Publications
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Bjorbækmo, Marit Frederikke Markussen; Brodie, Juliet; Krabberød, Anders Kristian; Logares, Ramiro; Fuss, Janina & Fredriksen, Stein
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(2023).
18S rDNA gene metabarcoding of microeukaryotes and epi-endophytes in the holobiome of seven species of large brown algae.
Journal of Phycology.
ISSN 0022-3646.
59(5),
p. 859–878.
doi:
10.1111/jpy.13377.
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Brown algae (Phaeophyceae) are habitat-forming species in coastal ecosystems and include kelp forests and seaweed beds that support a wide diversity of marine life. Host-associated microbial communities are an integral part of phaeophyte biology, and whereas the bacterial microbial partners have received considerable attention, the microbial eukaryotes associated with brown algae have hardly been studied. Here, we used broadly targeted “pan-eukaryotic” primers (metabarcoding) to investigate brown algal-associated eukaryotes (the eukaryome). Using this approach, we aimed to investigate the eukaryome of seven large brown algae that are important and common species in coastal ecosystems. We also aimed to assess whether these macroalgae harbor novel eukaryotic diversity and to ascribe putative functional roles to the host-associated eukaryome based on taxonomic affiliation and phylogenetic placement. We detected a significant diversity of microeukaryotic and algal lineages associated with the brown algal species investigated. The operational taxonomic units (OTUs) were taxonomically assigned to 10 of the eukaryotic major supergroups, including taxonomic groups known to be associated with seaweeds as epibionts, endobionts, parasites, and commensals. Additionally, we revealed previously unrecorded sequence types, including novel phaeophyte OTUs, particularly in the Fucus spp. samples, that may represent fucoid genomic variants, sequencing artifacts, or undescribed epi-/endophytes. Our results provide baseline data and technical insights that will be useful for more comprehensive seaweed eukaryome studies investigating the evidently lineage-rich and functionally diverse symbionts of brown algae.
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Sommerer, Yasmine; Dobricic, Valerija; Schilling, Marcel; Ohlei, Olena; Sabet, Sanaz Sedghpour & Wesse, Tanja
[Show all 12 contributors for this article]
(2023).
Entorhinal cortex epigenome-wide association study highlights four novel loci showing differential methylation in Alzheimer’s disease.
Alzheimer's Research & Therapy.
15(1).
doi:
10.1186/s13195-023-01232-7.
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Background Studies on DNA methylation (DNAm) in Alzheimer’s disease (AD) have recently highlighted several genomic loci showing association with disease onset and progression. Methods Here, we conducted an epigenome-wide association study (EWAS) using DNAm profiles in entorhinal cortex (EC) from 149 AD patients and control brains and combined these with two previously published EC datasets by meta-analysis (total n = 337). Results We identified 12 cytosine-phosphate-guanine (CpG) sites showing epigenome-wide significant association with either case–control status or Braak’s tau-staging. Four of these CpGs, located in proximity to CNFN/LIPE, TENT5A, PALD1/PRF1, and DIRAS1, represent novel findings. Integrating DNAm levels with RNA sequencing-based mRNA expression data generated in the same individuals showed significant DNAm-mRNA correlations for 6 of the 12 significant CpGs. Lastly, by calculating rates of epigenetic age acceleration using two recently proposed “epigenetic clock” estimators we found a significant association with accelerated epigenetic aging in the brains of AD patients vs. controls. Conclusion In summary, our study represents the hitherto most comprehensive EWAS in AD using EC and highlights several novel differentially methylated loci with potential effects on gene expression.
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Teubner, Marlene; Lenzen, Benjamin; Espenberger, Lucas Bernal; Fuss, Janina; Nickelsen, Jörg & Krause, Kirsten
[Show all 8 contributors for this article]
(2020).
The Chloroplast Ribonucleoprotein CP33B Quantitatively Binds the psbA mRNA.
Plants.
9(3).
doi:
10.3390/plants9030367.
