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IJMS
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Transcriptome and Proteome Analysis of Fungi
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Transcriptome and Proteome Analysis of Fungi

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (30 July 2024) | Viewed by 1881

Special Issue Editor

Prof. Dr. Antonio Pisabarro

E-Mail Website
Guest Editor
Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006 Pamplona, Spain
Interests: fungal genome; transcriptome and proteome analysis; fungal biotechnology; fungal metabolism; infectious diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Advancements in genomic, transcriptomic, and proteomic analyses yield an expanding data stream, often surpassing personal handling capacity. The abundance of details hinders a comprehensive view. Typically, we operate within the paradigm of one gene, one enzyme, one function, or, at best, many genes, many enzymes, and many functions. However, integrative analysis methods lack comprehensive insights into biological processes. While we can read, our comprehension is limited. In recent years, remarkable progress has unfolded in two thriving scientific fields: data science and artificial intelligence. In this Special Issue of IJMS, we aim to explore the intersection of transcriptomics and proteomics in the emerging landscape of data science and artificial intelligence. We invite researchers to submit innovative works to contribute to this melting pot. To achieve this, we focus on fungi as biologically complex yet manageable systems, considering their genome size and developmental processes.

Prof. Dr. Antonio Pisabarro
Guest Editor

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Keywords

  • transcriptomic
  • proteomic
  • fungi

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Published Papers (3 papers)

