Biology subjects

Siemers, M.

Publications and source records attributed to Siemers, M..

5 recordsLinked to original sources

bioRxiv2025

Widespread synchronization of codon usage in functionally related genes

The usage of synonymous codons varies along the genome, with strong biases in conserved and highly expressed genes that are optimized for efficient translation. The extent to which selection shapes codon usage in other genes, as well as the associations between gene function, gene expression, and codon usage, remains an important open question. We developed and optimized a novel approach to detect synchronized changes in codon usage patterns and applied it to 15,005 species-representative bacterial genomes spanning the 15 most represented phyla. We show that codon usage is extensively shaped by selection in both highly and lowly expressed genes, with at least [~]20-46% of gene families showing synchronized codon usage evolution across genomes. We reveal that gene pairs with parallel codon usage adaptation are co-expressed, co-regulated, metabolically connected, and functionally associated. By identifying synchronized codon usage evolution between gene pairs, we have generated a genome-wide set of functional associations reflecting correlated expression across species. This underappreciated layer of coordinated codon usage adaptation has important implications for function discovery and engineering.

genomics↗

bioRxiv2025

A 3UTR-derived small RNA modulates the life-cycle of the cholera toxin-encoding filamentous phage, CTXphi

Bacteriophages (phages) are well known to be one of the major driving forces in bacterial evolution. This also applies to virulent microorganisms, such as the major human pathogen Vibrio cholerae, whose pathogenic potential and epidemic proliferation largely depends on the interaction with environmental phages. Specifically, integration of the CTX{phi} phage genome into the first chromosome of V. cholerae also introduced the ctxAB genes, encoding the primary toxin responsible for the severe acute diarrheal disease, cholera. Whereas the mechanisms underlying CTX{phi}-associated horizontal gene transfer and transcriptional control of the ctxAB genes have been intensively studied over the past years, post-transcriptional regulation affecting the CTX{phi} life-cycle has not been documented. Here, we report the discovery and characterization of the CisR small RNA (sRNA) that is produced from the 3UTR (untranslated region) of the prtV gene and inhibits the expression of the CTX{phi}-encoded cep mRNA. CisR-mediated repression of cep involves Hfq-assisted base-pairing of the two transcripts and results in reduced CTX{phi} production under stress conditions. We further demonstrate that transcription of prtV-cisR requires both the master quorum-sensing regulator HapR and CRP, a global regulator of carbon metabolism. Taken together, our work provides evidence that V. cholerae employs sRNA-mediated post-transcriptional gene regulation to coordinate CTX{phi} activation with both cell density and nutrient availability. SIGNIFICANCE STATEMENTThe integration of the CTX{phi} phage genome, which carries the ctxAB toxin genes, is essential for cholera pathogenesis in humans. While transcriptional control of CTX{phi} and ctxAB has been well-studied, post-transcriptional mechanisms remain unexplored. Here, we identify and characterize CisR, a small RNA derived from the 3' untranslated region of prtV, which inhibits the CTX{phi}-encoded cep mRNA through Hfq-dependent base-pairing. CisR-mediated regulation limits phage production under stress conditions and is co-regulated by the quorum-sensing factor HapR and the metabolic regulator CRP. Our findings reveal a new RNA-based mechanism linking CTX{phi} phage activation to cell density and nutrient status of V. cholerae.

microbiology↗

bioRxiv2024

MftG is crucial for alcohol metabolism of mycobacteria by linking mycofactocin oxidation to respiration

Mycofactocin is a redox cofactor essential for the alcohol metabolism of mycobacteria.. While the biosynthesis of mycofactocin is well established, the gene mftG, which encodes an oxidoreductase of the glucose-methanol-choline superfamily, remained functionally uncharacterized. Here, we show that MftG enzymes are almost exclusively found in genomes containing mycofactocin biosynthetic genes and are present in 75% of organisms harboring these genes. Gene deletion experiments in Mycolicibacterium smegmatis demonstrated a growth defect of the {Delta}mftG mutant on ethanol as a carbon source, accompanied by an arrest of cell division reminiscent of mild starvation. Investigation of carbon and cofactor metabolism implied a defect in mycofactocin reoxidation. Cell-free enzyme assays and respirometry using isolated cell membranes indicated that MftG acts as a mycofactocin dehydrogenase shuttling electrons toward the respiratory chain. Transcriptomics studies also indicated remodeling of redox metabolism to compensate for a shortage of redox equivalents. In conclusion, this work closes an important knowledge gap concerning the mycofactocin system and adds a new pathway to the intricate web of redox reactions governing the metabolism of mycobacteria.

microbiology↗

bioRxiv2023

ChimericFragments: Computation, analysis, and visualization of global RNA networks

RNA-RNA interactions are key for post-transcriptional gene regulation in all domains of life. While ever more experimental protocols are being developed to study RNA-RNA interactions on a genome-wide scale, computational methods to analyze the underlying data are lagging behind. Here, we present ChimericFragments, an analysis and visualization framework for RNA-seq experiments producing chimeric RNA molecules. ChimericFragments implements a novel statistical method based on the complementarity of the base-pairing RNAs around their ligation site and is compatible with several widely used experimental procedures. We demonstrate that ChimericFragments enables the systematic identification of RNA regulators and RNA-RNA pairs and outperforms existing approaches.

bioinformatics↗

bioRxiv2020

A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2

Corona virus spike protein S is a large homo-trimeric protein embedded in the membrane of the virion particle. Protein S binds to angiotensin-converting-enzyme 2, ACE2, of the host cell, followed by proteolysis of the spike protein, drastic protein conformational change with exposure of the fusion peptide of the virus, and entry of the virion into the host cell. The structural elements that govern conformational plasticity of the spike protein are largely unknown. Here, we present a methodology that relies upon graph and centrality analyses, augmented by bioinformatics, to identify and characterize large H-bond clusters in protein structures. We apply this methodology to protein S ectodomain and find that, in the closed conformation, the three protomers of protein S bring the same contribution to an extensive central network of H-bonds, has a relatively large H-bond cluster at the receptor binding domain, and a cluster near a protease cleavage site. Markedly different H-bonding at these three clusters in open and pre-fusion conformations suggest dynamic H-bond clusters could facilitate structural plasticity and selection of a protein S protomer for binding to the host receptor, and proteolytic cleavage. From analyses of spike protein sequences we identify patches of histidine and carboxylate groups that could be involved in transient proton binding.

bioinformatics↗