Biology subjects

Viehoever, P.

Publications and source records attributed to Viehoever, P..

11 recordsLinked to original sources

bioRxiv2026

Tuning into xanthan: A conserved yet flexible polysaccharide utilization system in Microbacterium

Bacteria encounter structurally complex extracellular polysaccharides in natural environments, yet the regulatory and evolutionary basis of their utilization remains poorly understood. Here, we isolated a soil-derived Microbacterium strain, named Microbacterium xanthanicum UB-LE1, that grows on xanthan as the sole carbon source. We dissected the genetic and regulatory architecture underlying this capability. Genome sequencing combined with transcriptomic and proteomic profiling uncovered a discrete, strongly inducible regulon associated with xanthan utilization, encoding 23 proteins with five secreted proteins and three candidate transcriptional regulators. DNA-affinity purification sequencing confirmed two regulators binding to operons within the xanthan utilization locus. Comparative genomics across the Microbacteriaceae revealed conserved and lineage-specific features of this system and supports recent acquisition and modular integration of the locus, with at least two predominant architectural variants possibly shaped by substrate availability and ecological specialization. Coordinated induction at both the transcript and protein levels, together with two experimentally validated regulators, points to tight regulatory control of complex polysaccharide degradation in Microbacterium xanthanicum UB-LE1. Together, these findings provide mechanistic and evolutionary insight into how bacteria adapt to complex extracellular carbohydrates, expand current knowledge of xanthan turnover in microbial ecosystems, and establish a framework for exploring the emergence and diversification of specialized polysaccharide utilization pathways across bacterial taxa. IMPORTANCEMicroorganisms are central drivers of carbon turnover in soils and other terrestrial ecosystems, determining the availability of nutrients and shaping microbial community structure. A significant portion of soil carbon is contained in extracellular polysaccharides, yet the pathways by which microorganisms degrade these complex polymers remain poorly understood. Xanthan, a structurally complex and widely produced microbial exopolysaccharide, represents a persistent and largely overlooked carbon pool. By dissecting the genetic, regulatory, and evolutionary basis of xanthan utilization in Microbacterium xanthanicum UB-LE1, this study advances our understanding of how soil bacteria adapt to complex extracellular carbohydrates and how substrate availability shapes the emergence and diversification of specialized metabolic pathways. Importantly, the identification of additional xanthan-active enzymes and regulatory components in M. xanthanicum UB-LE1 opens opportunities for targeted modification of xanthan structure and properties, paving the way for new biotechnological applications in food, materials, and industrial biotechnology, while linking microbial ecology to functional innovation.

microbiology↗

bioRxiv2024

Study of excess manganese stress response highlights the central role of manganese exporter Mnx for holding manganese homeostasis in the cyanobacterium Synechocystis sp. PCC 6803

Cellular levels of the essential micronutrient manganese (Mn) need to be carefully balanced within narrow boarders. In cyanobacteria, sufficient Mn supply is critical for assuring the function of the oxygen-evolving complex as central part of the photosynthetic machinery. However, Mn accumulation is fatal for the cells. The reason for the observed cytotoxicity is unclear. To understand the causality behind Mn toxicity in cyanobacteria, we investigated the impact of excess Mn on physiology and global gene expression in the model organism Synechocystis sp. PCC 6803. We compared the response of the wild type and the knock-out mutant in the manganese exporter (Mnx), {Delta}mnx, which is disabled in the export of surplus Mn and thus functions as model for toxic Mn overaccumulation. While growth and pigment accumulation in {Delta}mnx was severely impaired 24 h after addition of 10-fold Mn, the wild type was not affected and thus mounted an adequate transcriptional response. RNA-seq data analysis revealed that the Mn stress transcriptomes were partly resembling an iron limitation transcriptome. However, the expression of iron limitation signature genes isiABDC was not affected by the Mn treatment, indicating that Mn excess is not accompanied by iron limitation in Synechocystis. We suggest that the Ferric uptake regulator, Fur, gets partially mismetallated under Mn excess conditions and thus interferes with an iron-dependent transcriptional response. To encounter mismetallation and other Mn-dependent problems on protein level, the cells invest into transcripts of ribosomes, proteases, and chaperones. In case of the {Delta}mnx mutant the consequences of the disability to export excess Mn from the cytosol manifest in additionally impaired energy metabolism and oxidative stress transcriptomes with fatal outcome. This study emphasizes the central importance of Mn homeostasis and the transporter Mnxs role in restoring and holding it.

