Biology subjects

Jansen, R. S.

Publications and source records attributed to Jansen, R. S..

10 recordsLinked to original sources

bioRxiv2026

A new stress-response pathway in Mycobacterium tuberculosis

Metabolic adaptations are key in the virulence of the pathogen Mycobacterium tuberculosis (Mtb). However, our current understanding of these adaptations is limited to common pathways in central carbon metabolism. Here we apply an untargeted bottom-up approach to discover unknown stress-responsive metabolites and their biosynthetic enzyme. We show that upon exposure to hypoxia, nitric oxide and activated macrophages, Mtb rapidly produces high levels of an unknown metabolite that we identify as 6-{gamma}-amino-butyric acid-trehalose (GABA-trehalose). Formation of millimolar GABA-trehalose levels under these stresses is driven by a rapid rise in GABA, which is also excreted. We demonstrate that GABA-trehalose is produced from GABA and trehalose by the uncharacterized ATP-grasp enzyme Rv1722, involving a carboxylate-hydroxyl ligation that is non-canonical for ATP-grasp enzymes. Phylogenetic analyses demonstrate that the gene rv1722 is present in most slow-growing mycobacteria but absent in most rapid-growing mycobacteria. While the role of GABA-trehalose in Mtb metabolism remains unclear, we postulate that the increased NADH/NAD+ ratio under hypoxia and nitric oxide exposure promotes GABA formation and inhibits its breakdown, leading to GABA accumulation and excretion. Rv1722-driven coupling of GABA and trehalose constitutes an alternative to excretion that conserves carbon and nitrogen. Taken together, our bottom-up approach reveals a new stress-response pathway in Mtb that rapidly produces large quantities of GABA-trehalose. These findings extend our knowledge of the metabolic adaptations that a major human pathogen utilizes in response to immune system-imposed stresses.

biochemistry↗

bioRxiv2026

The molecular mechanism and activity of Kuenenia stuttgartiensis hydrazine synthase

Anaerobic ammonium-oxidizing (anammox) bacteria convert ammonium and nitrite into dinitrogen gas via the intermediates nitric oxide and hydrazine. To produce hydrazine, anammox bacteria harbor a biochemically unique enzyme: hydrazine synthase. Based on the hydrazine synthase crystal structure it was hypothesized that hydrazine is produced in a two-step mechanism. In this hypothesis, nitric oxide is first reduced to hydroxylamine (first half-reaction), followed by condensation of hydroxylamine with ammonium to hydrazine (second half-reaction). Here, we experimentally investigated the proposed molecular mechanism of hydrazine synthase and characterized and optimized the in vitro activity. First, we optimized the activity of isolated hydrazine synthase from anammox bacterium Kuenenia stuttgartiensis strain MBR1 via an anaerobic isolation method. We further compared hydrazine synthase activity measured via a coupled assay versus that of a newly established direct LC-MS assay. Next, the hypothesized second half-reaction was investigated via the direct LC-MS assay, quantifying biologically produced hydrazine from hydroxylamine and ammonium. Despite variation in hydrazine synthase activity across assays, we determined ammonium and hydroxylamine affinity and investigated product inhibition. Finally, we found that hydrazine synthesis from ammonium and hydroxylamine by isolated hydrazine synthase is oxygen-tolerant, strongly suggesting that the second half-reaction is initiated on an oxidized heme within hydrazine synthase. Taken together, the results corroborate that condensation of ammonium with hydroxylamine to form hydrazine is the second half-reaction of the proposed two-step mechanism for hydrazine synthesis by hydrazine synthase.

microbiology↗

bioRxiv2026

Quantification of hydrazine in biochemical assays and anammox bacteria using LC-MS

Hydrazine is an industrially valuable product. Strikingly, hydrazine is also a key intermediate in the energy metabolism of anaerobic ammonium-oxidizing (anammox) bacteria, where it is formed by hydrazine synthase. To study the molecular mechanism and activity of isolated hydrazine synthase, a sensitive, relatively fast and easy method to quantify hydrazine is needed. However, reported methods such as colorimetric assays, MALDI-TOF MS, and enzymatic conversion of hydrazine to dinitrogen gas, are either insensitive or laborious. In this study, we describe the validation and application of a fast and simple liquid chromatography-mass spectrometry (LC-MS) method to reproducibly quantify hydrazine produced by anammox hydrazine synthase. Hydrazine was derivatized with benzaldehyde, and directly injected onto a C18 column coupled to a Q-TOF MS. To increase assay performance, 15N2-hydrazine was included as internal standard. The response ratio of hydrazine was linearly proportional to the hydrazine concentration from 0.05-1 {micro}M with an average correlation coefficient of 0.9925. Intra- and inter-day accuracy lay between 88-113% and 95-105%, respectively. Intra- and inter-day precision (RSD, %) [≤] 11%. Hydrazine and derivatized hydrazine were stable when stored at -70{degrees}C or in the autosampler. We successfully applied the LC-MS method to determine hydrazine production by isolated hydrazine synthase and within cell lysate of anammox bacteria.

