Translational control of fungal gene expression during the wheat-Fusarium graminearum interaction

To date, translational regulation of key genes controlling infection-related processes in fungal pathogens during their interactions with plants has not been studied. Here, we employed ribosome profiling (ribo-seq) to study translational responses and how such responses are coordinated with transcriptional changes in the fungal pathogen Fusarium graminearum (Fg), which causes Fusarium head blight (FHB), a destructive disease of cereal crops worldwide. Transcription and translation were not always coordinated with approximately 22% of Fg genes showing a discordant relationship during wheat infection. Nitrite reductase, which we show here as an important component of fungal virulence, is only regulated at the translational level in Fg. In addition, more than 1000 new open reading frames (ORFs), many of which are short and highly conserved, were identified in the Fg genome. Like in higher eukaryotes, translation is controlled by upstream ORFs (uORFs) in Fg during infection. Similarly, miRNAs control both transcription and translation in Fg during wheat infection. However, Fgdicer2-dependent miRNAs do not have a significant effect on transcriptional gene expression at the global outset. The ribo-seq study undertaken here for the first time in any fungal pathogen discovered novel insights about the biology of an important plant pathogen.

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uORFs: Important Cis-Regulatory Elements in Plants

International Journal of Molecular Sciences ◽

10.3390/ijms21176238 ◽

2020 ◽

Vol 21 (17) ◽

pp. 6238

Author(s):

Ting Zhang ◽

Anqi Wu ◽

Yaping Yue ◽

Yu Zhao

Keyword(s):

Gene Expression ◽

Translation Initiation ◽

Translational Control ◽

Translational Regulation ◽

Regulatory Elements ◽

Ribosome Profiling ◽

Open Reading Frames ◽

Post Translational Modification ◽

Cis Acting ◽

Eukaryotic Mrnas

Gene expression is regulated at many levels, including mRNA transcription, translation, and post-translational modification. Compared with transcriptional regulation, mRNA translational control is a more critical step in gene expression and allows for more rapid changes of encoded protein concentrations in cells. Translation is highly regulated by complex interactions between cis-acting elements and trans-acting factors. Initiation is not only the first phase of translation, but also the core of translational regulation, because it limits the rate of protein synthesis. As potent cis-regulatory elements in eukaryotic mRNAs, upstream open reading frames (uORFs) generally inhibit the translation initiation of downstream major ORFs (mORFs) through ribosome stalling. During the past few years, with the development of RNA-seq and ribosome profiling, functional uORFs have been identified and characterized in many organisms. Here, we review uORF identification, uORF classification, and uORF-mediated translation initiation. More importantly, we summarize the translational regulation of uORFs in plant metabolic pathways, morphogenesis, disease resistance, and nutrient absorption, which open up an avenue for precisely modulating the plant growth and development, as well as environmental adaption. Additionally, we also discuss prospective applications of uORFs in plant breeding.

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Upstream Open Reading Frames (uORFs) in the Apicomplexan Parasites Plasmodium falciparum and Toxoplasma gondii: Small yet Powerful Regulators of Translation

10.20944/preprints202104.0680.v1 ◽

2021 ◽

Author(s):

Chhaminder Kaur ◽

Swati Patankar

Keyword(s):

Gene Expression ◽

Plasmodium Falciparum ◽

Toxoplasma Gondii ◽

Translational Regulation ◽

Life Cycles ◽

Ribosome Profiling ◽

Open Reading Frames ◽

Apicomplexan Parasites ◽

Upstream Open Reading Frames ◽

Reading Frames

During their complex life cycles, the Apicomplexan parasites, Plasmodium falciparum and Toxoplasma gondii employ several genetic switches to regulate their gene expression. One such switch is mediated at the level of translation through upstream Open Reading Frames (uORFs). As uORFs are found in the upstream regions of a majority of genes in both the parasites, it is essential that their roles in translational regulation be appreciated to a greater extent. This review provides a comprehensive summary of studies that show uORF-mediated gene regulation in these parasites and highlights examples of clinically and physiologically relevant proteins that exhibit uORF-mediated regulation. In addition to these examples, several studies that use bioinformatics, transcriptomics, proteomics, and ribosome profiling also indicate the possibility of widespread translational regulation by uORFs. Further analysis of genome-wide datasets will reveal novel genes involved in key biological pathways such as cell-cycle progression, stress-response, and pathogenicity. The cumulative evidence from studies presented in this review suggests that uORFs will play crucial roles in regulating gene expression during clinical disease caused by these important human pathogens.

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A spatiotemporal translatome of mouse tissue development

10.1101/2020.04.14.041079 ◽

2020 ◽

Author(s):

Hongwei Wang ◽

Yan Wang ◽

Jiaqi Yang ◽

Nan Tang ◽

Huihui Li ◽

...

