 10.1002/yea.3433] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/04/2019] [Accepted: 07/07/2019] [Indexed: 11/10/2022] Open
Abstract
Replicative senescence, which is induced by telomere shortening, underlies the loss of regeneration capacity of organs and is ultimately detrimental to the organism. At the same time, it is required to protect organisms from unlimited cell proliferation that may arise from numerous stimuli or deregulations. One important feature of replicative senescence is its high level of heterogeneity and asynchrony, which promote genome instability and senescence escape. Characterizing this heterogeneity and investigating its sources are thus critical to understanding the robustness of replicative senescence. Here we review the different aspects of senescence driven by telomere attrition that are subject to variation in Saccharomyces cerevisiae, the current understanding of the molecular processes at play, and the consequences of heterogeneity in replicative senescence.
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Affiliation(s)
- Zhou Xu
- CNRS, UMR7238, Institut de Biologie Paris‐Seine, Laboratory of Computational and Quantitative BiologySorbonne UniversitéParisFrance
| | - Maria Teresa Teixeira
- CNRS, UMR8226, Institut de Biologie Physico‐Chimique, Laboratory of Molecular and Cell Biology of EukaryotesSorbonne Université, PSL Research UniversityParisFrance
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Guo R, Chen D, Xiong C, Hou C, Zheng Y, Fu Z, Diao Q, Zhang L, Wang H, Hou Z, Li W, Kumar D, Liang Q. Identification of long non-coding RNAs in the chalkbrood disease pathogen Ascospheara apis. J Invertebr Pathol 2018; 156:1-5. [PMID: 29894727 DOI: 10.1016/j.jip.2018.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 06/04/2018] [Accepted: 06/08/2018] [Indexed: 01/14/2023]
Abstract
Ascospheara apis is a widespread fungal pathogen that exclusively invades honeybee larvae. Thus far, non-coding RNA in A. apis has not yet been documented. In this study, we sequenced A. apis using strand specific cDNA library construction and Illumina RNA sequencing methods, and identified 379 lncRNAs, including antisense lncRNAs, lincRNAs, intronic lncRNAs and sense lncRNAs. Additionally, these lncRNAs were found to be shorter in length and have fewer exons and transcript isoforms than protein-coding genes, similar to those identified in mammals and plants. Furthermore, the existence of 15 predicted lncRNAs of A. apis was confirmed using RT-PCR and expression levels of 11 were lower than those of adjacent protein-coding genes. Our findings not only enlarge the lncRNA database for fungi, but also lay a foundation for further investigation of potential lncRNA-mediated regulation of genes in A. apis.
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Affiliation(s)
- Rui Guo
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dafu Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Cuiling Xiong
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chunsheng Hou
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Yanzhen Zheng
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongmin Fu
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qingyun Diao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Lu Zhang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hongquan Wang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhixian Hou
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wendong Li
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dhiraj Kumar
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Qin Liang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Wang M, Liu W, Jiao J, Li J, Wang C, Zhang L. Expression Profiling of mRNAs and Long Non-Coding RNAs in Aged Mouse Olfactory Bulb. Sci Rep 2017; 7:2079. [PMID: 28522862 PMCID: PMC5437011 DOI: 10.1038/s41598-017-02329-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/10/2017] [Indexed: 12/20/2022] Open
Abstract
Age-related decline in olfactory function affects the quality of life in elderly people and also potentially represents an early clinical symptom of neurodegenerative disorder. Olfactory bulb (OB) plays a central role in olfactory information transmitting and signal processing. The mechanisms underlying this impairment remain unclear. In the current study, microarray was used to investigate differentially expressed protein coding genes (PCGs) and long non-coding RNAs (lncRNAs) in OBs from three groups of mice of different ages (2 months-old young adults, 6 months-old mature adults and 20 months-old aged adults), for their potential roles in olfactory impairment. Gene Ontology and pathway analysis results showed that the differentially expressed PCGs in the OBs from aged mice were mainly associated with signal transduction, regulation of gene expression and cellular microenvironment. Similarly, gene set enrichment analysis identified two differentially and inversely expressed lncRNAs (NONMMUT004524 and NONMMUT000384), both of which were significantly associated with neuroactive ligand-receptor interaction pathway in the OBs of aged mice. These findings suggest that a decline of olfactory function in aged mice may be linked to differential expression of specific lncRNAs and their potentially adverse effects on the neuroactive ligand-receptor interaction pathway in the OB.
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Affiliation(s)
- Ming Wang
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, China.,Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, 100005, China
| | - Wei Liu
- The National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
| | - Jian Jiao
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, China.,Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, 100005, China
| | - Jingyun Li
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, China.,Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, 100005, China
| | - Chengshuo Wang
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, China.,Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, 100005, China
| | - Luo Zhang
- Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, China. .,Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, 100005, China. .,Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, China.