biochemistry↗

bioRxiv2025

Mini-bacterioferritins: Structural insight into a new type of ferritin-like protein from an anaerobic methane-oxidising archaeon

Ferritins are ubiquitous among life forms, as they are essential for iron homeostasis. Here, we unveiled a novel member of the ferritin family, baptised mini-bacterioferritin. The characterised mini-bacterioferritin was isolated from a microbial enrichment dominated by the methanotrophic archaeon Candidatus Methanoperedens BLZ2. Its atomic resolution crystal structure reveals a 12-mer assembly with a diiron ferroxidase centre located within a four-helix bundle. Redox cycling experiments on protein crystals reveal a shift in iron position at the active site, which follows the established ferritin catalytic cycle. The 12-mer sphere-like structure harboured six Fe-coproporphyrin III ligands, positioned at the interdimeric interface, a characteristic previously only found in 24-mer bacterioferritins. Phylogenetics, together with structure predictions of closely related proteins, revealed that mini-bacterioferritins form a new clade within the ferritin family that might conserve ancestral traits. Future research will need to investigate the physiological roles of these enzymes, which were unsuspectingly widely distributed among prokaryotes. TeaserA novel ferritin family, the heme-binding mini-bacterioferritin, assembles as a dodecamer and is widely distributed among microbes.

biochemistry↗

bioRxiv2025

Nitric oxide-forming nitrite reductases in the anaerobic ammonium oxidizer Kuenenia stuttgartiensis

Anaerobic ammonium-oxidizing (anammox) bacteria contribute to the global nitrogen cycle by removing fixed nitrogen from the environment. They do so via the anaerobic oxidation of ammonium to dinitrogen gas, with nitrite as terminal electron acceptor. The first step in this so-called anammox reaction is the conversion of nitrite to nitric oxide by nitrite reductase. Next, nitric oxide is combined with ammonium to form hydrazine by hydrazine synthase, after which hydrazine is oxidized to dinitrogen gas by hydrazine dehydrogenase. In contrast to the other catabolic anammox enzymes, different anammox species encode different potential nitrite reductase enzymes. On top of that, there is a redundancy in genes encoding for nitrite reductase in single anammox species. The unusual diversity and redundancy in anammox nitrite reductases is unexplained. The genome of the model anammox species "Candidatus Kuenenia stuttgartiensis" encodes for three putative nitrite reductases. Here, we investigated which of these nitrite reductases is or are active in K. stuttgartiensis. Active nitric oxide-producing nitrite reductases were enriched from K. stuttgartiensis cells via fast protein liquid chromatography. Nitric oxide production by the enriched nitrite reductases was followed with membrane inlet mass spectrometry. Combining the activity assays with proteomics analysis indicated that the soluble nitrite reductases NirS and HAOr most strongly correlated with enzyme activity. This indicates that K. stuttgartiensis employs two distinct nitrite reductases to keep its nitric oxide pool replenished.

microbiology↗

bioRxiv2024

From Eggs to Guts: Symbiotic Association of Sodalis nezarae sp. nov. with the Southern Green Shield Bug Nezara viridula

Phytophagous insects engage in symbiotic relationships with bacteria that contribute to digestion, nutrient supplementation, and development of the host. The analysis of shield bug microbiomes has been mainly focused on the gut intestinal tract predominantly colonized by Pantoea symbionts, and other microbial community members in the gut or other organs have hardly been investigated. In this study, we reveal that the Southern green shield bug Nezara viridula harbours a Sodalis symbiont in several organs, with a notable prevalence in salivary glands, and anterior regions of the midgut. Removing external egg microbiota via sterilization profoundly impacted insect viability but did not disrupt the vertical transmission of Sodalis and Pantoea symbionts. Based on the dominance of Sodalis in testes, we deduce that N. viridula males could be involved in symbiont vertical transmission. Genomic analyses comparing Sodalis species revealed that Sodalis sp. Nvir shares characteristics with both free- living and obligate insect-associated Sodalis spp. Sodalis sp. Nvir also displays genome instability typical of endosymbiont lineages, which suggests ongoing speciation to an obligate endosymbiont. Together, our study reveals that shield bugs harbour unrecognized symbionts that might be paternally transmitted.

