1
|
Lelandais G, Remy D, Malagnac F, Grognet P. New insights into genome annotation in Podospora anserina through re-exploiting multiple RNA-seq data. BMC Genomics 2022; 23:859. [PMID: 36581831 PMCID: PMC9801653 DOI: 10.1186/s12864-022-09085-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/16/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Publicly available RNA-seq datasets are often underused although being helpful to improve functional annotation of eukaryotic genomes. This is especially true for filamentous fungi genomes which structure differs from most well annotated yeast genomes. Podospora anserina is a filamentous fungal model, which genome has been sequenced and annotated in 2008. Still, the current annotation lacks information about cis-regulatory elements, including promoters, transcription starting sites and terminators, which are instrumental to integrate epigenomic features into global gene regulation strategies. RESULTS Here we took advantage of 37 RNA-seq experiments that were obtained in contrasted developmental and physiological conditions, to complete the functional annotation of P. anserina genome. Out of the 10,800 previously annotated genes, 5'UTR and 3'UTR were defined for 7554, among which, 3328 showed differential transcriptional signal starts and/or transcriptional end sites. In addition, alternative splicing events were detected for 2350 genes, mostly due alternative 3'splice sites and 1732 novel transcriptionally active regions (nTARs) in unannotated regions were identified. CONCLUSIONS Our study provides a comprehensive genome-wide functional annotation of P. anserina genome, including chromatin features, cis-acting elements such as UTRs, alternative splicing events and transcription of non-coding regions. These new findings will likely improve our understanding of gene regulation strategies in compact genomes, such as those of filamentous fungi. Characterization of alternative transcripts and nTARs paves the way to the discovery of putative new genes, alternative peptides or regulatory non-coding RNAs.
Collapse
Affiliation(s)
- Gaëlle Lelandais
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Damien Remy
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Fabienne Malagnac
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Pierre Grognet
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| |
Collapse
|
2
|
Chai H, Liu P, Ma Y, Chen W, Tao N, Zhao Y. Organization and Unconventional Integration of the Mating-Type Loci in Morchella Species. J Fungi (Basel) 2022; 8:jof8070746. [PMID: 35887501 PMCID: PMC9318749 DOI: 10.3390/jof8070746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 02/01/2023] Open
Abstract
True morels (Morchella spp.) are a group of delicious fungi in high demand worldwide, and some species of morels have been successfully cultivated in recent years. To better understand the sexual reproductive mechanisms of these fungi, we characterized the structure of the mating-type loci from ten morel species, and seven of them were obtained using long-range PCR amplification. Among the studied species, eight were heterothallic, two were homothallic, and four types of composition were observed in the MAT loci. In three of the five black morel species, the MAT1-1-1, MAT1-1-10, and MAT1-1-11 genes were in the MAT1-1 idiomorph, and only the MAT1-2-1 gene was in the MAT1-2 idiomorph, while an integration event occurred in the other two species and resulted in the importation of the MAT1-1-11 gene into the MAT1-2 idiomorph and survival as a truncated fragment in the MAT1-1 idiomorph. However, the MAT1-1-11 gene was not available in the four yellow morels and one blushing morel species. M. rufobrunnea, a representative species of the earliest diverging branch of true morels, along with another yellow morel Mes-15, were confirmed to be homothallic, and the MAT1-1-1, MAT1-1-10, and MAT1-2-1 genes were arranged in a tandem array. Therefore, we hypothesized that homothallism should be the ancestral reproductive state in Morchella. RT-PCR analyses revealed that four mating genes could be constitutively expressed, while the MAT1-1-10 gene underwent alternative splicing to produce different splice variants.
Collapse
Affiliation(s)
- Hongmei Chai
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.C.); (P.L.); (Y.M.); (W.C.); (N.T.)
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming 650205, China
- Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming 650205, China
| | - Ping Liu
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.C.); (P.L.); (Y.M.); (W.C.); (N.T.)
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming 650205, China
- Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming 650205, China
| | - Yuanhao Ma
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.C.); (P.L.); (Y.M.); (W.C.); (N.T.)
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming 650205, China
- Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming 650205, China
| | - Weimin Chen
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.C.); (P.L.); (Y.M.); (W.C.); (N.T.)
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming 650205, China
- Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming 650205, China
| | - Nan Tao
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.C.); (P.L.); (Y.M.); (W.C.); (N.T.)
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming 650205, China
- Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming 650205, China
| | - Yongchang Zhao
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.C.); (P.L.); (Y.M.); (W.C.); (N.T.)