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Chloroplast RNAs are stabilized and processed by a multitude of nuclear-encoded RNA-binding proteins, often in response to external stimuli like light and temperature. A particularly interesting RNA-based regulation occurs with the <i>psbA</i> mRNA, which shows light-dependent translation. Recently, the chloroplast ribonucleoprotein CP33B was identified as a ligand of the <i>psbA</i> mRNA. We here characterized the interaction of CP33B with chloroplast RNAs in greater detail using a combination of RIP-chip, quantitative dot-blot, and RNA-Bind-n-Seq experiments. We demonstrate that CP33B prefers <i>psbA</i> over all other chloroplast RNAs and associates with the vast majority of the <i>psbA</i> transcript pool. The RNA sequence target motif, determined in vitro, does not fully explain CP33B’s preference for <i>psbA</i>, suggesting that there are other determinants of specificity in vivo.
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Straumfors, Anne; Foss, Oda Astrid Haarr; Fuss, Janina; Mollerup, Steen Kristen; Kauserud, Håvard & Mundra, Sunil
(2019).
The inhalable mycobiome of sawmill workers: Exposure characterization and diversity.
Applied and Environmental Microbiology.
ISSN 0099-2240.
85(21),
p. 1–17.
doi:
10.1128/AEM.01448-19.
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Exposure to fungal spores has been associated with respiratory symptoms and allergic alveolitis among sawmill workers, but the complexity of sawmill workers' fungal exposure has been poorly studied.
We characterized the fungal diversity in air samples from sawmill workers' breathing zone, and identified differences in richness, diversity and taxonomic composition between companies, departments, wood types and seasons. Full-shift personal inhalable dust samples (n=86) collected from 11 industrial saw-, sorting-, and planer mill companies processing spruce and/or pine were subjected to DNA metabarcoding using the fungal Internal Transcribed Spacer (ITS) region 2.
The workers were exposed to a higher total number of operational taxonomic units (OTUs) in summer compared to winter, and when processing spruce compared with pine. Workers in the saw department had the richest fungal exposure followed by workers in the planing department and sorting of dry timber department. Sawmills explained 11% of the variation in fungal community composition of the exposure, followed by season (5%) and departments (3%). The fungal composition of the exposure differed between season, sawmills, wood types and departments also at the taxonomic levels, from phylum to species level. The differences in exposure diversity suggests that potential health effects of fungal inhalation also may be different, hence a risk assessment based on the fungal diversity differences should be performed.
This study may serve as a basis towards establishing a fungal profile of signature species that are specific for sawmills and can be measured quantitatively in future risk assessments of sawmill workers.
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Bråte, Jon; Fuss, Janina; Mehrotra, Shruti; Jakobsen, Kjetill Sigurd & Klaveness, Dag
(2019).
Draft genome assembly and transcriptome sequencing of the golden algae Hydrurus foetidus (Chrysophyceae).
F1000 Research.
8(401),
p. 1–12.
doi:
10.12688/f1000research.16734.3.
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Hydrurus foetidus is a freshwater alga belonging to the phylum Heterokonta. It thrives in cold rivers in polar and high alpine regions. It has several morphological traits reminiscent of single-celled eukaryotes, but can also form macroscopic thalli. Despite its ability to produce polyunsaturated fatty acids, its life under cold conditions and its variable morphology, very little is known about its genome and transcriptome. Here, we present an extensive set of next-generation sequencing data, including genomic short reads from Illumina sequencing and long reads from Nanopore sequencing, as well as full length cDNAs from PacBio IsoSeq sequencing and a small RNA dataset (smaller than 200 bp) sequenced with Illumina. We combined this data with, to our knowledge, the first draft genome assembly of a chrysophyte algae. The assembly consists of 5069 contigs to a total assembly size of 171 Mb and a 77% BUSCO completeness. The new data generated here may contribute to a better understanding of the evolution and ecological roles of chrysophyte algae, as well as to resolve the branching patterns within the Heterokonta.