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Long Noncoding RNAs in the Yeast S. cerevisiae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1008:119-132. [PMID: 28815538 DOI: 10.1007/978-981-10-5203-3_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Long noncoding RNAs have recently been discovered to comprise a sizeable fraction of the RNA World. The scope of their functions, physical organization, and disease relevance remain in the early stages of characterization. Although many thousands of lncRNA transcripts recently have been found to emanate from the expansive DNA between protein-coding genes in animals, there are also hundreds that have been found in simple eukaryotes. Furthermore, lncRNAs have been found in the bacterial and archaeal branches of the tree of life, suggesting they are ubiquitous. In this chapter, we focus primarily on what has been learned so far about lncRNAs from the greatly studied single-celled eukaryote, the yeast Saccharomyces cerevisiae. Most lncRNAs examined in yeast have been implicated in transcriptional regulation of protein-coding genes-often in response to forms of stress-whereas a select few have been ascribed yet other functions. Of those known to be involved in transcriptional regulation of protein-coding genes, the vast majority function in cis. There are also some yeast lncRNAs identified that are not directly involved in regulation of transcription. Examples of these include the telomerase RNA and telomere-encoded transcripts. In addition to its role as a template-encoding telomeric DNA synthesis, telomerase RNA has been shown to function as a flexible scaffold for protein subunits of the RNP holoenzyme. The flexible scaffold model provides a specific mechanistic paradigm that is likely to apply to many other lncRNAs that assemble and orchestrate large RNP complexes, even in humans. Looking to the future, it is clear that considerable fundamental knowledge remains to be obtained about the architecture and functions of lncRNAs. Using genetically tractable unicellular model organisms should facilitate lncRNA characterization. The acquired basic knowledge will ultimately translate to better understanding of the growing list of lncRNAs linked to human maladies.
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Kyriakou D, Stavrou E, Demosthenous P, Angelidou G, San Luis BJ, Boone C, Promponas VJ, Kirmizis A. Functional characterisation of long intergenic non-coding RNAs through genetic interaction profiling in Saccharomyces cerevisiae. BMC Biol 2016; 14:106. [PMID: 27927215 PMCID: PMC5142380 DOI: 10.1186/s12915-016-0325-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/09/2016] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Transcriptome studies have revealed that many eukaryotic genomes are pervasively transcribed producing numerous long non-coding RNAs (lncRNAs). However, only a few lncRNAs have been ascribed a cellular role thus far, with most regulating the expression of adjacent genes. Even less lncRNAs have been annotated as essential hence implying that the majority may be functionally redundant. Therefore, the function of lncRNAs could be illuminated through systematic analysis of their synthetic genetic interactions (GIs). RESULTS Here, we employ synthetic genetic array (SGA) in Saccharomyces cerevisiae to identify GIs between long intergenic non-coding RNAs (lincRNAs) and protein-coding genes. We first validate this approach by demonstrating that the telomerase RNA TLC1 displays a GI network that corresponds to its well-described function in telomere length maintenance. We subsequently performed SGA screens on a set of uncharacterised lincRNAs and uncover their connection to diverse cellular processes. One of these lincRNAs, SUT457, exhibits a GI profile associating it to telomere organisation and we consistently demonstrate that SUT457 is required for telomeric overhang homeostasis through an Exo1-dependent pathway. Furthermore, the GI profile of SUT457 is distinct from that of its neighbouring genes suggesting a function independent to its genomic location. Accordingly, we show that ectopic expression of this lincRNA suppresses telomeric overhang accumulation in sut457Δ cells assigning a trans-acting role for SUT457 in telomere biology. CONCLUSIONS Overall, our work proposes that systematic application of this genetic approach could determine the functional significance of individual lncRNAs in yeast and other complex organisms.
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Affiliation(s)
- Dimitris Kyriakou
- Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus
| | - Emmanouil Stavrou
- Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus
| | | | - Georgia Angelidou
- Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus
| | - Bryan-Joseph San Luis
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Charles Boone
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Vasilis J Promponas
- Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus
| | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus.
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Abstract
Aging is a universal, intrinsic, and time-dependent biological decay that is linked to intricate cellular processes including cellular senescence, telomere shortening, stem cell exhaustion, mitochondrial dysfunction, and deregulated metabolism. Cellular senescence is accepted as one of the core processes of aging at the organism level. Understanding the molecular mechanism underlying senescence could facilitate the development of potential therapeutics for aging and age-related diseases. Recently, the discovery of long non-coding RNAs (lncRNA) provided insights into a novel regulatory layer that can intervene with cellular senescence. Increasing evidence indicates that targeting lncRNAs may impact on senescence pathways. In this review, we will focus on lncRNAs involved in mechanistic pathways governing cellular senescence.
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Affiliation(s)
- Ufuk Degirmenci
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Sun Lei
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS, Singapore
- *Correspondence: Sun Lei,
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