Keyword(s):

Gene Expression ◽

Translational Control ◽

Translational Regulation ◽

Regulation Of Gene Expression ◽

Open Reading Frames ◽

Mouse Tissue ◽

Specific Gene ◽

Translational Efficiency ◽

Tissue Development ◽

Mouse Tissues

AbstractThe precise regulation of gene expression in mammalian tissues during development results in their functional specification. Although previous transcriptomic and proteomic analyses have provided great biological insights into tissue-specific gene expression and the physiological relevance of these tissues in development, our understanding of translational regulation in developing tissues is lacking. In this study, we performed a spatiotemporally resolved translatome analysis of six mouse tissues at the embryonic and adult stages to quantify the effects of translational regulation and identify new translational components. We quantified the spatial and temporal divergences of gene expression and detected specific changes in gene expression and pathways underlying these divergences. We further showed that dynamic translational control can be achieved by modulating the translational efficiency, which resulted in the enhancement of tissue specificity during development. We also discovered thousands of actively translated upstream open reading frames (ORFs) that exhibited spatiotemporal patterns and demonstrated their regulatory roles in translational regulation. Furthermore, we identified known and novel micropeptides encoded by small ORFs from long noncoding RNAs that are functionally relevant to tissue development. Our data and analyses facilitate a better understanding of the complexity of translational regulation across tissue and developmental spectra and serve as a useful resource of the mouse translatome.

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Translation of ABCE1 Is Tightly Regulated by Upstream Open Reading Frames in Human Colorectal Cells

Biomedicines ◽

10.3390/biomedicines9080911 ◽

2021 ◽

Vol 9 (8) ◽

pp. 911

Author(s):

Joana Silva ◽

Pedro Nina ◽

Luísa Romão

Keyword(s):

Translational Regulation ◽

Regulatory Elements ◽

Ribosome Profiling ◽

Leader Sequence ◽

Open Reading Frames ◽

Regulatory Function ◽

Coding Sequence ◽

Abc Protein ◽

Upstream Open Reading Frames ◽

Reading Frames

ATP-binding cassette subfamily E member 1 (ABCE1) belongs to the ABC protein family of transporters; however, it does not behave as a drug transporter. Instead, ABCE1 actively participates in different stages of translation and is also associated with oncogenic functions. Ribosome profiling analysis in colorectal cancer cells has revealed a high ribosome occupancy in the human ABCE1 mRNA 5′-leader sequence, indicating the presence of translatable upstream open reading frames (uORFs). These cis-acting translational regulatory elements usually act as repressors of translation of the main coding sequence. In the present study, we dissect the regulatory function of the five AUG and five non-AUG uORFs identified in the human ABCE1 mRNA 5′-leader sequence. We show that the expression of the main coding sequence is tightly regulated by the ABCE1 AUG uORFs in colorectal cells. Our results are consistent with a model wherein uORF1 is efficiently translated, behaving as a barrier to downstream uORF translation. The few ribosomes that can bypass uORF1 (and/or uORF2) must probably initiate at the inhibitory uORF3 or uORF5 that efficiently repress translation of the main ORF. This inhibitory property is slightly overcome in conditions of endoplasmic reticulum stress. In addition, we observed that these potent translation-inhibitory AUG uORFs function equally in cancer and in non-tumorigenic colorectal cells, which is consistent with a lack of oncogenic function. In conclusion, we establish human ABCE1 as an additional example of uORF-mediated translational regulation and that this tight regulation contributes to control ABCE1 protein levels in different cell environments.

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Molecular Characterization and Functional Analysis of PR-1-Like Proteins Identified from the Wheat Head Blight Fungus Fusarium graminearum

Phytopathology ◽

10.1094/phyto-08-17-0268-r ◽

2018 ◽

Vol 108 (4) ◽

pp. 510-520 ◽

Cited By ~ 3

Author(s):

Shunwen Lu ◽

Michael C. Edwards

Keyword(s):