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Teubner, Marlene; Fuss, Janina; Kühn, Kristina; Krause, Kirsten & Schmitz-Linneweber, Christian
(2016).
The RRM protein CP33A is a global ligand of chloroplast mRNAs and is essential for plastid biogenesis and plant development.
The Plant Journal.
ISSN 0960-7412.
89(3),
p. 472–485.
doi:
10.1111/tpj.13396.
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Fuss, Janina; Liegmann, Oliver; Krause, Kirsten & Rensing, Stefan A.
(2013).
Green Targeting Predictor and Ambiguous Targeting Predictor 2: the pitfalls of plant protein targeting prediction and of transient protein expression in heterologous systems.
New Phytologist.
ISSN 0028-646X.
doi:
10.1111/nph.12433.
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The challenges of plant protein targeting prediction are the existence of dual subcellular targets and the bias of experimentally confirmed data towards few and mostly nonplant model species.
To assess whether training with proteins from evolutionarily distant species has a negative impact on prediction accuracy, we developed the Green Targeting Predictor tool, which was trained with a species-specific data set for Physcomitrella patens. Its performance was compared with that of the same tool trained with a mixed data set. In addition, we updated the Ambiguous Targeting Predictor.
We found that predictions deviated from in vivo observations predominantly for proteins diverging within the green lineage, as well as for dual targeted proteins. To evaluate the usefulness of heterologous expression systems, selected proteins were subjected to localization studies in P. patens, Arabidopsis thaliana and Nicotiana tabacum. Four out of six proteins that show dual targeting in the original plant system were located only in a single compartment in one or both heterologous systems.
We conclude that targeting signals of divergent plant species exhibit differences, calling for custom in silico and in vivo approaches when aiming to unravel the actual distribution patterns of proteins within a plant cell.
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Krause, Kirsten; Herrmann, Ullrich; Fuss, Janina; Miao, Ying & Krupinska, Karin
(2009).
Whirly proteins as communicators between plant organelles and the nucleus?
Endocytobiosis and cell research.
ISSN 0256-1514.
19,
p. 51–62.
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Whirly proteins belong to a small family of proteins with a characteristic secondary structure and a conserved DNA binding domain that is found mainly in angiosperms. At least one member of the Whirly protein family, Whirly1, is dually targeted to the nucleus and to the chloroplasts and it was shown that apart from its initially described function as a transcriptional regulator of nuclear disease resistance genes, this protein comprises many more functions. It seems to fulfil roles in nuclear telomere homeostasis and possibly chloroplast rRNA metabolism as well as chloroplast intron splicing. A homologous protein with a mitochondrial presequence, Whirly2, in contrast, is presumably involved in the replication of the mitochondrial genome and in mitochondrial gene expression. In addition, it seems to affect the expression of a small subset of nuclear genes. Both Whirly proteins show an antagonistic effect on leaf senescence. Although direct evidence for a nuclear localisation of Whirly2 has yet to be obtained, we hypothesise that all members of the Whirly family are intriguing candidates for organelle-to-nucleus crosstalk with an intricate interaction between each other.
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Haraldsen, Arthur Alexander Blørstad; Bjorbækmo, Marit Markussen; Mangot, Jean-Francois; Fuss, Janina; Shalchian-Tabrizi, Kamran & Hansen, Haakon
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(2015).
Protist diversity in a marine and lacustrine system: Patterns across a salinity gradient.
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During the last decade, the improvement of high-throughput sequencing (HTS) techniques has substantially increased our insight into microbial ecology, by capturing a much more detailed picture of their diversity. Due to the increasing amount of data obtained by HTS methods, specific questions on the biogeography and factors explaining the distribution of these microorganisms can now be fully examined. Here, the composition and structure of a metabolically active benthic protistan community was investigated along a salinity gradient of closely associated marine and freshwater systems. Amplicons of rDNA and rRNA, were sequenced using the Illumina MiSeq technology. This approach seemed to successfully capture the majority of the protist community in these habitats. The marine environments displayed a higher species richness compared to the lacustrine systems investigated, and a considerable difference in protist composition was observed between marine and freshwater systems. Nevertheless, some protists were found in both saline and freshwater environments, indicating the ability to survive rather diverse environmental conditions. It is noteworthy that some of the OTUs from both habitats form putative new clades in the enigmatic X-cell group.