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming 650205, China
- Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming 650205, China
- Correspondence: ; Tel.: +86-871-6514-0446
| |
Collapse
|
3
|
Cao X, Xu X, Dong J, Xue Y, Sun L, Zhu Y, Liu T, Jin Q. Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages. BMC Genomics 2022; 23:21. [PMID: 34983376 PMCID: PMC8725419 DOI: 10.1186/s12864-021-08184-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 11/18/2021] [Indexed: 12/28/2022] Open
Abstract
Background Circular RNAs (circRNAs) are a group of noncoding RNAs that participate in gene expression regulation in various pathways. The essential roles of circRNAs have been revealed in many species. However, knowledge of circRNAs in fungi is still not comprehensive. Results Trichophyton rubrum (T. rubrum) is considered a model organism of human pathogenic filamentous fungi and dermatophytes. In this study, we performed a genome-wide investigation of circRNAs in T. rubrum based on high-throughput sequencing and ultimately identified 4254 circRNAs. Most of these circRNAs were specific to the conidial or mycelial stage, revealing a developmental stage-specific expression pattern. In addition, 940 circRNAs were significantly differentially expressed between the conidial and mycelial stages. PCR experiments conducted on seven randomly selected differentially expressed (DE-) circRNAs confirmed the circularized structures and relative expression levels of these circRNAs. Based on their genome locations, most circRNAs originated from intergenic regions, unlike those in plants and animals. Furthermore, we constructed circRNA-miRNA-mRNA regulatory networks that included 661 DE-circRNAs targeting 140 miRNAs and further regulating 2753 mRNAs. The relative expression levels of two randomly selected circRNA-miRNA-mRNA axes were investigated by qRT-PCR, and the competing endogenous RNA (ceRNA) network theory was validated. Functional enrichment analysis of the target genes suggested that they were significantly involved in posttranscriptional processes and protein synthesis as well as some small-molecule metabolism processes. CircRNAs are relatively more conserved in closely related dermatophytes but rarely conserved in distantly related species. Tru_circ07138_001 is a highly conserved circRNA that was conserved in all ten dermatophytes analyzed in our study and three distantly related species. Its host gene TERG_07138 was also highly conserved in two of these distantly related species Gallus gallus and Caenorhabditis elegans. The specific role of this circRNA deserves further exploration. Conclusions Our study is the first to provide a global profile of circRNAs in T. rubrum as well as dermatophytes. These results could serve as valuable resources for research on circRNA regulatory mechanisms in fungi and reveal new insights for further investigation of the physical characteristics of these significant human fungal pathogens. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08184-y.
Collapse
Affiliation(s)
- Xingwei Cao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Xingye Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Jie Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Ying Xue
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Lilian Sun
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Yafang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Tao Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.
| |
Collapse
|
4
|
Muzafar S, Sharma RD, Chauhan N, Prasad R. Intron distribution and emerging role of alternative splicing in fungi. FEMS Microbiol Lett 2021; 368:6414529. [PMID: 34718529 DOI: 10.1093/femsle/fnab135] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/28/2021] [Indexed: 12/16/2022] Open
Abstract
Spliceosomal introns are noncoding sequences that are spliced from pre-mRNA. They are ubiquitous in eukaryotic genomes, although the average number of introns per gene varies considerably between different eukaryotic species. Fungi are diverse in terms of intron numbers ranging from 4% to 99% genes with introns. Alternative splicing is one of the most common modes of posttranscriptional regulation in eukaryotes, giving rise to multiple transcripts from a single pre-mRNA and is widespread in metazoans and drives extensive proteome diversity. Earlier, alternative splicing was considered to be rare in fungi, but recently, increasing numbers of studies have revealed that alternative splicing is also widespread in fungi and has been implicated in the regulation of fungal growth and development, protein localization and the improvement of survivability, likely underlying their unique capacity to adapt to changing environmental conditions. However, the role of alternative splicing in pathogenicity and development of drug resistance is only recently gaining attention. In this review, we describe the intronic landscape in fungi. We also present in detail the newly discovered functions of alternative splicing in various cellular processes and outline areas particularly in pathogenesis and clinical drug resistance for future studies that could lead to the development of much needed new therapeutics.
Collapse
Affiliation(s)
- Suraya Muzafar
- Amity Institute of Integrative Sciences and Health, Amity University Gurgaon, Gurgaon 122413, Haryana, India
| | - Ravi Datta Sharma
- Amity Institute of Integrative Sciences and Health, Amity University Gurgaon, Gurgaon 122413, Haryana, India
| | - Neeraj Chauhan
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Rajendra Prasad
- Amity Institute of Integrative Sciences and Health, Amity University Gurgaon, Gurgaon 122413, Haryana, India
| |
Collapse
|
5
|
Li Z, Yang J, Peng J, Cheng Z, Liu X, Zhang Z, Bhadauria V, Zhao W, Peng YL. Transcriptional Landscapes of Long Non-coding RNAs and Alternative Splicing in Pyricularia oryzae Revealed by RNA-Seq. FRONTIERS IN PLANT SCIENCE 2021; 12:723636. [PMID: 34589103 PMCID: PMC8475275 DOI: 10.3389/fpls.2021.723636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Pyricularia oryzae causes the rice blast, which is one of the most devastating crop diseases worldwide, and is a model fungal pathogen widely used for dissecting the molecular mechanisms underlying fungal virulence/pathogenicity. Although the whole genome sequence of P. oryzae is publicly available, its current transcriptomes remain incomplete, lacking the information on non-protein coding genes and alternative splicing. Here, we performed and analyzed RNA-Seq of conidia and hyphae, resulting in the identification of 3,374 novel genes. Interestingly, the vast majority of these novel genes likely transcribed long non-coding RNAs (lncRNAs), and most of them were localized in the intergenic regions. Notably, their expressions were concomitant with the transcription of neighboring genes thereof in conidia and hyphae. In addition, 2,358 genes were found to undergo alternative splicing events. Furthermore, we exemplified that a lncRNA was important for hyphal growth likely by regulating the neighboring protein-coding gene and that alternative splicing of the transcription factor gene CON7 was required for appressorium formation. In summary, results from this study indicate that lncRNA transcripts and alternative splicing events are two important mechanisms for regulating the expression of genes important for conidiation, hyphal growth, and pathogenesis, and provide new insights into transcriptomes and gene regulation in the rice blast fungus.
