Biology subjects

Böhm, M.

Publications and source records attributed to Böhm, M..

6 recordsLinked to original sources

bioRxiv2026

Self-Sufficient Maturation and Catalysis of a Clade E CODH Encoded in a CooCTJ-Operon from Clostridium pasteurianum BC1

Carbon monoxide dehydrogenases (CODHs) are metalloenzymes central to microbial CO metabolism and CO2 fixation. We report the heterologous production and characterisation of Clostridium pasteurianum BC1 CODH-III (CpBC1CODH-III), from the phylogenetic clade E, co-expressed with its maturation machinery CooCTJ. CpBC1CODH-III shows moderate CO oxidation (150 U/mg) and CO2 reduction (0.568 U/mg) activities. Electron paramagnetic resonance (EPR) spectroscopy under varying redox conditions identified a rhombic signal at g {approx} 2.0, characteristic of reduced B-clusters, and a C-clusters at different stages (g {approx} 1.75, g {approx} 1.72), indicative of a bound CO2. Investigation of maturation effects showed that co-expression of CooCTJ stabilised CpBC1CODH-III production, but did not enhance maximum activity, which was primarily influenced by nickel availability. Comparative operon analysis with the well-studied clade F Rhodospirillum rubrum CODH (RrCODH) revealed high structural similarity in CODH and CooC, but significant divergence in CooJ, with conserved metal-binding regions identified via AlphaFold3 modelling and dot plot analysis. CpBC1CODH-III represents a unique example of a clade E CODH within a clade F genomic context, demonstrating intrinsic robustness in maturation and activity

biochemistry↗

bioRxiv2025

Investigating the native functions of -carbon monoxide dehydrogenase through genomic context analysis

Carbon monoxide dehydrogenases containing nickel-iron active sites ([NiFe]-CODHs) catalyze the reversible oxidation of CO to CO2, representing key targets for biocatalytic CO2 reduction. Despite dramatic differences in catalytic rates and O2 tolerance between CODH variants, the molecular basis for this functional diversity remains poorly understood. We applied comparative genomics and synteny analysis to investigate the biochemical roles of CODH clades A-F using 1,376 CODH and 1,545 hybrid cluster protein sequences. Around 30% of genomes encode multiple CODH isoforms. Analysis revealed distinct gene clustering patterns correlating with biochemical function. Clades A, E, and F exhibit a degree of distributional exclusivity. Clades C and D frequently co-occur with active CODHs, suggesting auxiliary roles. Operon architecture analysis revealed functional specialization: clade A links to acetyl-CoA synthase; clades A, E and F contain essential maturation machinery (CooC, CooJ, CooT) correlating with catalytic activity; clade B associates with transporters; clade C with electron transfer partners; clade D with transcriptional regulators. High CODH-HCP co-occurrence (except clade A) suggests functional or environmental interdependency. These findings establish clades A, E and F as primary biocatalyst targets while defining regulatory functions for clades C and D, providing a genomics framework for predicting CODH phenotypes.

bioinformatics↗

bioRxiv2024

Quantifying the IUCN Red List: Using historical assessments to calculate future extinction risk

The IUCN Red List of Threatened Species assigns species to discrete categories based on a common set of criteria to capture relative extinction risk. Some quantitative analyses require a continuous probability of extinction not provided by discrete categories. Furthermore, the criteria may not translate to extinction risk in a universal way across species, because some species attributes are not incorporated into the criteria. Here we calculate extinction risk using Markov Models parameterised with historical IUCN Red List assessment data, and we provide quantitative extinction risk for use in downstream analyses. We find that taxonomy, body size, and habitat specialism interact with extinction risk in ways not fully captured by the existing categories. For example, an Endangered habitat specialist appears equally at risk compared to a Critically Endangered habitat generalist. We hope our findings will support more accurate quantitative biodiversity analyses of species extinctions and declines using Red List data.

