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Omics Approaches in Trichoderma Research
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Omics Approaches in Trichoderma Research

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Genomics, Genetics and Molecular Biology".

Deadline for manuscript submissions: closed (31 October 2024) | Viewed by 771

Special Issue Editors

Dr. Artemio Mendoza-Mendoza

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Guest Editor
Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
Interests: signalling; biocontrol; plant–microbe interactions; molecular biology; biochemistry; cell biology; microbial bioactive compounds; Trichoderma
Special Issues, Collections and Topics in MDPI journals
Dr. José M. Villalobos-Escobedo

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Guest Editor
Plant and Microbial Biology, University of California, Berkeley, CA, USA
Interests: Trichoderma and how they interact with their plant hosts

Special Issue Information

Dear Colleagues,

Trichoderma spp. are cosmopolitan fungi with infinite plasticity to interact with diverse organisms, including bacteria, fungi, oomycetes, nematodes, and plants. Trichoderma spp. induce abiotic and biotic stress protection in plants by using different mechanisms that can be direct or indirect. Trichoderma is an excellent model for studying differentiation, cell wall degrading enzyme production, mycoparasitism, and secondary metabolism production. 

The Journal of Fungi is pleased to announce a Special Issue on "Omics Approaches in Trichoderma Research" and welcomes original, high-quality papers in research articles, reviews, and short communications. This Special Issue covers a wide range of research where omics tools are applied to understand the biology of Trichoderma. These omics can include but are not limited to whole genome sequencing (WGS), transcriptomics, proteomics, metabolomics, epigenomics, metatranscriptomics, and metagenomics in complex systems to understand the microbial association of Trichoderma with other microorganisms, for example.   

Dr. Artemio Mendoza
Dr. José M. Villalobos-Escobedo
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Journal of Fungi is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Trichoderma
  • genomics
  • transcriptomics
  • proteomics
  • metabolomics
  • ISR
  • rhizospheric microbial community
  • biocontrol
  • mycoparasitism
  • Trichoderma–plant interaction
  • cell-wall degrading enzymes
  • suppressive soils
  • conidiation

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Further information on MDPI's Special Issue polices can be found here.

Published Papers (1 paper)

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Research

25 pages, 5613 KiB  
Article
Regulatory Role of Vacuolar Calcium Transport Proteins in Growth, Calcium Signaling, and Cellulase Production in Trichoderma reesei
by Letícia Harumi Oshiquiri, Lucas Matheus Soares Pereira, David Batista Maués, Elizabete Rosa Milani, Alinne Costa Silva, Luiz Felipe de Morais Costa de Jesus, Julio Alves Silva-Neto, Flávio Protásio Veras, Renato Graciano de Paula and Roberto Nascimento Silva
J. Fungi 2024, 10(12), 853; https://doi.org/10.3390/jof10120853 - 11 Dec 2024
Viewed by 299
Abstract
Recent research has revealed the calcium signaling significance in the production of cellulases in Trichoderma reesei. While vacuoles serve as the primary calcium storage within cells, the function of vacuolar calcium transporter proteins in this process remains unclear. In this study, we [...] Read more.
Recent research has revealed the calcium signaling significance in the production of cellulases in Trichoderma reesei. While vacuoles serve as the primary calcium storage within cells, the function of vacuolar calcium transporter proteins in this process remains unclear. In this study, we conducted a functional characterization of four vacuolar calcium transport proteins in T. reesei. This was accomplished by the construction of the four mutant strains ∆trpmc1, ∆tryvc1, ∆tryvc3, and ∆tryvc4. These mutants displayed enhanced growth when subjected to arabinose, xylitol, and xylose. Furthermore, the mutants ∆trpmc1, ∆tryvc1, and ∆tryvc4 showed a reduction in growth under conditions of 100 mM MnCl2, implying their role in manganese resistance. Our enzymatic activity assays revealed a lack of the expected augmentation in cellulolytic activity that is typically seen in the parental strain following the introduction of calcium. This was mirrored in the expression patterns of the cellulase genes. The vacuolar calcium transport genes were also found to play a role in the expression of genes involved with the biosynthesis of secondary metabolites. In summary, our research highlights the crucial role of the vacuolar calcium transporters and, therefore, of the calcium signaling in orchestrating cellulase and hemicellulase expression, sugar utilization, and stress resistance in T. reesei. Full article
(This article belongs to the Special Issue Omics Approaches in Trichoderma Research)
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Figure 1