Collapse
Affiliation(s)
- Zhigang Li
- College of Plant Protection/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jun Yang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Junbo Peng
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhihua Cheng
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xinsen Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Vijai Bhadauria
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Wensheng Zhao
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - You-Liang Peng
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| |
Collapse
|
6
|
Bühring S, Yemelin A, Michna T, Tenzer S, Jacob S. Evidence of a New MoYpd1p Phosphotransferase Isoform in the Multistep Phosphorelay System of Magnaporthe oryzae. J Fungi (Basel) 2021; 7:jof7050389. [PMID: 34063560 PMCID: PMC8156605 DOI: 10.3390/jof7050389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/05/2021] [Accepted: 05/14/2021] [Indexed: 01/01/2023] Open
Abstract
Different external stimuli are perceived by multiple sensor histidine kinases and transmitted by phosphorylation via the phosphotransfer protein Ypd1p in the multistep phosphorelay system of the high osmolarity glycerol signaling pathway of filamentous fungi. How the signal propagation takes place is still not known in detail since multiple sensor histidine kinase genes in most filamentous fungi are coded in the genome, whereas only one gene for Ypd1p exists. That raises the hypothesis that various Ypd1p isoforms are produced from a single gene sequence, perhaps by alternative splicing, facilitating a higher variability in signal transduction. We found that the mRNA of MoYPD1 in the rice blast fungus Magnaporthe oryzae is subjected to an increased structural variation and amplified putative isoforms on a cDNA level. We then generated mutant strains overexpressing these isoforms, purified the products, and present here one previously unknown MoYpd1p isoform on a proteome level. Alternative splicing was found to be a valid molecular mechanism to increase the signal diversity in eukaryotic multistep phosphorelay systems.
Collapse
Affiliation(s)
- Sri Bühring
- Institute for Biotechnology and Drug Research gGmbH, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; (S.B.); (A.Y.)
| | - Alexander Yemelin
- Institute for Biotechnology and Drug Research gGmbH, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; (S.B.); (A.Y.)
| | - Thomas Michna
- Institut für Immunologie, Universitätsmedizin der Johannes-Gutenberg Universität Mainz, Langenbeckstr. 1, 55131 Mainz, Germany; (T.M.); (S.T.)
| | - Stefan Tenzer
- Institut für Immunologie, Universitätsmedizin der Johannes-Gutenberg Universität Mainz, Langenbeckstr. 1, 55131 Mainz, Germany; (T.M.); (S.T.)
| | - Stefan Jacob
- Institute for Biotechnology and Drug Research gGmbH, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; (S.B.); (A.Y.)
- Correspondence:
| |
Collapse
|
7
|
Kumar S, Mutturi S. Alternative splicing regulates the α-glucosidase synthesis in Aspergillus neoniger NCIM 1400. Fungal Biol 2021; 125:658-665. [PMID: 34281659 DOI: 10.1016/j.funbio.2021.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 02/26/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
Aspergillus neoniger NCIM 1400 whose cell-free fraction was earlier established for transglycosylation activity conferred by α-glucosidase gene (agdA), was subjected to sequence analysis. Preliminary results revealed certain dynamics in the intron splicing mechanism, and to ascertain these molecular events, a detailed study was carried. The electrophoresis results from the cDNA portion (B-fragment) of agdA showed multiple bands, indicating the amplification of one or more fragments. The sequence results of cDNA cloned vector revealed the retention type of alternative splicing in the agdA. The splicing mechanism of agdA in NCIM 1400 was compared to different A. niger strains, which harbours agdA orthologues, using PCR. It was observed that effective intron splicing leads to higher α-glucosidase activity from these selected Aspergillus spp. To explore the dynamics of intron retention in A. neoniger NCIM 1400, time-course analysis of intron retention, enzyme activity, and sugar consumption were carried over a period of 168 h of fungal growth. RT-qPCR results revealed that introns retention was not detected during the initial growth phase when the maltose and its hydrolysed product, glucose were consumed. Here we demonstrate that exhaustion of maltose causes increase in retention of introns in the mRNA transcripts of agdA gene, and this could be the possible mode of regulating this gene.
Collapse
Affiliation(s)
- Sandeep Kumar
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, 570020, India; AcSIR-Academy of Scientific & Innovative Research, Ghaziabad, UP, 201002, India
| | - Sarma Mutturi
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, 570020, India; AcSIR-Academy of Scientific & Innovative Research, Ghaziabad, UP, 201002, India.
| |
Collapse
|
8
|
Rossi A, Martins MP, Bitencourt TA, Peres NTA, Rocha CHL, Rocha FMG, Neves-da-Rocha J, Lopes MER, Sanches PR, Bortolossi JC, Martinez-Rossi NM. Reassessing the Use of Undecanoic Acid as a Therapeutic Strategy for Treating Fungal Infections. Mycopathologia 2021; 186:327-340. [PMID: 33835367 DOI: 10.1007/s11046-021-00550-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/21/2021] [Indexed: 12/15/2022]
Abstract
Treating fungal infections is challenging and frequently requires long-term courses of antifungal drugs. Considering the limited number of existing antifungal drugs, it is crucial to evaluate the possibility of repositioning drugs with antifungal properties and to revisit older antifungals for applications in combined therapy, which could widen the range of therapeutic possibilities. Undecanoic acid is a saturated medium-chain fatty acid with known antifungal effects; however, its antifungal properties have not been extensively explored. Recent advances indicate that the toxic effect of undecanoic acid involves modulation of fungal metabolism through its effects on the expression of fungal genes that are critical for virulence. Additionally, undecanoic acid is suitable for chemical modification and might be useful in synergic therapies. This review highlights the use of undecanoic acid in antifungal treatments, reinforcing its known activity against dermatophytes. Specifically, in Trichophyton rubrum, against which the activity of undecanoic acid has been most widely studied, undecanoic acid elicits profound effects on pivotal processes in the cell wall, membrane assembly, lipid metabolism, pathogenesis, and even mRNA processing. Considering the known antifungal activities and associated mechanisms of undecanoic acid, its potential use in combination therapy, and the ability to modify the parent compound structure, undecanoic acid shows promise as a novel therapeutic against fungal infections.