ecology↗

bioRxiv2022

Past, present, and future of the Living Planet Index

As we enter the next phase of international policy commitments to halt biodiversity loss (e.g. Post-2020 Biodiversity Framework), biodiversity indicators will play an important role forming the robust basis upon which targeted, and time sensitive conservation actions are developed. Population trend indicators are perhaps the most powerful tool in biodiversity monitoring due to their responsiveness to changes over short timescales and their ability to aggregate species trends from global down to at a sub-national or even local scale. We consider how the project behind the foremost population level indicator - the Living Planet Index - has evolved over the last 25 years, its value to the field of biodiversity monitoring, and how its components have portrayed a compelling account of the changing status of global biodiversity through its application at policy, research and practice levels. We explore ways the project can develop to enhance our understanding of the state of biodiversity and share lessons learned to inform indicator development and mobilise action. O_TEXTBOXBox 1. The Living Planet Index Project The Living Planet Index project (the index, methodology, and database) and its secondary outputs (methods papers and R code, database and website, global index, and subset indices) have had wide-ranging applications within the fields of biodiversity monitoring and research, as well as across policy, education, and outreach. The Living Planet Index (LPI) is a biodiversity indicator which tracks trends in the relative abundance of wild vertebrate populations (where population is defined as to a single species in a defined location rather than the biological definition). Relative abundance captures how populations are changing over time on average in comparison to a reference point, or "baseline" (the LPI uses 1970). It is often described as analogous to a stock market index for species. The index is comprised of thousands of population time-series for vertebrate species from locations around the world; the trends from these populations are averaged to produce terrestrial, freshwater, and marine indices, which are further aggregated to a global LPI. The latest global LPI shows a decline of 68% between 1970 and 2016 globally 1. This is an average trend based on time-series data from 20,811 populations of 4,392 species of mammals, birds, reptiles, amphibians, and fish. The LPI database (LPD) can include population data for any species for which time-series population data could be found, regardless of threat status, or whether they show increasing or declining trends. These population time-series are sourced from scientific papers, online databases, government, and expert led published reports. They can be searched and downloaded from the project website (www.livingplanetindex.org). More technical information is available on the LPI stats website (http://stats.livingplanetindex.org/). C_TEXTBOX

ecology↗

bioRxiv2022

Automated assessment reveals extinction risk of reptiles is widely underestimated across space and phylogeny

The Red List of Threatened Species, published by the International Union for Conservation of Nature (IUCN), is a crucial tool for conservation decision making. However, despite substantial effort, numerous species remain unassessed, or have insufficient data available to be assigned a Red List threat category. Moreover, the Red Listing process is subject to various sources of uncertainty and bias. The development of robust automated assessment methods could serve as an efficient and highly useful tool to accelerate the assessment process and offer provisional assessments. Here we aimed to: 1) present a machine learning based automated threat assessment method that can be used on less known species; 2) offer provisional assessments for all reptiles - the only major tetrapod group without a comprehensive Red List assessment; and 3) evaluate potential effects of human decision biases on the outcome of assessments. We use the method presented here to assess 4,369 reptile species that are currently unassessed or classified as Data Deficient by the IUCN. Our models range in accuracy from 88% to 93% for classifying species as threatened/non-threatened, and from 82% to 87% for predicting specific threat categories. Unassessed and Data Deficient reptiles were more likely to be threatened than assessed species, adding to mounting evidence that they should be considered threatened by default. The overall proportion of threatened species greatly increased when we included our provisional assessments. Assessor identities strongly affected prediction outcomes, suggesting that assessor effects need to be carefully considered in extinction risk assessments. Regions and taxa we identified as likely to be more threatened should be given increased attention in new assessments and conservation planning. Lastly, the method we present here can be easily implemented to help bridge the assessment gap on other less known taxa.

ecology↗

bioRxiv2021

Differentially accessible Cdc4 phospho-degrons regulate Ctf19CCAN kinetochore subunit stability in mitosis

Kinetochores are multi-subunit protein assemblies that link chromosomes to microtubules of the mitotic and meiotic spindle. How effective, yet strictly centromere-dependent kinetochore assembly is coupled to cell cycle progression is incompletely understood. Here, by combining comprehensive phosphorylation analysis of native Ctf19CCAN subunits with biochemical and functional assays in the model system budding yeast, we demonstrate that Cdk1 phosphorylation activates phospho-degrons on the essential subunit Ame1CENP-U which are recognized by the E3 ubiquitin ligase complex SCF-Cdc4. Gradual phosphorylation of degron motifs culminates in M-Phase and targets the protein for degradation. Binding of the Mtw1 complex shields the proximal phospho-degron, protecting kinetochore-bound Ame1 from the degradation machinery. Artificially increasing degron strength partially suppresses the temperature-sensitivity of a cdc4 mutant, while overexpression of Ame1-Okp1 is toxic to cells, demonstrating the physiological importance of this mechanism. We propose that phospho-regulated clearance of excess CCAN subunits protects against ectopic kinetochore assembly and contributes to mitotic checkpoint silencing. Our results suggest a novel strategy for how phospho-degrons can be used to regulate the assembly of multi-subunit complexes.

cell biology↗