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Fuss, Janina; Liegmann, Oliver; Rensing, Stefan A. & Krause, Kirsten
(2011).
Protein targeting in the moss Physcomitrella patens and the angiosperm Arabidopsis thaliana - how compatible are transport systems after 450 Ma of divergent evolution?
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Fuss, Janina; Herrmann, Ullrich & Krause, Kirsten
(2009).
Crosstalk between nucleus and organelles: Dual targeting of transcription factors exemplified by members of the SEBF-like, GeBP and C3H families of Arabidopsis.
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Fuss, Janina; Krause, Kirsten & Fischer, Karsten
(2012).
Plant regulatory networks : RNA binding proteins as mediators of communication between DNA containing compartments by dual targeting.
UiT Norges arktiske universitet.
ISSN 9788282660297.
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The endosymbiosis-derived organelles within a plant cell, plastids and mitochondria, have to be equipped with a certain set of proteins to be fully functional. This set of proteins is encoded by different genomes: the organellar genomes and the nuclear genomes. This setup poses some interesting challenges for the regulation of gene expression and protein transport. On the one hand, the targeting signals that transport proteins to the organelles have to be highly specific and on the other hand, the communication between the DNA containing compartments to coordinate their gene expression has to be transmitted somehow, not only from the nucleus but also from the organelles back to the nucleus. In this thesis, two prediction programs are introduced. One of them can predict dual targeted proteins to both organelles (ATP, ambiguous targeting predictor) and the other one is species- specific for Physcomitrella patens (GTP_Pp; green targeting predictor – P. patens-specific). The first predictor can help to gain a more complete picture of the proteins potentially present in the organelles. With the help of that predictor, we predicted that the amount of proteins with dual targeting signals is higher than anticipated and that we to date know only a minor part of actually dual targeted proteins. The second predictor can help to answer the question on the evolutionary consistency of targeting signals within the plant kingdom and the importance of having species-specific approaches in analyzing protein targeting. We actually observed a surprisingly big difference in composition and recognition of mitochondrial and dual-targeting protein signals, which led to the conclusion, that species-specific approaches always should be considered as the optimal option for both, in silico and in vivo experiments. The second part of this thesis focuses the mechanisms of communication between nucleus and the organelles, especially the plastid possibly mediated by dual targeting. We chose several plastid RNA-/DNA-binding proteins to analyze their sub-plastidic localization and their potential additional nuclear localization. Those candidates were AtWHY1 (Arabidopsis thaliana Whirly1), four members of the AtcpRNP (chloroplast ribonucleoprotein) family and AtEF-Tu (elongation factor thermo-unstable). The analyzed members of the AtcpRNP family reflect their described multiple functions within the plastid also in a multiple localization pattern. Furthermore, we were able to show interactions of different members of the AtcpRNP family by yeast-two-hybrid interaction assays. The localization pattern of AtEF-Tu was very similar to the one observed for the AtcpRNPs, which indicated, together with a confirmed localization within the transcriptionally active chromosome, a multiple function for AtEF-Tu. The sub-plastidic localization data suggest overlapping networks of activity for the proteins by observed co-localizations. This was also shown with respect to several marker proteins for plastid functions. For AtEF-Tu and the AtcpRNPs, we also showed experimentally that a second localization in the nucleus is possible for the mature protein, which makes them interesting candidates for a possible mediation of plastid signals to the nucleus next to AtWHY1. For AtWHY1, we were able to show an effect of the DNA binding domain on the known localization pattern which seemed to reflect an aberration in transport processes through the envelope. This offers a potential regulatory mechanism that needs to be explored in detail in the future.
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Published
May 22, 2014 4:00 PM
- Last modified
Apr. 24, 2015 10:56 AM