Collapse
Affiliation(s)
- Antonio Rossi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, USP, Ribeirão Preto, SP, 14049-900, Brazil
| | - Maíra P Martins
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, USP, Ribeirão Preto, SP, 14049-900, Brazil
| | - Tamires A Bitencourt
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, USP, Ribeirão Preto, SP, 14049-900, Brazil
| | - Nalu T A Peres
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Carlos H L Rocha
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, USP, Ribeirão Preto, SP, 14049-900, Brazil
| | - Flaviane M G Rocha
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, USP, Ribeirão Preto, SP, 14049-900, Brazil
| | - João Neves-da-Rocha
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, USP, Ribeirão Preto, SP, 14049-900, Brazil
| | - Marcos E R Lopes
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, USP, Ribeirão Preto, SP, 14049-900, Brazil
| | - Pablo R Sanches
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, USP, Ribeirão Preto, SP, 14049-900, Brazil
| | - Júlio C Bortolossi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, USP, Ribeirão Preto, SP, 14049-900, Brazil
| | - Nilce M Martinez-Rossi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, USP, Ribeirão Preto, SP, 14049-900, Brazil.
| |
Collapse
|
9
|
Lim CS, Weinstein BN, Roy SW, Brown CM. Analysis of fungal genomes reveals commonalities of intron gain or loss and functions in intron-poor species. Mol Biol Evol 2021; 38:4166-4186. [PMID: 33772558 PMCID: PMC8476143 DOI: 10.1093/molbev/msab094] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Previous evolutionary reconstructions have concluded that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had intron-rich genomes. By contrast, some extant eukaryotes have few introns, underscoring the complex histories of intron–exon structures, and raising the question as to why these few introns are retained. Here, we have used recently available fungal genomes to address a variety of questions related to intron evolution. Evolutionary reconstruction of intron presence and absence using 263 diverse fungal species supports the idea that massive intron reduction through intron loss has occurred in multiple clades. The intron densities estimated in various fungal ancestors differ from zero to 7.6 introns per 1 kb of protein-coding sequence. Massive intron loss has occurred not only in microsporidian parasites and saccharomycetous yeasts, but also in diverse smuts and allies. To investigate the roles of the remaining introns in highly-reduced species, we have searched for their special characteristics in eight intron-poor fungi. Notably, the introns of ribosome-associated genes RPL7 and NOG2 have conserved positions; both intron-containing genes encoding snoRNAs. Furthermore, both the proteins and snoRNAs are involved in ribosome biogenesis, suggesting that the expression of the protein-coding genes and noncoding snoRNAs may be functionally coordinated. Indeed, these introns are also conserved in three-quarters of fungi species. Our study shows that fungal introns have a complex evolutionary history and underappreciated roles in gene expression.
Collapse
Affiliation(s)
- Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Brooke N Weinstein
- Quantitative & Systems Biology, School of Natural Sciences, University of California-Merced, Merced, CA, USA.,Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Scott W Roy
- Quantitative & Systems Biology, School of Natural Sciences, University of California-Merced, Merced, CA, USA.,Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Chris M Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| |
Collapse
|
10
|
Fang S, Hou X, Qiu K, He R, Feng X, Liang X. The occurrence and function of alternative splicing in fungi. FUNGAL BIOL REV 2020. [DOI: 10.1016/j.fbr.2020.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
11
|
Barth E, Sieber P, Stark H, Schuster S. Robustness during Aging-Molecular Biological and Physiological Aspects. Cells 2020; 9:E1862. [PMID: 32784503 PMCID: PMC7465392 DOI: 10.3390/cells9081862] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/27/2020] [Accepted: 08/05/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding the process of aging is still an important challenge to enable healthy aging and to prevent age-related diseases. Most studies in age research investigate the decline in organ functionality and gene activity with age. The focus on decline can even be considered a paradigm in that field. However, there are certain aspects that remain surprisingly stable and keep the organism robust. Here, we present and discuss various properties of robust behavior during human and animal aging, including physiological and molecular biological features, such as the hematocrit, body temperature, immunity against infectious diseases and others. We examine, in the context of robustness, the different theories of how aging occurs. We regard the role of aging in the light of evolution.
Collapse
Affiliation(s)
- Emanuel Barth
- RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Patricia Sieber
- Matthias Schleiden Institute, Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Heiko Stark
- Institute of Zoology and Evolutionary Research with Phyletic Museum, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Stefan Schuster
- Matthias Schleiden Institute, Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany;
| |
Collapse
|
12
|
Global identification of alternative splicing in Shiraia bambusicola and analysis of its regulation in hypocrellin biosynthesis. Appl Microbiol Biotechnol 2019; 104:211-223. [PMID: 31768612 DOI: 10.1007/s00253-019-10189-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/21/2019] [Accepted: 10/03/2019] [Indexed: 01/24/2023]
Abstract
Hypocrellins, as natural pigments from Shiraia bambusicola, have extensive applications in the agricultural, cosmetic, food, and feed industries, and play a vital role in photodynamic therapy for anticancer and antiviral treatments. However, environmental stresses are always the bottlenecks for increasing hypocrellin yield during the process of fermentation. Pre-mRNA alternative splicing (AS) is an essential mechanism in the defense of abiotic stresses in the animal and plant kingdom, but is seldom involved in fungi. In this study, AS from genome-wide sequencing and RNA-seq data for S. bambusicola was analyzed for the first time. Interestingly, the proportion of AS in S. bambusicola was 38.44% (most of them participated in metabolic processes, covering pigmentation and response to stimulus), a much higher ratio than seen in that of other fungal species (1.3-18%). Here, we identified the relationship of AS and secondary metabolic (SM) biosynthesis under a series of abiotic stresses. Suitable fungicides suppressed hypocrellin production significantly, and AS occurred in key functional genes (sbFLO, sbMFS, sbPKS) of hypocrellin biosynthesis. In contrast, H2O2 improved the yield of hypocrellins, but AS were not found in the corresponding gene cluster. A further study showed that overexpressing an isoform of sbPKS (sbPKSa) in Shiraia bambusicola could dramatically down-regulate the expression of the original gene sbPKS and nearly inhibit the production of hypocrellins. Altogether, our study strongly supported the hypothesis that AS had a vital role in the regulation of hypocrellin biosynthesis under stresses, and initially explored whether SM functional genes were relevant for fungi.