Functional Analysis ◽

Fusarium Graminearum ◽

Expression Patterns ◽

Polyacrylamide Gel Electrophoresis ◽

Sodium Dodecyl ◽

Transcriptional Analysis ◽

Fungal Genome ◽

Dimensional Structure ◽

Head Blight ◽

Fungal Virulence

The group 1 pathogenesis-related (PR-1) proteins originally identified from plants and their homologs are also found in other eukaryotic kingdoms. Studies on nonplant PR-1-like (PR-1L) proteins have been pursued widely in humans and animals but rarely in filamentous ascomycetes. Here, we report the characterization of four PR-1L proteins identified from the ascomycete fungus Fusarium graminearum, the primary cause of Fusarium head blight of wheat and barley (designated FgPR-1L). Molecular cloning revealed that the four FgPR-1L proteins are all encoded by small open reading frames (612 to 909 bp) that are often interrupted by introns, in contrast to plant PR-1 genes that lack introns. Sequence analysis indicated that all FgPR-1L proteins contain the PR-1-specific three-dimensional structure, and one of them features a C-terminal transmembrane (TM) domain that has not been reported for any stand-alone PR-1 proteins. Transcriptional analysis revealed that the four FgPR-1L genes are expressed in axenic cultures and in planta with different spatial or temporal expression patterns. Phylogenetic analysis indicated that fungal PR-1L proteins fall into three major groups, one of which harbors FgPR-1L-2-related TM-containing proteins from both phytopathogenic and human-pathogenic ascomycetes. Low-temperature sodium dodecyl sulfate polyacrylamide gel electrophoresis and proteolytic assays indicated that the recombinant FgPR-1L-4 protein exists as a monomer and is resistant to subtilisin of the serine protease family. Functional analysis confirmed that deletion of the FgPR-1L-4 gene from the fungal genome results in significantly reduced virulence on susceptible wheat. This study provides the first example that the F. graminearum–wheat interaction involves a pathogen-derived PR-1L protein that affects fungal virulence on the host.

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Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation

10.1101/021501 ◽

2015 ◽

Cited By ~ 2

Author(s):

David E Weinberg ◽

Premal Shah ◽

Stephen W Eichhorn ◽

Jeffrey A Hussmann ◽

Joshua B Plotkin ◽

...

Keyword(s):

Translational Control ◽

Nucleotide Composition ◽

Ribosome Profiling ◽

Open Reading Frames ◽

Untranslated Regions ◽

Coding Regions ◽

Genome Wide ◽

Upstream Open Reading Frames ◽

Improved Methods ◽

Reading Frames

Ribosome-footprint profiling provides genome-wide snapshots of translation, but technical challenges can confound its analysis. Here, we use improved methods to obtain ribosome-footprint profiles and mRNA abundances that more faithfully reflect gene expression in Saccharomyces cerevisiae. Our results support proposals that both the beginning of coding regions and codons matching rare tRNAs are more slowly translated. They also indicate that emergent polypeptides with as few as three basic residues within a 10-residue window tend to slow translation. With the improved mRNA measurements, the variation attributable to translational control in exponentially growing yeast was less than previously reported, and most of this variation could be predicted with a simple model that considered mRNA abundance, upstream open reading frames, cap-proximal structure and nucleotide composition, and lengths of the coding and 5′- untranslated regions. Collectively, our results reveal key features of translational control in yeast and provide a framework for executing and interpreting ribosome- profiling studies.

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Promoter architecture determines co-translational regulation of mRNA

10.1101/192195 ◽

2017 ◽

Author(s):

Lorena Espinar ◽

Miquel Àngel Schikora Tamarit ◽

Júlia Domingo ◽

Lucas B. Carey

Keyword(s):

Gene Expression ◽

Translational Regulation ◽

Open Reading Frames ◽

Mrna Levels ◽

Rna Seq ◽

Linear Interaction ◽

Information Encoding ◽

Inducible Promoters ◽

Promoter Architecture ◽

Inducible Genes

AbstractInformation that regulates gene expression is encoded throughout each gene but if different regulatory regions can be understood in isolation, or if they interact, is unknown. Here we measure mRNA levels for 10,000 open reading frames (ORFs) transcribed from either an inducible or constitutive promoter. We find that the strength of co-translational regulation on mRNA levels is determined by promoter architecture. Using a novel computational-genetic screen of 6402 RNA-seq experiments we identify the RNA helicase Dbp2 as the mechanism by which co-translational regulation is reduced specifically for inducible promoters. Finally, we find that for constitutive genes, but not inducible genes, most of the information encoding regulation of mRNA levels in response to changes in growth rate is encoded in the ORF and not in the promoter. Thus the ORF sequence is a major regulator of gene expression, and a non-linear interaction between promoters and ORFs determines mRNA levels.

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Molecular Characterization of a Novel Strain of Fusarium graminearum Virus 1 Infecting Fusarium graminearum

Viruses ◽

10.3390/v12030357 ◽

2020 ◽

Vol 12 (3) ◽

pp. 357 ◽

Cited By ~ 2

Author(s):

Lihang Zhang ◽

Xiaoguang Chen ◽

Pallab Bhattacharjee ◽

Yue Shi ◽

Lihua Guo ◽

...

