Biology subjects

Heiniger, B.

Publications and source records attributed to Heiniger, B..

5 recordsLinked to original sources

bioRxiv2026

GenomeCompendium: A database for the integrated analysis of repeats, assembly quality and functional content of complete prokaryotic genomes

Microorganisms hold great promise for urgent global needs such as increasing sustainable agricultural production while reducing chemical fertilizer and pesticide use or providing novel classes of antimicrobials/therapeutics. Moving from analyzing microbiome composition to applying synthetic communities and studying their functions requires access to isolates and complete genome sequences. By spanning the frequent repeats, long-read sequencing can resolve complex prokaryotic genomes, yet error-prone short-read assemblies dominate. We here release the GenomeCompendium, a public database and interactive analysis tool for complete prokaryotic genomes (https://genome-compendium.com/). Using NCBI RefSeq (~47,000) and GenBank (~13,000) genomes, we integrated available metadata, GTDB taxonomy and computed features including repeat classes and gene content screening, intragenomic 16S rRNA sequence identity, and biosynthetic gene cluster co-occurrences. Evaluating repeat content and assembly complexity metrics, we identify taxonomic ranks dominated by difficult-to-assemble genomes and show that complex, repeat-rich genomes are more common than previously estimated. By mining metadata, our quality control flags 6.3% of RefSeq assemblies as potentially erroneous or incomplete. As valuable reference for data mining and to track taxonomic coverage, the GenomeCompendium links ~90 features across genomes, offers downloadable reports and -as unique features- pre-computed proteogenomics databases to improve genome annotations of RefSeq strains and the ability to analyze any uploaded prokaryotic genome.

genomics↗

bioRxiv2026

Proteogenomic discovery of novel small proteins in clinical Mycobacterium tuberculosis strains

Even though our meta-analysis ranks Mycobacterium tuberculosis genomes among the bacterial pathogens that are most straightforward to assemble, most available assemblies relied on short-read sequencing and contain genomic blind spots that miss functionally important genes. Complete genomes are essential for functional genomics, particularly for identifying small ORF-encoded proteins (SEPs; [≤]100 amino acids), which can play critical biological roles yet are frequently missed by standard annotations. Here, we generated complete long-read assemblies for six clinical reference strains representing lineage 1 and the more pathogenic lineage 2, followed by comparative genomic and proteogenomic analyses. We additionally provide software to predict comprehensive sets of mycobacteria-specific proline-glutamic acid (PE) and PPE family genes, including lineage-specific variants. Using parallel accumulation-serial fragmentation mass spectrometry, we detected approximately two-thirds of each strains annotated proteome from unfractionated cell extracts. Extending our proteogenomic framework across related strains, and adding rigorous control of proteogenomic discovery rates using entrapment strategies, we revealed 12-24 previously unannotated proteins per strain, predominantly SEPs, 56-60 alternative translation start sites, and 9-17 expressed pseudogenes. Newly identified proteins included conserved and lineage-specific SEPs, an antitoxin, candidate antimicrobial peptides and novel proteins under purifying selection. Overall, applying this improved proteogenomics method to phylogenomically selected clinical reference strains provides a valuable approach for discovering candidate diagnostics or therapeutics, as illustrated here for a WHO-listed critical bacterial pathogen.

microbiology↗

bioRxiv2025

A revised genome annotation of the model cyanobacterium Synechocystis based on start and stop codon-enriched ribosome profiling and proteogenomics

Cyanobacteria are important primary producers and are used as microbial cell factories due to their ability to use solar light for oxygenic photosynthesis. Synechocystis sp. PCC 6803 is a popular model cyanobacterium, yet there are ambiguities in the precise coding regions of many genes, and numerous genes encoding small proteins have remained undetected. Here we present the results of a riboproteogenomic analysis, combining ribosome profiling (Ribo-seq) analysis involving inhibitors that stall ribosomes at translation initiation and termination sites (TIS- and TTS-Ribo-seq), with a proteogenomic reevaluation and reannotation of its entire genome. We report evidence for the translation of 3,055 annotated genes based on proteogenomics (83%), of 3,492 based on Ribo-seq (95.2%), and of 3,018 supported by both methods (82%). The data suggested unannotated protein-coding genes and corrections for annotated ones. We validated 15 small proteins translated from antisense RNAs, from intergenic and intragenic regions and provide proteogenomic support for up to 69 further, mostly small proteins. With slr0489, slr1079 and slr1082 we identified three genes with intragenic out-of-frame translons and show that both the internal and host reading frames are translated and that the resulting proteins interact with each other. Our data can be accessed via an intuitive and interactive genome browser platform at https://www.bioinf.uni-freiburg.de/[~]ribobase/. They illustrate the enormous value of consolidating genome annotations in the context of integrated experimental data.