Collapse
|
13
|
Alternative Splicing in Heat Shock Protein Transcripts as a Mechanism of Cell Adaptation in Trichophyton rubrum. Cells 2019; 8:cells8101206. [PMID: 31590387 PMCID: PMC6830096 DOI: 10.3390/cells8101206] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/27/2019] [Accepted: 10/02/2019] [Indexed: 12/16/2022] Open
Abstract
Heat shock proteins (HSPs) are involved in critical processes like host tissue invasion, resistance, and pathogenicity in dermatophytes. RNA-Seq analysis of Trichophyton rubrum exposed to undecanoic acid (UDA) revealed intron retention events in HSP transcripts. Because HSPs are modulated in response to various stimuli and as alternative splicing (AS) can result in a broad diversity in the proteome of eukaryotic cells, our objective was to confirm the aforementioned retention events, investigating their consequences and extent. Furthermore, we aimed to determine: (1) the expression profile of HSP genes in an infection-like scenario and (2) the importance of Hsp90 for the keratinolytic potential of T. rubrum. RT and qPCR analyses comparing the exposure to UDA and terbinafine (TRB) confirmed the presence of two mRNA isoforms of the hsp7-like gene, with distinct expression patterns in response to UDA and TRB. The HSP expression profile revealed two upregulated, three downregulated, and four unmodulated transcripts; Hsp90 inhibition by 17-AAG resulted in a significant decrease in keratinolytic potential at 37 °C. Altogether, these results broaden the current knowledge on the importance of HSP-mediated pathways for cell adaptation and other aspects of dermatophyte biology, indicating that HSP network proteins can be potential targets for antifungal therapy.
Collapse
|
14
|
Alternative Splicing of the Aflatoxin-Associated Baeyer⁻Villiger Monooxygenase from Aspergillus flavus: Characterisation of MoxY Isoforms. Toxins (Basel) 2018; 10:toxins10120521. [PMID: 30563144 PMCID: PMC6315744 DOI: 10.3390/toxins10120521] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/01/2018] [Accepted: 12/03/2018] [Indexed: 01/24/2023] Open
Abstract
Aflatoxins are carcinogenic mycotoxins that are produced by the filamentous fungus Aspergillus flavus, a contaminant of numerous food crops. Aflatoxins are synthesised via the aflatoxin biosynthesis pathway, with the enzymes involved encoded by the aflatoxin biosynthesis gene cluster. MoxY is a type I Baeyer–Villiger monooxygenase (BVMO), responsible for the conversion of hydroxyversicolorone (HVN) and versicolorone (VN) to versiconal hemiacetal acetate (VHA) and versiconol acetate (VOAc), respectively. Using mRNA data, an intron near the C-terminus was identified that is alternatively spliced, creating two possible MoxY isoforms which exist in vivo, while analysis of the genomic DNA suggests an alternative start codon leading to possible elongation of the N-terminus. These four variants of the moxY gene were recombinantly expressed in Escherichia coli, and their activity evaluated with respect to their natural substrates HVN and VN, as well as surrogate ketone substrates. Activity of the enzyme is absolutely dependent on the additional 22 amino acid residues at the N-terminus. Two MoxY isoforms with alternative C-termini, MoxYAltN and MoxYAltNC, converted HVN and VN, in addition to a range of ketone substrates. Stability and flavin-binding data suggest that MoxYAltN is, most likely, the dominant isoform. MoxYAltNC is generated by intron splicing, in contrast to intron retention, which is the most prevalent type of alternative splicing in ascomycetes. The alternative C-termini did not alter the substrate acceptance profile, or regio- or enantioselectivity of the enzyme, but did significantly affect the solubility and stability.
Collapse
|
15
|
Sieber P, Voigt K, Kämmer P, Brunke S, Schuster S, Linde J. Comparative Study on Alternative Splicing in Human Fungal Pathogens Suggests Its Involvement During Host Invasion. Front Microbiol 2018; 9:2313. [PMID: 30333805 PMCID: PMC6176087 DOI: 10.3389/fmicb.2018.02313] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 09/11/2018] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing (AS) is an important regulatory mechanism in eukaryotes but only little is known about its impact in fungi. Human fungal pathogens are of high clinical interest causing recurrent or life-threatening infections. AS can be well-investigated genome-wide and quantitatively with the powerful technology of RNA-Seq. Here, we systematically studied AS in human fungal pathogens based on RNA-Seq data. To do so, we investigated its effect in seven fungi during conditions simulating ex vivo infection processes and during in vitro stress. Genes undergoing AS are species-specific and act independently from differentially expressed genes pointing to an independent mechanism to change abundance and functionality. Candida species stand out with a low number of introns with higher and more varying lengths and more alternative splice sites. Moreover, we identified a functional difference between response to host and other stress conditions: During stress, AS affects more genes and is involved in diverse regulatory functions. In contrast, during response-to-host conditions, genes undergoing AS have membrane functionalities and might be involved in the interaction with the host. We assume that AS plays a crucial regulatory role in pathogenic fungi and is important in both response to host and stress conditions.
