Christian H Ahrens

Agroscope & SIB Swiss Institute of Bioinformatics

Accurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to fully exploit the rapidly growing repertoire of completely sequenced prokaryotic genomes. However, large discrepancies among the number of CDSs annotated by different resources, missed functional short open reading frames (sORFs), and overprediction of spurio...

Increasing antibacterial resistance presents a major challenge in antibiotic discovery. One attractive target in Gram-negative bacteria is the unique asymmetric outer membrane (OM), which acts as a permeability barrier that protects the cell from external stresses such as the presence of antibiotics. We describe a novel β-hairpin macrocyclic peptid...

Unlabelled: Proteomics data provide unique insights into biological systems, including the predominant subcellular localization (SCL) of proteins, which can reveal important clues about their functions. Here we analyzed data of a complete prokaryotic proteome expressed under two conditions mimicking interaction of the emerging pathogen Bartonella...

Prokaryotes are, due to their moderate complexity, particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and proteins extracted from matched samples. Saturated...

Many bacteria produce extracellular and surface-associated components such as membrane vesicles (MVs), extracellular DNA and moonlighting cytosolic proteins for which the biogenesis and export pathways are not fully understood. Here we show that the explosive cell lysis of a sub-population of cells accounts for the liberation of cytosolic content i...

Rhizobia fix nitrogen within root nodules of host plants where nitrogenase expression is strictly controlled by its key regulator NifA. We recently discovered that in nodules infected by the beta-rhizobial strain Paraburkholderia phymatum STM815, NifA controls expression of two bacterial auxin synthesis genes. Both the iaaM and iaaH transcripts, as...

Bisphenols are used in the process of polymerization of polycarbonate plastics and epoxy resins. Bisphenols can easily migrate out of plastic products and enter the gastrointestinal system. By increasing colonic inflammation in mice, disrupting the intestinal bacterial community structure and altering the microbial membrane transport system in zebr...

The general stress response (GSR) enables bacteria to sense and overcome a variety of environmental stresses. In alphaproteobacteria, stress-perceiving histidine kinases of the HWE and HisKA_2 families trigger a signaling cascade that leads to phosphorylation of the response regulator PhyR and, consequently, to activation of the GSR σ factor σ EcfG...

Cyberlindnera sargentensis strain SHA 17.2, isolated from a Swiss soil sample, exhibited strong antagonistic activity against several plant pathogenic fungi in vitro and was highly competitive against other yeasts in soil. As a basis for identifying the mechanisms underlying its strong antagonistic activity, we have sequenced the genome of C. sarge...

Pseudomonas aeruginosa biofilms exhibit an intrinsic resistance to antibiotics and constitute a considerable clinical threat. In cystic fibrosis, a common feature of biofilms formed by P. aeruginosa in the airway is the occurrence of mutants deficient in flagellar motility. This study investigates the impact of flagellum deletion on the structure a...

Small proteins of up to ∼50 amino acids are an abundant class of biomolecules across all domains of life. Yet, due to the challenges inherent in their size, they are often missed in genome annotations, and are difficult to identify and characterize using standard experimental approaches. Consequently, we still know few small proteins even in well-s...

Compost applications vary in their plant growth promotion and plant disease suppression, likely due to differences in physico-chemical and biological parameters. Our hypothesis was that bacteria are important for plant growth promotion and disease suppression of composts and, therefore, composts having these traits would contain similar sets of ind...

Paraburkholderia phymatum STM815, a rhizobial strain of the Burkholderiaceae family, is able to nodulate a broad range of legumes including the agriculturally important Phaseolus vulgaris (common bean). P. phymatum harbors two type VI Secretion Systems (T6SS-b and T6SS-3) in its genome that contribute to its high interbacterial competitiveness in v...

Aureobasidium pullulans is an extremotolerant, cosmopolitan yeast-like fungus that successfully colonises vastly different ecological niches. The species is widely used in biotechnology and successfully applied as a commercial biocontrol agent against postharvest diseases and fireblight. However, the exact mechanisms that are responsible for its an...