Keyword(s):

Fusarium Graminearum ◽

Pathogenic Fungi ◽

Open Reading Frames ◽

Chinese Isolate ◽

The Novel ◽

Fungal Virulence ◽

Host Interaction ◽

Short Orfs ◽

Rapid Amplification ◽

Fungal Viruses

Fungal viruses (mycoviruses) have attracted more attention for their possible hypovirulence (attenuation of fungal virulence) trait, which may be developed as a biocontrol agent of plant pathogenic fungi. However, most discovered mycoviruses are asymptomatic in their hosts. In most cases, mycovirus hypovirulent factors have not been explored clearly. In this study, we characterized a ssRNA mycovirus in Fusarium graminearum strain HB56-9. The complete nucleotide genome was obtained by combining random sequencing and rapid amplification of cDNA ends (RACE). The full genome was 6621-nucleotides long, excluding the poly(A) tail. The mycovirus was quite interesting because it shared 95.91% nucleotide identities with previously reported Fusarium graminearum virus 1 strain DK21 (FgV1-DK21), while the colony morphology of their fungal hosts on PDA plates were very different. The novel virus was named Fusarium graminearum virus 1 Chinese isolate (FgV1-ch). Like FgV1-DK21, FgV1-ch also contains four putative open reading frames (ORFs), including one long and three short ORFs. A phylogenetic analysis indicated that FgV1-ch is clustered into a proposed family Fusariviridae. FgV1-ch, unlike FgV1-DK21, had mild or no effects on host mycelial growth, spore production and virulence. The nucleotide differences between FgV1-ch and FgV1-DK21 will help to elucidate the hypovirulence determinants during mycovirus–host interaction.

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Nutrient Control of mRNA Translation

Annual Review of Nutrition ◽

10.1146/annurev-nutr-120919-041411 ◽

2020 ◽

Vol 40 (1) ◽

pp. 51-75 ◽

Cited By ~ 2

Author(s):

Xin Erica Shu ◽

Robert V. Swanda ◽

Shu-Bing Qian

Keyword(s):

Gene Expression ◽

Translational Control ◽

Translational Regulation ◽

Mrna Translation ◽

Nutrient Sensing ◽

Control Networks ◽

Genome Wide ◽

Nutrient Signaling ◽

Specific Proteins ◽

Cellular Dna

The emergence of genome-wide analyses to interrogate cellular DNA, RNA, and protein content has revolutionized the study of control networks that mediate cellular homeostasis. mRNA translation represents the last step of genetic flow and primarily defines the proteome. Translational regulation is thus critical for gene expression, in particular under nutrient excess or deficiency. Until recently, it was unclear how the global effects of translational control are orchestrated by nutrient signaling pathways. An emerging concept of translational reprogramming addresses how to maintain the expression of specific proteins during nutrient stress by translation of selective mRNAs. In this review, we describe recent advances in our understanding of translational control principles; nutrient-sensing mechanisms; and their dysregulation in human diseases such as diabetes, cancer, and aging. The mechanistic understanding of translational regulation in response to different nutrient conditions may help identify potential dietary and therapeutic targets to improve human health.

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Novel Genes of Fusarium graminearum That Negatively Regulate Deoxynivalenol Production and Virulence

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-22-12-1588 ◽

2009 ◽

Vol 22 (12) ◽

pp. 1588-1600 ◽

Cited By ~ 76

Author(s):

Donald M. Gardiner ◽

Kemal Kazan ◽

John M. Manners

Keyword(s):

Gene Expression ◽

Fusarium Graminearum ◽

Global Analysis ◽

Gene Clusters ◽

Head Blight ◽

Knock Out ◽

Serious Disease ◽

Amine Compounds ◽

Fungal Genes ◽

Fungal Gene Expression

Fusarium head blight of wheat, caused by Fusarium graminearum, is a serious disease resulting in both reduced yields and contamination of grain with trichothecene toxins, with severe consequences for mammalian health. Recently, we have identified several related amine compounds such as agmatine and putrescine that promote the production of high levels of trichothecene toxins, such as deoxynivalenol (DON), in culture by F. graminearum and F. sporotrichioides. Here, a global analysis of fungal gene expression using the Affymetrix Fusarium GeneChip during culture under DON-inducing conditions compared with noninducing conditions is reported. Agmatine differentially regulated a large number of fungal genes, including both known and previously uncharacterized putative secondary metabolite biosynthetic gene clusters. In silico prediction of binding sites for the transcriptional regulator (TRI6) controlling TRI gene expression and gene expression analysis in a TRI6 mutant of F. graminearum showed that three of the differentially regulated genes were under the control of TRI6. Gene knock-out mutations of two of these genes resulted in mutants with massively increased production of DON and increased aggressiveness toward wheat. Our results not only identify a novel mechanism of negative regulation of DON production and virulence in F. graminearum but also point out the potential of this pathogen to evolve with an ability to produce massively increased amounts of toxins and increased virulence.

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