microbiology↗

bioRxiv2022

Small proteome of the nitrogen-fixing plant symbiont Sinorhizobium meliloti

The soil-dwelling plant symbiont Sinorhizobium meliloti is a major model organism of Alphaproteobacteria. Despite numerous detailed OMICS studies, information about small open reading frame (sORF)-encoded proteins (SEPs) is largely missing, because sORFs are poorly annotated, and SEPs are hard to detect experimentally. However, given that SEPs can fulfill important functions, cataloging the full complement of translated sORFs is critical for analyzing their roles in bacterial physiology. Ribosome profiling (Ribo-seq) can detect translated sORFs with high sensitivity, but is not yet routinely applied to bacteria because it must be adapted for each species. Here, we established a Ribo-seq procedure for S. meliloti 2011 based on RNase I digestion and detected translation for 60% of the annotated coding sequences during growth in minimal medium. Using ORF prediction tools based on Ribo-seq data, subsequent filtering, and manual curation, the translation of 37 non-annotated sORFs with [≤] 70 amino acids was predicted with high confidence. The Ribo-seq data were supplemented by mass spectrometry (MS) analyses from three sample preparation approaches and two integrated proteogenomic search databases (iPtgxDBs). Searches against a standard and a 20-fold smaller Ribo-seq data-informed custom iPtgxDB confirmed many annotated SEPs and identified 11 additional novel SEPs. Epitope tagging and Western blot analysis confirmed the translation of 15 out of 20 SEPs selected from the translatome map. Overall, by applying MS and Ribo-seq as complementary approaches, the small proteome of S. meliloti was substantially expanded by 48 novel SEPs. Several of them are conserved from Rhizobiaceae to Bacteria, suggesting important physiological functions.

molecular biology↗

bioRxiv2021

Genome-wide association study reveals complex genetic architecture of cadmium and mercury accumulation and tolerance traits in Medicago truncatula

Heavy metals are an increasing problem due to contamination from human sources that and can enter the food chain by being taken up by plants. Understanding the genetic basis of accumulation and tolerance in plants is important for reducing the uptake of toxic metals in crops and crop relatives, as well as for removing heavy metals from soils by means of phytoremediation. Following exposure of Medicago truncatula seedlings to cadmium (Cd) and mercury (Hg), we conducted a genome-wide association study using relative root growth (RRG) and leaf accumulation measurements. Cd and Hg accumulation and RRG had heritability ranging 0.44 - 0.72 indicating high genetic diversity for these traits. The Cd and Hg trait associations were broadly distributed throughout the genome, indicated the traits are polygenic and involve several quantitative loci. For all traits, candidate genes included several membrane associated ATP-binding cassette transporters, P-type ATPase transporters, several oxidative stress response genes and stress related UDP-glycosyltransferases. The P-type ATPase transporters and ATP-binding cassette protein-families have roles in vacuole transport of heavy metals, and our findings support their wide use in physiological plant responses to heavy metals and abiotic stresses. We also found associations between Cd RRG with the genes CAX3 and PDR3, two linked adjacent genes, and leaf accumulation of Hg associated with the genes NRAMP6 and CAX9. When plant genotypes with the most extreme phenotypes were compared, we found significant divergence in genomic regions using population genomics methods that contained metal transport and stress response gene ontologies. Several of these genomic regions show high linkage disequilibrium (LD) among candidate genes suggesting they have evolved together. Minor allele frequency (MAF) and effect size of the most significant SNPs was negatively correlated with large effect alleles being most rare. This is consistent with purifying selection against alleles that increase toxicity and abiotic stress. Conversely, the alleles with large affect that had higher frequencies that were associated with the exclusion of Cd and Hg. Overall, macroevolutionary conservation of heavy metal and stress response genes is important for improvement of forage crops by harnessing wild genetic variants in gene banks such as the Medicago HapMap collection.

plant biology↗