microbiology↗

bioRxiv2023

Multiple transcription factors mediate acclimation of Chlamydomonas to light stress

Light as a substrate for photosynthesis may be a boon or a bane. To thrive, photosynthetic organisms must constantly respond to changing light and CO2 conditions by balancing energy harvest and consumption in a highly dynamic way. Two major safeguard measures of photoacclimation, that is photoprotection and carbon concentrating mechanism, underlie tight transcriptional control, leading to expression changes under high light and limited CO2 with different dynamics for both systems. Here, by using a consensus gene regulatory network inferred by employing a compendium of 1,869 RNA-seq datasets, we identified and validated in vivo eight candidate transcription factors (TFs) that contribute to photoacclimation in Chlamydomonas reinhardtii. Target gene analyses indicate that the TFs act individually in associated pathways but also influence each other in expression, and function as network parts with partial redundancy with respect to photoprotection. The analyses unveil that stress responses in Chlamydomonas are mediated by a complex, interconnected network of TFs rather than a hierarchical system where multiple regulators can influence each other and target gene expression and thereby mitigate the effects of loss.

plant biology↗

bioRxiv2023

Genomic characterization of a nematode tolerance locus in sugar beet

BackgroundInfection by beet cyst nematodes (BCN, Heterodera schachtii) causes a serious disease of sugar beet, and climatic change is expected to improve the conditions for BCN infection. Yield and yield stability under adverse conditions are among the main breeding objectives. Breeding of BCN tolerant sugar beet cultivars offering high yield in the presence of the pathogen is therefore of high relevance. ResultsTo identify causal genes providing tolerance against BCN infection, we combined several experimental and bioinformatic approaches. Relevant genomic regions were detected through mapping-by-sequencing using a segregating F2 population. DNA sequencing of contrasting F2 pools and analyses of allele frequencies for variant positions identified a single genomic region which confers nematode tolerance. The genomic interval was confirmed and narrowed down by genotyping with newly developed molecular markers. To pinpoint the causal genes within the potential nematode tolerance locus, we generated long read-based genome sequence assemblies of the tolerant parental breeding line Strube U2Bv and the susceptible reference line 2320Bv. We analyzed continuous sequences of the potential locus with regard to functional gene annotation and differential gene expression upon BCN infection. A cluster of genes with similarity to the Arabidopsis thaliana gene encoding nodule inception protein-like protein 7 (NLP7) was identified. Gene expression analyses confirmed transcriptional activity and revealed clear differences between susceptible and tolerant genotypes. ConclusionsOur findings provide new insights into the genomic basis of plant-nematode interactions that can be used to design and accelerate novel management strategies against BCN.

plant biology↗

bioRxiv2023

Transcription factors mediating regulation of photosynthesis

Photosynthesis by which plants convert carbon dioxide to sugars using the energy of light is fundamental to life as it forms the basis of nearly all food chains. Surprisingly, our knowledge about its transcriptional regulation remains incomplete. Effort for its agricultural optimization have mostly focused on post-translational regulatory processes1-3 but photosynthesis is regulated at the post-transcriptional4 and the transcriptional level5. Stacked transcription factor mutations remain photosynthetically active5,6 and additional transcription factors have been difficult to identify possibly due to redundancy6 or lethality. Using a random forest decision tree-based machine learning approach for gene regulatory network calculation7 we determined ranked candidate transcription factors and validated five out of five tested transcription factors as controlling photosynthesis in vivo. The detailed analyses of previously published and newly identified transcription factors suggest that photosynthesis is transcriptionally regulated in a partitioned, non-hierarchical, interlooped network.