Collapse
Affiliation(s)
- Patricia Sieber
- Department of Bioinformatics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany.,Research Group Systems Biology, Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Kerstin Voigt
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Philipp Kämmer
- Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Sascha Brunke
- Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Jörg Linde
- Research Group PiDOMICS, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Institute for Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health-Friedrich-Loeffler-Institute, Jena, Germany
| |
Collapse
|
16
|
Nowrousian M. Genomics and transcriptomics to study fruiting body development: An update. FUNGAL BIOL REV 2018. [DOI: 10.1016/j.fbr.2018.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
17
|
Freitag J, Stehlik T, Stiebler AC, Bölker M. The Obvious and the Hidden: Prediction and Function of Fungal Peroxisomal Matrix Proteins. Subcell Biochem 2018; 89:139-155. [PMID: 30378022 DOI: 10.1007/978-981-13-2233-4_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fungal peroxisomes are characterized by a number of specific biological functions. To understand the physiology and biochemistry of these organelles knowledge of the proteome content is crucial. Here, we address different strategies to predict peroxisomal proteins by bioinformatics approaches. These tools range from simple text searches to network based learning strategies. A complication of this analysis is the existence of cryptic peroxisomal proteins, which are overlooked in conventional bioinformatics queries. These include proteins where targeting information results from transcriptional and posttranscriptional alterations. But also proteins with low efficiency targeting motifs that are predominantly localized in the cytosol, and proteins lacking any canonical targeting information, can play important roles within peroxisomes. Many of these proteins are so far unpredictable. Detection and characterization of these cryptic peroxisomal proteins revealed the presence of novel peroxisomal enzymatic reaction networks in fungi.
Collapse
Affiliation(s)
- Johannes Freitag
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Thorsten Stehlik
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Alina C Stiebler
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Michael Bölker
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany.
| |
Collapse
|
18
|
Dong WX, Ding JL, Gao Y, Peng YJ, Feng MG, Ying SH. Transcriptomic insights into the alternative splicing-mediated adaptation of the entomopathogenic fungus Beauveria bassiana
to host niches: autophagy-related gene 8 as an example. Environ Microbiol 2017; 19:4126-4139. [DOI: 10.1111/1462-2920.13862] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 07/16/2017] [Accepted: 07/16/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Wei-Xia Dong
- Institute of Microbiology, College of Life Sciences, Zhejiang University; Hangzhou 310058 China
| | - Jin-Li Ding
- Institute of Microbiology, College of Life Sciences, Zhejiang University; Hangzhou 310058 China
| | - Yang Gao
- Institute of Microbiology, College of Life Sciences, Zhejiang University; Hangzhou 310058 China
| | - Yue-Jin Peng
- Institute of Microbiology, College of Life Sciences, Zhejiang University; Hangzhou 310058 China
| | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University; Hangzhou 310058 China
| | - Sheng-Hua Ying
- Institute of Microbiology, College of Life Sciences, Zhejiang University; Hangzhou 310058 China
| |
Collapse
|
19
|
Workflow for Genome-Wide Determination of Pre-mRNA Splicing Efficiency from Yeast RNA-seq Data. BIOMED RESEARCH INTERNATIONAL 2016; 2016:4783841. [PMID: 28050562 PMCID: PMC5168555 DOI: 10.1155/2016/4783841] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/02/2016] [Indexed: 11/17/2022]
Abstract
Pre-mRNA splicing represents an important regulatory layer of eukaryotic gene expression. In the simple budding yeast Saccharomyces cerevisiae, about one-third of all mRNA molecules undergo splicing, and splicing efficiency is tightly regulated, for example, during meiotic differentiation. S. cerevisiae features a streamlined, evolutionarily highly conserved splicing machinery and serves as a favourite model for studies of various aspects of splicing. RNA-seq represents a robust, versatile, and affordable technique for transcriptome interrogation, which can also be used to study splicing efficiency. However, convenient bioinformatics tools for the analysis of splicing efficiency from yeast RNA-seq data are lacking. We present a complete workflow for the calculation of genome-wide splicing efficiency in S. cerevisiae using strand-specific RNA-seq data. Our pipeline takes sequencing reads in the FASTQ format and provides splicing efficiency values for the 5′ and 3′ splice junctions of each intron. The pipeline is based on up-to-date open-source software tools and requires very limited input from the user. We provide all relevant scripts in a ready-to-use form. We demonstrate the functionality of the workflow using RNA-seq datasets from three spliceosome mutants. The workflow should prove useful for studies of yeast splicing mutants or of regulated splicing, for example, under specific growth conditions.