Small proteins play essential roles in bacterial physiology and virulence, however, automated algorithms for genome annotation are often not yet able to accurately predict the corresponding genes. The accuracy and reliability of genome annotations, particularly for small open reading frames (sORFs), can be significantly improved by integrating prot...

Background The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 a...

A Correction to this paper has been published: https://doi.org/10.1038/s41597-020-00747-0

Pseudomonas aeruginosa MPAO1 is the parental strain of the widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and biofilm-associated antibiotic resistance. Our model employs a genomics-driven workflow to assemble the complete MPAO1 genome,...

Root-knot nematodes (genus Meloidogyne) are plant parasites causing huge economic loss in the agricultural industry and affecting severely numerous developing countries. Control methods against these plant pests are sparse, the preferred one being the deployment of plant cultivars bearing resistance genes against Meloidogyne species. However, M. en...

The application of biocontrol biopesticides based on plant growth–promoting rhizobacteria (PGPR), particularly members of the genus Bacillus, is considered a promising perspective to make agricultural practices sustainable and ecologically safe. Recent advances in genome sequencing by third-generation sequencing technologies, e.g., Pacific Bioscien...

Small open reading frame encoded proteins (SEPs) gained increasing interest during the last years due to their broad range of important functions in both, prokaryotes and eukaryotes. In bacteria, signalling, virulence or regulation of enzyme activities have been associated with SEPs. Nonetheless, the number of SEPs detected in large-scale proteome...

Soil-borne diseases cause significant yield losses worldwide, are difficult to treat and often only limited options for disease management are available. It has long been known that compost amendments, which are routinely applied in organic and integrated farming as a part of good agricultural practice to close nutrient cycles, can convey a protect...

Leader peptides encoded by transcription attenuators are widespread small proteins that are considered nonfunctional in trans . We found that the leader peptide peTrpL of the soil-dwelling plant symbiont Sinorhizobium meliloti is required for differential, posttranscriptional regulation of a multidrug resistance operon upon antibiotic exposure. Mul...

Small proteins play diverse and essential roles in bacterial physiology and virulence. Despite their importance, automated genome annotation algorithms still cannot accurately annotate all respective small open reading frames (sORFs), as they usually provide insufficient sequence information for domain and homology searches, tend to be species spec...

For plants, the advantages of associating with beneficial bacteria include plant growth promotion, reduction of abiotic and biotic stresses and enhanced protection against various pests and diseases. Beneficial bacteria rightly equipped for successful plant colonization and showing antagonistic activity toward plant pathogens seem to be actively re...

Supplemental Information to Varadarajan_Allan_et_al

Pseudomonas aeruginosa MPAO1 is the parental strain of the widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and antibiotic resistance. Our model employs a genomics-driven workflow to assemble the complete MPAO1 genome, identify unique and...

Bacillus velezensis strains are applied as ecologically safe biopesticides, plant growth promoting rhizobacteria (PGPR), and in veterinary probiotics. They are abundant in various environments including soil, plants, marine habitats, the intestinal micro-flora, etc. The mechanisms underlying this adaptive plasticity and bioactivity are not well unde...

Metschnikowia pulcherrima synthesizes the pigment pulcherrimin, from cyclodileucine (cyclo(Leu‐Leu)) as a precursor, and exhibits strong antifungal activity against notorious plant pathogenic fungi. This yeast therefore has great potential for biocontrol applications against fungal diseases; particularly in the phyllosphere where this species is fr...

Background: Complete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bacterial strain is in most cases straightforward, more informative data about co-existing bacteria as well as sy...

Listeria monocytogenes is an opportunistic foodborne pathogen responsible for listeriosis, a potentially fatal foodborne disease. Many different Listeria strains and serotypes exist, but a proteogenomic resource that bridges the gap in our molecular understanding of the relationships between the Listeria genotypes and phenotypes via proteotypes is...

Leaf phenotype of different legume hosts inoculated with Bradyrhizobium diazoefficiens 110spc4 or USDA 110. All tested host plants [Glycine max cv. Williams 82 and cv. Black jet (soybeans), Vigna radiata (mung bean), Vigna unguiculata (cowpea), Macroptillium atropurpureum (siratro), and Aeschynomene afraspera] displayed dark-green leaves when inocu...