Figure 1
<p>Cladogram of calcium transport proteins. We used sequences of characterized proteins present in the cell membrane, vacuoles, endoplasmic reticulum, and Golgi apparatus together with <span class="html-italic">T. reesei</span> proteins of unknown localization identified in this study. The support values from 1000 resamples are indicated by the black circles, varying from 0 to 1. The figure only shows values from 0.8 to 1, from smaller to larger size.</p> Full article ">Figure 2
<p>Comparative expression analysis of <span class="html-italic">T. reesei</span> putative vacuolar calcium transport proteins, homologous to <span class="html-italic">S. cerevisiae’</span>s YVC1 and PMC1. The RNA-Seq data were obtained from studies [<a href="#B6-jof-10-00853" class="html-bibr">6</a>,<a href="#B17-jof-10-00853" class="html-bibr">17</a>,<a href="#B18-jof-10-00853" class="html-bibr">18</a>,<a href="#B19-jof-10-00853" class="html-bibr">19</a>,<a href="#B20-jof-10-00853" class="html-bibr">20</a>,<a href="#B48-jof-10-00853" class="html-bibr">48</a>]. (<b>a</b>) <span class="html-italic">yvc1</span> expression in commonly used parental strains and (<b>b</b>) the mutant strains lacking <span class="html-italic">Xyr1</span>, <span class="html-italic">Azf1</span>, <span class="html-italic">Cre1</span>, <span class="html-italic">Tmk1</span>, <span class="html-italic">Tmk2</span> and <span class="html-italic">Epl2</span>, respectively. (<b>c</b>,<b>d</b>) <span class="html-italic">pmc1</span> expression under the same conditions. Cel = cellulose, Glu = glucose, Soph = sophorose, SCB = sugarcane bagasse, Gly = glycerol.</p> Full article ">Figure 3
<p>Growth of strains QM6a∆<span class="html-italic">tmus53</span>∆<span class="html-italic">pyr4</span> (parental), ∆<span class="html-italic">trpmc1</span>, ∆<span class="html-italic">tryvc1</span>, ∆<span class="html-italic">tryvc3</span>, and ∆<span class="html-italic">tryvc</span>4 in minimal media in the presence of 25 mM of different carbon sources for 72 h, with and without 10 mM CaCl<sub>2</sub> supplementation. The values represent the absorbance readings at 750 nm.</p> Full article ">Figure 4
<p>Growth of strains QM6a∆<span class="html-italic">tmus53</span>∆<span class="html-italic">pyr4</span> (parental), ∆<span class="html-italic">trpmc1</span>, ∆<span class="html-italic">tryvc1</span>, ∆<span class="html-italic">tryvc3</span>, and ∆<span class="html-italic">tryvc</span>4 in 25 mM xylose minimal media for 48 or 72 h in the presence of 10, 100, or 300 mM of the metals calcium (<b>a</b>,<b>b</b>), copper (<b>c</b>,<b>d</b>), manganese (<b>e</b>,<b>f</b>), cobalt (<b>g</b>,<b>h</b>), zinc (<b>i</b>,<b>j</b>), iron (<b>k</b>,<b>l</b>), magnesium (<b>m</b>,<b>n</b>) or aluminum (<b>o</b>,<b>p</b>). Significance levels are indicated as follows: * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, and *** <span class="html-italic">p</span> &lt; 0.001 in relation to the parental strain (Student’s <span class="html-italic">t</span>-test). The control condition (gray bars) was calculated for each microplate.</p> Full article ">Figure 5
<p>Growth of strains QM6a∆<span class="html-italic">tmus53</span>∆<span class="html-italic">pyr4</span> (parental), ∆<span class="html-italic">trpmc1</span>, ∆<span class="html-italic">tryvc1</span>, ∆<span class="html-italic">tryvc3</span>, and ∆<span class="html-italic">tryvc</span>4 in 25 mM xylose Minimal media in the presence of 0.5 M NaCl (<b>a</b>–<b>c</b>) or 0.5 M KCl (<b>d</b>–<b>f</b>) and in presence or absence of 10 mM CaCl<sub>2</sub>. * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, and *** <span class="html-italic">p</span> &lt; 0.001 in relation to the parental strain (two-way ANOVA, followed by Tukey’s multiple comparisons). Non-significant results are indicated as ‘ns’. The control condition (gray bars) was calculated for each microplate.</p> Full article ">Figure 6