plant biology↗

bioRxiv2022

Phased grapevine genome sequence assembly of an Rpv12 carrier for exploration of Rpv12 associated positional and functional Plasmopara viticola resistance genes

The downy mildew disease caused by the oomycete Plasmopara viticola is a serious threat for grapevine and can cause enormous yield losses in viticulture. The quantitative trait locus Rpv12, mediating resistance against P. viticola, was originally found in Asian Vitis amurensis. This locus and its genes were analyzed here in detail. A haplotype-separated genome sequence of the diploid Rpv12-carrier Gf.99-03 was created and annotated. The defense response against P. viticola was investigated in an infection time-course RNA-Seq experiment, revealing approximately 600 up-regulated Vitis genes during host-pathogen interaction. The Rpv12 regions of the resistance conferring and the sensitivity encoding Gf.99-03 haplotypes were structurally and functionally compared to each other. Two different clusters of resistance-related genes were identified within the Rpv12 locus. One cluster carries a set of four differentially expressed genes with three ACCELERATED CELL DEATH 6-like genes. The other cluster carries a set of six resistance gene analogues related to qualitative pathogen resistance. The Rpv12 locus and its candidate genes for P. viticola resistance provide a precious genetic resource for P. viticola resistance breeding. Newly developed co-segregating simple sequence repeat markers in close proximity to the R-genes enable its improved applicability in marker-assisted grapevine breeding.

plant biology↗

bioRxiv2022

A fully phased interspecific grapevine rootstock genome sequence representing V. riparia and V. cinerea and allele-aware annotation of the phylloxera resistance locus Rdv1

The phylloxera resistant rootstock cultivar Borner is an interspecific hybrid derived from Vitis riparia and V. cinerea and a valuable resource for Vitis disease resistances. We created a fully phased, high-quality Borner genome sequence named BoeRC using long PacBio reads. Comprehensive gene annotation of both Borner haplotypes, designated BoeRip and BoeCin, was applied to describe the phylloxera resistance locus Rdv1. Using a mapping population derived from a susceptible V. vinifera breeding line and Borner, the Rdv1 locus was further delimited. Rdv1, which is derived from V. cinerea and included in the haplotype BoeCin, was compared with sequences of phylloxera-susceptible and phylloxera-tolerant cultivars. Between flanking regions that display high synteny, we detected and precisely characterized a diverse sequence region that covers between 202 to 403 kbp in different haplotypes. In BoeCin, five putative disease resistance genes were identified that represent likely candidates for conferring resistance to phylloxera.

genomics↗

bioRxiv2021

Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives

BackgroundAs the major source of sugar in moderate climates, sugar-producing beets (Beta vulgaris subsp. vulgaris) have a high economic value. However, the low genetic diversity within cultivated beets requires introduction of new traits, for example to increase their tolerance and resistance attributes - traits that often reside in the crop wild relatives. For this, genetic information of wild beet relatives and their phylogenetic placements to each other are crucial. To answer this need, we sequenced and assembled the complete plastome sequences from a broad species spectrum across the beet genera Beta and Patellifolia, both embedded in the Betoideae (order Caryophyllales). This pan-plastome dataset was then used to determine the wild beet phylogeny in high-resolution. ResultsWe sequenced the plastomes of 18 closely related accessions representing 11 species of the Betoideae subfamily and provided high-quality plastome assemblies which represent an important resource for further studies of beet wild relatives and the diverse plant order Caryophyllales. Their assembly sizes range from 149,723 bp (Beta vulgaris subsp. vulgaris) to 152,816 bp (Beta nana), with most variability in the intergenic sequences. Combining plastome-derived phylogenies with read-based treatments based on mitochondrial information, we were able to suggest a unified and highly confident phylogenetic placement of the investigated Betoideae species. Our results show that the genus Beta can be divided into the two clearly separated sections Beta and Corollinae. Our analysis confirms the affiliation of B. nana with the other Corollinae species, and we argue against a separate placement in the Nanae section. Within the Patellifolia genus, the two diploid species Patellifolia procumbens and Patellifolia webbiana are, regarding the plastome sequences, genetically more similar to each other than to the tetraploid Patellifolia patellaris. Nevertheless, all three Patellifolia species are clearly separated. ConclusionIn conclusion, our wild beet plastome assemblies represent a new resource to understand the molecular base of the beet germplasm. Despite large differences on the phenotypic level, our pan-plastome dataset is highly conserved. For the first time in beets, our whole plastome sequences overcome the low sequence variation in individual genes and provide the molecular backbone for highly resolved beet phylogenomics. Hence, our plastome sequencing strategy can also guide genomic approaches to unravel other closely related taxa.

