Gene products and processes contributing to lanthanide homeostasis and methanol metabolism in Methylorubrum extorquens AM1

Abstract

Lanthanide elements have been recently recognized as “new life metals” yet much remains unknown regarding lanthanide acquisition and homeostasis. In Methylorubrum extorquens AM1, the periplasmic lanthanide-dependent methanol dehydrogenase XoxF1 produces formaldehyde, which is lethal if allowed to accumulate . This property enabled a transposon mutagenesis study and growth studies to confirm novel gene products required for XoxF1 function. The identified genes encode an MxaD homolog , an ABC-type transporter, an aminopeptidase, a putative homospermidine synthase, and two genes of unknown function annotated as orf6 and orf7 . Lanthanide transport and trafficking genes were also identified. Growth and lanthanide uptake were measured using strains lacking individual lanthanide transport cluster genes, and transmission electron microscopy was used to visualize lanthanide localization. We corroborated previous reports that a TonB-ABC transport system is required for lanthanide incorporation to the cytoplasm. However, cells were able to acclimate over time and bypass the requirement for the TonB outer membrane transporter to allow expression of xoxF1 and growth. Transcriptional reporter fusions show that excess lanthanides repress the gene encoding the TonB-receptor. Using growth studies along with energy dispersive X-ray spectroscopy and transmission electron microscopy, we demonstrate that lanthanides are stored as cytoplasmic inclusions that resemble polyphosphate granules.

Extracellular and Intracellular Lanthanide Accumulation in the Methylotrophic Beijerinckiaceae Bacterium RH AL1

“…Our RNAseqbased gene expression analysis made use of the fitness-increase upon lanthanide supplementation under heterotrophic growth conditions with pyruvate as carbon source. The observed, slight downregulation of the genes coding for homologs of the TonB-ABC transport system was in line with previous reports in M. extorquens AM1 and Methylotuvimicrobium buryatense 5GB1C that observed a down-regulation of this machinery in response to excess lanthanides (20,52). Similar observations are known from iron homeostasis (53,54).…”

“…The involvement of TonB-dependent receptors makes it likely that lanthanide uptake is linked to extracellular chelators similar to what is known for iron and copper uptake (17). Lanthanides are stored intracellularly in M. extorquens AM1 in mineral form (20). The widespread occurrence of lanthanide-dependent enzymes in (non-)methyotrophic organisms implies that multiple mechanisms for sensing, uptake, and on May 9, 2021 by guest http://aem.asm.org/ Downloaded from storing lanthanides exist in organisms that harness these metals for their metabolism.…”

“…This includes lanthanide uptake and storage. Recent work in Methylorubrum extorquens AM1 and M. extorquens PA1 has shown that lanthanide uptake is linked to TonB-ABC transport systems and lanthanide-shuttling proteins such as lanmodulin (18)(19)(20)(21) encoded by the lut (lanthanide utilization and transport) gene cluster. The involvement of TonB-dependent receptors makes it likely that lanthanide uptake is linked to extracellular chelators similar to what is known for iron and copper uptake (17).…”

Draft genome of a novel methanotrophic Methylobacter sp. from the volcanic soils of Pantelleria Island

“…Lanmodulin seems not to be encoded in the MAG. Other studies indicated that TonB-dependent transporters might be involved in REE transport over the outer membrane, which are encoded by tonB or cirA genes (Ochsner et al 2019;Roszczenko-Jasińska et al 2020). The draft genome of ''Ca.…”

Harnessing methylotrophs as a bacterial platform to reduce adverse effects of the use of the heavy lanthanide gadolinium in magnetic resonance imaging

“…M. fumariolicum SolV grows optimally in acidic conditions (pH 2-5) making Ln 3+ soluble for uptake and utilization, and as such does not have a known dedicated transport system for these metals. In contrast, methylotrophs that grow at neutral pH have an ABC transport system and specific TonB-dependent receptor encoded in a "lanthanide-utilization and transport" gene cluster (Roszczenko-Jasińska et al 2020;Ochsner et al 2019). Of such organisms known to date, only a genetically manipulated mutant strain of Methylotenera mobilis JLW8 has been reported to show indications of growth with Gd 3+ in the form of increased culture density (Huang, Yu, and Chistoserdova 2018).…”