<p>Growth analysis of strains QM6a∆<span class="html-italic">tmus53</span>∆<span class="html-italic">pyr4</span> (parental), ∆<span class="html-italic">trpmc1</span>, ∆<span class="html-italic">tryvc1</span>, ∆<span class="html-italic">tryvc3</span>, and ∆<span class="html-italic">tryvc</span>4 in MA with 1% carboxymethylcellulose (CMC) for 5 days or 2% glucose + 100 mM Congo red (CR) for 3 days. (<b>a</b>) growth in plates, (<b>b</b>) growth measurements in 1% CMC and (<b>c</b>) 100 mM CR. Significance levels are indicated as follows: * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, and *** <span class="html-italic">p</span> &lt; 0.001 (Student’s <span class="html-italic">t</span>-test). Non-significant results are indicated as ‘ns’.</p> Full article ">Figure 7
<p>CMCase activity of parental and mutant strains grown for 24 h in MA media with 1% cellulose with or without 10 mM CaCl<sub>2</sub> supplementation for 24 h (<b>a</b>), 48 h (<b>b</b>), 72 h (<b>c</b>), and 96 h (<b>d</b>), and gene expression of endoglucanase (<span class="html-italic">cel7b</span>) (<b>e</b>), cellobiohydrolases (<span class="html-italic">cel7a</span> and <span class="html-italic">cel6a</span>) (<b>f</b>,<b>g</b>) and beta-glucosidase (<span class="html-italic">cel3a</span>) (<b>h</b>). Significance levels are indicated as follows: * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, and *** <span class="html-italic">p</span> &lt; 0.001 (Student’s <span class="html-italic">t</span>-test). Non-significant results are indicated as ‘ns’.</p> Full article ">Figure 8
<p>Gene expression of transcription factors and calcium signaling components of parental and mutant strains grown on MA media with 1% cellulose for 24 h. Gene expression of <span class="html-italic">xyr1</span> (<b>a</b>), <span class="html-italic">ace3</span> (<b>b</b>), <span class="html-italic">hac1a</span> (<b>c</b>), <span class="html-italic">cre1</span> (<b>d</b>), <span class="html-italic">crz1</span> (<b>e</b>), <span class="html-italic">cam</span> (<b>f</b>), and <span class="html-italic">cna1</span> (<b>g</b>). * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, and *** <span class="html-italic">p</span> &lt; 0.001 (Student’s <span class="html-italic">t</span>-test). Non-significant results are indicated as ‘ns’.</p> Full article ">Figure 9
<p>Gene expression of xylose metabolism enzymes (<b>a</b>–<b>c</b>), calcium signaling components (<b>d</b>–<b>f</b>), xylanases (<b>g</b>,<b>h</b>), and secondary metabolites components (<b>i</b>–<b>k</b>) of parental and mutant strains grown on MA media with 25 mM xylose for 48 h. * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, and *** <span class="html-italic">p</span> &lt; 0.001 (Student’s <span class="html-italic">t</span>-test). Non-significant results are indicated as ‘ns’.</p> Full article ">Figure 10
<p>Confocal microscopy and analysis of cell wall thickness. (<b>a</b>) the strains were grown in MA media with 25 mM xylose supplemented with 10 mM CaCl<sub>2</sub> and stained with 5 µM Fluo-4/AM. (<b>b</b>) the strains were grown in MEX media supplemented with 0 or 10 mM CaCl<sub>2</sub> for 1 day in a microscope slide and stained with 0.001% calcofluor white. (<b>c</b>) measurements of cell wall thickness. ** <span class="html-italic">p</span> &lt; 0.01 and *** <span class="html-italic">p</span> &lt; 0.001 (Student’s <span class="html-italic">t</span>-test). Non-significant results are indicated as ‘ns’.</p> Full article ">Figure 11
<p>Putative model of the function of the vacuolar calcium transport proteins YVC1 and PMC1 of <span class="html-italic">T. reesei</span>. The deletion of these proteins impairs the dynamics of calcium transport in the vacuoles, therefore, when extracellular calcium enters the cells, the calcium-mediated signaling does not occur properly, as the expression of the transcription factors ACE3, CRZ1, CRE1, YPR1, and YPR2 are increased/decreased, causing a reduction in cellulases/hemicellulases expression, manganese and osmotic stress tolerance and an increase in xylose assimilation and in cell wall thickness. red arrows down—down-regulation effect and blue arrows up—up-regulation effect.</p> Full article ">
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