Collapse
|
20
|
Mendes NS, Silva PM, Silva-Rocha R, Martinez-Rossi NM, Rossi A. Pre-mRNA splicing is modulated by antifungal drugs in the filamentous fungus Neurospora crassa. FEBS Open Bio 2016; 6:358-68. [PMID: 27239448 PMCID: PMC4821360 DOI: 10.1002/2211-5463.12047] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 02/10/2016] [Accepted: 02/15/2016] [Indexed: 11/17/2022] Open
Abstract
For this study, we sought to identify pre‐mRNA processing events modulated by changes in extracellular pH, inorganic phosphate, and antifungal drugs. We examined genes with at least four putative introns whose transcriptional level responded to these effectors. We showed that the intron retention levels of genes encoding asparagine synthetase 2, C6‐zinc finger regulator (fluffy), and a farnesyltransferase respond to amphotericin B, ketoconazole, and other effectors. In general, the assayed antifungals promoted the disruption of the structural domains of these proteins probably leading to their inactivation, which emphasize the complexity of the metabolic modulation exerted by antifungal signaling.
Collapse
Affiliation(s)
- Niege S Mendes
- Department of Genetics Ribeirão Preto Medical School University of São Paulo Ribeirão Preto SP Brazil
| | - Patricia M Silva
- Department of Genetics Ribeirão Preto Medical School University of São Paulo Ribeirão Preto SP Brazil
| | - Rafael Silva-Rocha
- Department of Molecular and Cellular Biology Ribeirão Preto Medical School University of São Paulo Ribeirão Preto SP Brazil
| | - Nilce M Martinez-Rossi
- Department of Genetics Ribeirão Preto Medical School University of São Paulo Ribeirão Preto SP Brazil
| | - Antonio Rossi
- Department of Genetics Ribeirão Preto Medical School University of São Paulo Ribeirão Preto SP Brazil
| |
Collapse
|
21
|
Al-Rasheed MM, Alzahrani AS, Macadam A, Overall A, Gard P, Dzimiri N. The potential role of the sodium iodide symporter gene polymorphism in the development of differentiated thyroid cancer. Gene 2015; 572:163-8. [PMID: 26160439 DOI: 10.1016/j.gene.2015.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 06/05/2015] [Accepted: 07/02/2015] [Indexed: 01/09/2023]
Abstract
The sodium iodide symporter (NIS) (solute carrier family 5; SLC5A), mediates the active transport of iodine anion (I(-)) into thyroid follicular cells to facilitate thyroid hormone biosynthesis. Considering its fundamental role in thyroid function, our objective in this study is to explore its potential involvement in the pathogenesis of differentiated thyroid cancer (DTC). Following a preliminary sequencing of the gene in a representative sample of the general population, five variants, (1) rs45602038, (2) rs4808708, (3) rs4808709, (4) rs7250346 and (5) rs12327843, were selected for a larger population-based association study consisting of 507 cases and 597 controls, of which only the rs45602038_TT [Odds ratio (95% confidence interval)=1.90 (1.26-2.88); p=0.002] was associated with disease following adjustment for other confounders using the multivariate analysis. Furthermore, a 5-mer haplotype CGAGT constructed from the five studied SNPs conferred a significant risk (χ(2)=10.98; p=0.0009) for DTC. This association trickled down through shorter derivatives, with the 4-mer haplotype CGAG (χ(2)=13.25; p=0.0003) displaying the most significant association and the 3-mer GAG (χ(2)=11.80; p=0.0006) being equally strongly linked to the disease. Comparison of the flanking derivatives of the primary 5-mer haplotype also indicated that the 3-mer CGA (χ(2)=4.04; p=0.045) constructed from SNP block 1-3 was a lot weaker than that of the AGT (χ(2)=6.73; p=0.0095) constructed from the blocks 3-5 from the other end of the gene. Put together, these data implicate the three nucleotide changes at the rs4808708, rs4808709 and rs7250346 loci (blocks 2-4) as the core for this relationship.
Collapse
Affiliation(s)
- Maha M Al-Rasheed
- Clinical Pharmacy Department, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia; King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK.
| | - Ali S Alzahrani
- King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia.
| | - Angela Macadam
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK.
| | - Andrew Overall
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK.
| | - Paul Gard
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK.
| | - Nduna Dzimiri
- King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia.
| |
Collapse
|
22
|
Ág N, Flipphi M, Karaffa L, Scazzocchio C, Fekete E. Alternatively spliced, spliceosomal twin introns in Helminthosporium solani. Fungal Genet Biol 2015; 85:7-13. [PMID: 26514742 DOI: 10.1016/j.fgb.2015.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 10/23/2015] [Accepted: 10/24/2015] [Indexed: 11/24/2022]
Abstract
Spliceosomal twin introns, "stwintrons", have been defined as complex intervening sequences that carry a second intron ("internal intron") interrupting one of the conserved sequence domains necessary for their correct splicing via consecutive excision events. Previously, we have described and experimentally verified stwintrons in species of Sordariomycetes, where an "internal intron" interrupted the donor sequence of an "external intron". Here we describe and experimentally verify two novel stwintrons of the potato pathogen Helminthosporium solani. One instance involves alternative splicing of an internal intron interrupting the donor domain of an external intron and a second one interrupting the acceptor domain of an overlapping external intron, both events leading to identical mature mRNAs. In the second case, an internal intron interrupts the donor domain of the external intron, while an alternatively spliced intron leads to an mRNA carrying a premature chain termination codon. We thus extend the stwintron concept to the acceptor domain and establish a link of the occurrence of stwintrons with that of alternative splicing.