Quality assessment of the shotgun proteomics samples (3 biological replicates each for growth under oxic and microoxic conditions) by a clustering analysis (heatmap based on semi-quantitative spectral count data).

List of 26 USDA 110 genes affected by a frameshift caused by a single nucleotide insertion or deletion compared to strain 110spc4. We also list which of the encoded proteins (based on a search against the USDA 110 protein database) and their respective 110spc4 orthologs (based on a search against the 110spc4 protein database) were found to be expre...

List of antibodies and conditions applied in western blot experiments performed in this study.

PCR verification of the ~202 kb deletion present in Bradyrhizobium diazoefficiens USDA 110 derivatives 110spc4 (Regensburger and Hennecke, 1983) and 110rif 15 (Regensburger and Hennecke, 1984). (A) Schematic representation of the genomic region comprising the deletion between genome position no. 8,974,768 and 70,634 in the reference strain USDA 110...

Venn diagram showing the overlap of 110spc4 orthologs (see section Materials and Methods) of the 506 previously identified microoxia-specific transcribed genes (Pessi et al., 2007) with the 288 proteins uniquely expressed in microoxia (this study) and 2,900 proteins expressed in oxia (this study). The overlap revealed that 647 genes/proteins were o...

List of references included in the Supplementary Material.

List of the 91 B. diazoefficiens microoxia-induced genes (log2 fold change ≥ 1; i.e., FC ≥ 2) whose corresponding protein product was not induced under microoxic conditions compared to oxic conditions (log2 FC ≤ 0.5 or multiple testing corrected p-value ≥ 0.9).

Example of proteogenomic evidence for novelties based on genome sequence differences. (A) The correct genomic sequence of strain 110spc4 is shown for a region of interest along with that of the USDA 110 reference strain and the respective annotations. Bdiaspc4_16655 is annotated as a sugar ABC transporter gene in strain 110spc4 (upper panel), predi...

List of 223 CDS located in the ~202 kb genomic region that is deleted in B. diazoefficiens 110spc4 compared to the USDA110 NCBI reference genome (corresponding to nucleotide positions 8,974,768–9,105,828 and 1–70,634). The respective COG classification was determined using the eggNOG database “bactNOG” (Huerta-Cepas et al., 2016) and is shown for 1...

Lookup “master” table containing 6 sheets with different lists of proteins (corresponding to the results section) from B. diazoefficiens 110spc4, their locustag identifiers, genomic coordinates, the respective equivalent protein-coding gene (with locustag and coordinates) in B. diazoefficiens USDA 110 as well as functional annotations. The “Overvie...

The adaptation of rhizobia from the free-living state in soil to the endosymbiotic state comprises several physiological changes in order to cope with the extremely low oxygen availability (microoxia) within nodules. To uncover cellular functions required for bacterial adaptation to microoxia directly at the protein level, we applied a systems biol...

Ribosome-mediated transcription attenuation in bacteria is an important regulatory mechanism that is controlled by the translation of a short upstream ORF (uORF). Efficient uORF translation causes transcription termination downstream of the uORF. The resulting leader peptide and small attenuator RNA are generally considered nonfunctional. Here, we...

Root-knot nematodes (genus Meloidogyne ) are plant parasitic species that cause huge economic loss in the agricultural industry and affect the prosperity of communities in developing countries. Control methods against these plant pests are sparse and the current preferred method is deployment of plant cultivars bearing resistance genes against Melo...

Metschnikowia pulcherrima synthesizes the red pigment pulcherrimin, from cyclodileucine (cyclo(Leu-Leu)) as a precursor, and exhibits strong antifungal activity against notorious plant pathogenic fungi such as Botrytis and Gibberella (i.e., Fusarium ). This yeast therefore has great potential for biocontrol applications against fungal diseases; par...

Background Complete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bacterial strain is in most cases straightforward, more informative data about co-existing bacteria as well as syne...

Generating a complete, de novo genome assembly for prokaryotes is often considered a solved problem. However, we here show that Pseudomonas koreensis P19E3 harbors multiple, near identical repeat pairs up to 70 kilobase pairs in length, which contained several genes that may confer fitness advantages to the strain. Its complex genome, which also in...