genomics↗

bioRxiv2021

Characterization of the Brassica napus flavonol synthase gene family reveals bifunctional flavonol synthases

Flavonol synthase (FLS) is a key enzyme for the formation of flavonols, which are a subclass of the flavonoids. FLS catalyses the conversion of dihydroflavonols to flavonols. The enzyme belongs to the 2-oxoglutarate-dependent dioxygenases (2-ODD) superfamily. We characterized the FLS gene family of Brassica napus that covers 13 genes, based on the genome sequence of the B. napus cultivar Express 617. The goal was to unravel which BnaFLS genes are relevant for seed flavonol accumulation in the amphidiploid species B. napus. Two BnaFLS1 homeologs were identified and shown to encode bifunctional enzymes. Both exhibit FLS activity as well as flavanone 3-hydroxylase (F3H) activity, which was demonstrated in vivo and in planta. BnaFLS1-1 and -2 are capable of converting flavanones into dihydroflavonols and further into flavonols. Analysis of spatio-temporal transcription patterns revealed similar expression profiles of BnaFLS1 genes. Both are mainly expressed in reproductive organs and co-expressed with the genes encoding early steps of flavonoid biosynthesis. Our results provide novel insights into flavonol biosynthesis in B. napus and contribute information for breeding targets with the aim to modify the flavonol content in rapeseed.

plant biology↗

bioRxiv2019

25 years of propagation in suspension cell culture results in substantial alterations of the Arabidopsis thaliana genome

Arabidopsis thaliana is one of the best studied plant model organisms. Besides cultivation in greenhouses, cells of this plant can also be propagated in suspension cell culture. At7 is one such cell line that has been established about 25 years ago. Here we report the sequencing and the analysis of the At7 genome. Large scale duplications and deletions compared to the Col-0 reference sequence were detected. The number of deletions exceeds the number of insertions thus indicating that a haploid genome size reduction is ongoing. Patterns of small sequence variants differ from the ones observed between A. thaliana accessions e.g. the number of single nucleotide variants matches the number of insertions/deletions. RNA-Seq analysis reveals that disrupted alleles are less frequent in the transcriptome than the native ones.

genomics↗

bioRxiv2019

Genome sequencing of Musa acuminata Dwarf Cavendish reveals a chromosome arm duplication

Different Musa species, subspecies, and cultivars are currently investigated to reveal their genomic diversity. Here, we compare the genome sequence of one of the commercially most important cultivars, Musa acuminata Dwarf Cavendish, against the Pahang reference genome assembly. Numerous small sequence variants were detected and the ploidy of the cultivar presented here was determined as triploid based on sequence variant frequencies. Illumina sequence data also revealed a duplication of a large segment on the long arm of chromosome 2 in the Dwarf Cavendish genome. Comparison against previously sequenced cultivars provided evidence that this duplication is unique to Dwarf Cavendish. Although no functional relevance of this duplication was identified, this example shows the potential of plants to tolerate such aneuploidies.

genomics↗