Collapse
Affiliation(s)
- Norbert Ág
- Dept. of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary
| | - Michel Flipphi
- Dept. of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary.
| | - Levente Karaffa
- Dept. of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary
| | - Claudio Scazzocchio
- Dept. of Microbiology, Imperial College, London SW7 2AZ, United Kingdom; Institut de Biologie Intégrative de la Cellule (I2BC), UMR CEA/CNRS/Université Paris-Sud, 91405 Orsay Cedex, France
| | - Erzsébet Fekete
- Dept. of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary
| |
Collapse
|
23
|
Ulrich A, Wahl MC. Structure and evolution of the spliceosomal peptidyl-prolyl cis-trans isomerase Cwc27. ACTA ACUST UNITED AC 2014; 70:3110-23. [PMID: 25478830 DOI: 10.1107/s1399004714021695] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 10/01/2014] [Indexed: 11/10/2022]
Abstract
Cwc27 is a spliceosomal cyclophilin-type peptidyl-prolyl cis-trans isomerase (PPIase). Here, the crystal structure of a relatively protease-resistant N-terminal fragment of human Cwc27 containing the PPIase domain was determined at 2.0 Å resolution. The fragment exhibits a C-terminal appendix and resides in a reduced state compared with the previous oxidized structure of a similar fragment. By combining multiple sequence alignments spanning the eukaryotic tree of life and secondary-structure prediction, Cwc27 proteins across the entire eukaryotic kingdom were identified. This analysis revealed the specific loss of a crucial active-site residue in higher eukaryotic Cwc27 proteins, suggesting that the protein evolved from a prolyl isomerase to a pure proline binder. Noting a fungus-specific insertion in the PPIase domain, the 1.3 Å resolution crystal structure of the PPIase domain of Cwc27 from Chaetomium thermophilum was also determined. Although structurally highly similar in the core domain, the C. thermophilum protein displayed a higher thermal stability than its human counterpart, presumably owing to the combined effect of several amino-acid exchanges that reduce the number of long side chains with strained conformations and create new intramolecular interactions, in particular increased hydrogen-bond networks.
Collapse
Affiliation(s)
- Alexander Ulrich
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Markus C Wahl
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| |
Collapse
|
24
|
Meijueiro ML, Santoyo F, Ramirez L, Pisabarro AG. Transcriptome characteristics of filamentous fungi deduced using high-throughput analytical technologies. Brief Funct Genomics 2014; 13:440-50. [DOI: 10.1093/bfgp/elu033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
|
25
|
Ishida K, Kuboshima M, Morita H, Maeda H, Okamoto A, Takeuchi M, Yamagata Y. Diversity in mRNA expression of the serine-type carboxypeptidase ocpG in Aspergillus oryzae through intron retention. Biosci Biotechnol Biochem 2014; 78:1328-36. [PMID: 25130734 DOI: 10.1080/09168451.2014.923291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Alternative splicing is thought to be a means for diversification of products by mRNA modification. Although some intron retentions are predicted by transcriptome analysis in Aspergillus oryzae, its physiological significance remains unknown. We found that intron retention occurred occasionally in the serine-type carboxypeptidase gene, ocpG. Analysis under various culture conditions revealed that extracellular nitrogen conditions influence splicing patterns; this suggested that there might be a correlation between splicing efficiency and the necessity of OcpG activity for obtaining a nitrogen source. Since further analysis showed that splicing occurred independently in each intron, we constructed ocpG intron-exchanging strain by interchanging the positions of intron-1 and intron-2. The splicing pattern indicated the probability that ocpG intron retention was affected by the secondary structures of intronic mRNA.
Collapse
Affiliation(s)
- Ken Ishida
- a Department of Agriscience and Bioscience , Tokyo University of Agriculture and Technology , Tokyo , Japan
| | | | | | | | | | | | | |
Collapse
|
26
|
Kollath-Leiß K, Bönniger C, Sardar P, Kempken F. BEM46 shows eisosomal localization and association with tryptophan-derived auxin pathway in Neurospora crassa. EUKARYOTIC CELL 2014; 13:1051-63. [PMID: 24928924 PMCID: PMC4135797 DOI: 10.1128/ec.00061-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/06/2014] [Indexed: 11/20/2022]
Abstract
BEM46 proteins are evolutionarily conserved, but their functions remain elusive. We reported previously that the BEM46 protein in Neurospora crassa is targeted to the endoplasmic reticulum (ER) and is essential for ascospore germination. In the present study, we established a bem46 knockout strain of N. crassa. This Δbem46 mutant exhibited a level of ascospore germination lower than that of the wild type but much higher than those of the previously characterized bem46-overexpressing and RNA interference (RNAi) lines. Reinvestigation of the RNAi transformants revealed two types of alternatively spliced bem46 mRNA; expression of either type led to a loss of ascospore germination. Our results indicated that the phenotype was not due to bem46 mRNA downregulation or loss but was caused by the alternatively spliced mRNAs and the peptides they encoded. Using the N. crassa ortholog of the eisosomal protein PILA from Aspergillus nidulans, we further demonstrated the colocalization of BEM46 with eisosomes. Employing the yeast two-hybrid system, we identified a single interaction partner: anthranilate synthase component II (encoded by trp-1). This interaction was confirmed in vivo by a split-YFP (yellow fluorescent protein) approach. The Δtrp-1 mutant showed reduced ascospore germination and increased indole production, and we used bioinformatic tools to identify a putative auxin biosynthetic pathway. The genes involved exhibited various levels of transcriptional regulation in the different bem46 transformant and mutant strains. We also investigated the indole production of the strains in different developmental stages. Our findings suggested that the regulation of indole biosynthesis genes was influenced by bem46 overexpression. Furthermore, we uncovered evidence of colocalization of BEM46 with the neutral amino acid transporter MTR.
Collapse
Affiliation(s)
- K Kollath-Leiß
- Abteilung Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - C Bönniger
- Abteilung Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - P Sardar
- Abteilung Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - F Kempken
- Abteilung Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| |
Collapse
|