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Research

15 pages, 1613 KiB  
Article
Highly Repetitive Genome of Coniella granati (syn. Pilidiella granati), the Causal Agent of Pomegranate Fruit Rot, Encodes a Minimalistic Proteome with a Streamlined Arsenal of Effector Proteins
by Antonios Zambounis, Elisseos I. Maniatis, Annamaria Mincuzzi, Naomi Gray, Mohitul Hossain, Dimitrios I. Tsitsigiannis, Epaminondas Paplomatas, Antonio Ippolito, Leonardo Schena and James K. Hane
Int. J. Mol. Sci. 2024, 25(18), 9997; https://doi.org/10.3390/ijms25189997 - 17 Sep 2024
Viewed by 546
Abstract
This study describes the first genome sequence and analysis of Coniella granati, a fungal pathogen with a broad host range, which is responsible for postharvest crown rot, shoot blight, and canker diseases in pomegranates. C. granati is a geographically widespread pathogen which [...] Read more.
This study describes the first genome sequence and analysis of Coniella granati, a fungal pathogen with a broad host range, which is responsible for postharvest crown rot, shoot blight, and canker diseases in pomegranates. C. granati is a geographically widespread pathogen which has been reported across Europe, Asia, the Americas, and Africa. Our analysis revealed a 46.8 Mb genome with features characteristic of hemibiotrophic fungi. Approximately one third of its genome was compartmentalised within ‘AT-rich’ regions exhibiting a low GC content (30 to 45%). These regions primarily comprised transposable elements that are repeated at a high frequency and interspersed throughout the genome. Transcriptome-supported gene annotation of the C. granati genome revealed a streamlined proteome, mirroring similar observations in other pathogens with a latent phase. The genome encoded a relatively compact set of 9568 protein-coding genes with a remarkable 95% having assigned functional annotations. Despite this streamlined nature, a set of 40 cysteine-rich candidate secreted effector-like proteins (CSEPs) was predicted as well as a gene cluster involved in the synthesis of a pomegranate-associated toxin. These potential virulence factors were predominantly located near repeat-rich and AT-rich regions, suggesting that the pathogen evades host defences through Repeat-Induced Point mutation (RIP)-mediated pseudogenisation. Furthermore, 23 of these CSEPs exhibited homology to known effector and pathogenicity genes found in other hemibiotrophic pathogens. The study establishes a foundational resource for the study of the genetic makeup of C. granati, paving the way for future research on its pathogenicity mechanisms and the development of targeted control strategies to safeguard pomegranate production. Full article
(This article belongs to the Special Issue Transcriptome and Proteome Analysis of Fungi)
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25 pages, 1439 KiB  
Article
An Interplay between Transcription Factors and Recombinant Protein Synthesis in Yarrowia lipolytica at Transcriptional and Functional Levels—The Global View
by Maria Gorczyca, Paulina Korpys-Woźniak and Ewelina Celińska
Int. J. Mol. Sci. 2024, 25(17), 9450; https://doi.org/10.3390/ijms25179450 - 30 Aug 2024
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Abstract
Transcriptional regulatory networks (TRNs) associated with recombinant protein (rProt) synthesis in Yarrowia lipolytica are still under-described. Yet, it is foreseen that skillful manipulation with TRNs would enable global fine-tuning of the host strain’s metabolism towards a high-level-producing phenotype. Our previous studies investigated the [...] Read more.
Transcriptional regulatory networks (TRNs) associated with recombinant protein (rProt) synthesis in Yarrowia lipolytica are still under-described. Yet, it is foreseen that skillful manipulation with TRNs would enable global fine-tuning of the host strain’s metabolism towards a high-level-producing phenotype. Our previous studies investigated the transcriptomes of Y. lipolytica strains overproducing biochemically different rProts and the functional impact of transcription factors (TFs) overexpression (OE) on rProt synthesis capacity in this species. Hence, much knowledge has been accumulated and deposited in public repositories. In this study, we combined both biological datasets and enriched them with further experimental data to investigate an interplay between TFs and rProts synthesis in Y. lipolytica at transcriptional and functional levels. Technically, the RNAseq datasets were extracted and re-analyzed for the TFs’ expression profiles. Of the 140 TFs in Y. lipolytica, 87 TF-encoding genes were significantly deregulated in at least one of the strains. The expression profiles were juxtaposed against the rProt amounts from 125 strains co-overexpressing TF and rProt. In addition, several strains bearing knock-outs (KOs) in the TF loci were analyzed to get more insight into their actual involvement in rProt synthesis. Different profiles of the TFs’ transcriptional deregulation and the impact of their OE or KO on rProts synthesis were observed, and new engineering targets were pointed. Full article
(This article belongs to the Special Issue Transcriptome and Proteome Analysis of Fungi)
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22 pages, 1528 KiB  
Article
Strategies to Maintain Redox Homeostasis in Yeast Cells with Impaired Fermentation-Dependent NADPH Generation
by Magdalena Kwolek-Mirek, Roman Maslanka, Sabina Bednarska, Michał Przywara, Kornelia Kwolek and Renata Zadrag-Tecza
Int. J. Mol. Sci. 2024, 25(17), 9296; https://doi.org/10.3390/ijms25179296 - 27 Aug 2024
Viewed by 587
Abstract
Redox homeostasis is the balance between oxidation and reduction reactions. Its maintenance depends on glutathione, including its reduced and oxidized form, GSH/GSSG, which is the main intracellular redox buffer, but also on the nicotinamide adenine dinucleotide phosphate, including its reduced and oxidized form, [...] Read more.
Redox homeostasis is the balance between oxidation and reduction reactions. Its maintenance depends on glutathione, including its reduced and oxidized form, GSH/GSSG, which is the main intracellular redox buffer, but also on the nicotinamide adenine dinucleotide phosphate, including its reduced and oxidized form, NADPH/NADP+. Under conditions that enable yeast cells to undergo fermentative metabolism, the main source of NADPH is the pentose phosphate pathway. The lack of enzymes responsible for the production of NADPH has a significant impact on yeast cells. However, cells may compensate in different ways for impairments in NADPH synthesis, and the choice of compensation strategy has several consequences for cell functioning. The present study of this issue was based on isogenic mutants: Δzwf1, Δgnd1, Δald6, and the wild strain, as well as a comprehensive panel of molecular analyses such as the level of gene expression, protein content, and enzyme activity. The obtained results indicate that yeast cells compensate for the lack of enzymes responsible for the production of cytosolic NADPH by changing the content of selected proteins and/or their enzymatic activity. In turn, the cellular strategy used to compensate for them may affect cellular efficiency, and thus, the ability to grow or sensitivity to environmental acidification. Full article
(This article belongs to the Special Issue Transcriptome and Proteome Analysis of Fungi)
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