microbiology↗

bioRxiv2022

MS2Query: Reliable and Scalable MS2 Mass Spectral-based Analogue Search

Metabolomics-driven discoveries of biological samples remain hampered by the grand challenge of metabolite annotation and identification. Only few metabolites have an annotated spectrum in spectral libraries; hence, searching only for exact library matches generally returns a few hits. An attractive alternative is searching for so-called analogues as a starting point for structural annotations; analogues are library molecules which are not exact matches, but display a high chemical similarity. However, current analogue search implementations are not yet very reliable and relatively slow. Here, we present MS2Query, a machine learning-based tool that integrates mass spectral embedding-based chemical similarity predictors (Spec2Vec and MS2Deepscore) as well as detected precursor masses to rank potential analogues and exact matches. Benchmarking MS2Query on reference mass spectra and experimental case studies demonstrates an improved reliability and scalability. Thereby, MS2Query offers exciting opportunities for further increasing the annotation rate of complex metabolite mixtures and for discovering new biology.

bioinformatics↗

bioRxiv2021

Multiple acyl-CoA dehydrogenase deficiency kills Mycobacterium tuberculosis in vitro and during infection

The human pathogen Mycobacterium tuberculosis (Mtb) devotes a significant fraction of its genome to fatty acid metabolism. Although Mtb depends on host fatty acids as a carbon source, fatty acid {beta}-oxidation is mediated by genetically redundant enzymes, which has hampered the development of antitubercular drugs targeting this metabolic pathway. Here, we identify rv0338c, referred to as etfDMtb, to encode a membrane dehydrogenase essential for fatty acid {beta}-oxidation in Mtb. An etfD deletion mutant ({Delta}etfD) was incapable of growing on fatty acids in vitro, with long-chain fatty acids being bactericidal, and failed to grow and survive in mice. The {Delta}etfD metabolome revealed a block in {beta}-oxidation at the step catalyzed by acyl-CoA dehydrogenases (ACADs). In many organisms, including humans, ACADs are functionally dependent on an electron transfer flavoprotein (ETF) and cognate dehydrogenase. Immunoprecipitation identified EtfD in complex with FixA (EtfBMtb). FixA (EtfBMtb) and FixB (EtfAMtb) are homologous to the human ETF subunits. Our results demonstrate that EtfBAMtb constitutes Mtbs ETF, while EtfDMtb, although not homologous to human EtfD, functions as the dehydrogenase. These findings identify Mtbs fatty acid {beta}-oxidation as a novel potential target for TB drug development.

microbiology↗

bioRxiv2019

Ankylosis homologue (ANKH) controls extracellular citrate and pyrophosphate homeostasis and affects bone mechanical performance

The membrane protein Ankylosis homologue (ANKH, mouse orthologue: ANK) prevents mineralization of joint-space and articular cartilage. The accepted view is that ANKH mediates cellular release of inorganic pyrophosphate (PPi), a strong physiological inhibitor of mineralization. Using global metabolite profiling, we identified citrate as the most prominent metabolite leaving HEK293 cells in an ANKH-dependent manner. Although PPi levels were increased in culture medium of HEK293-ANKH cells, PPi was formed extracellularly after release of ATP and other nucleoside triphosphates. Ankank/ank mice, which lack functional ANK, had substantially reduced concentrations of citrate in plasma and urine, while citrate was undetectable in urine of a human patient lacking functional ANKH. Bone hydroxyapatite of Ankank/ank mice also contained markedly reduced levels of citrate and PPi and displayed diminished strength. Together, our data show that ANKH is a crucial factor in extracellular citrate and PPi homeostasis that is essential for normal bone development.

developmental biology↗

bioRxiv2019

Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis

Organisms are defined by their genomes, yet many distinguishing features of a given organism are encoded by genes that are functionally unannotated. Mycobacterium tuberculosis (Mtb), the leading cause of death due to a single microbe, co-evolved with humans as its only known natural reservoir, yet the factors mediating Mtbs pathogenicity remain incompletely defined. rv3722c is a gene of unknown function predicted to encode a pyridoxal phosphate binding protein and to be essential for in vitro growth of Mtb. Using metabolomic, genetic and structural approaches, we show that Rv3722c is the primary aspartate aminotransferase of Mtb and mediates an essential but underrecognized role in metabolism: nitrogen distribution. Together with the attenuation of Rv3722c-deficient Mtb in macrophages and mice, these results identify aspartate biosynthesis and nitrogen distribution as potential species-selective drug targets in Mtb.

microbiology↗