Biology subjects

Komeili, A.

Publications and source records attributed to Komeili, A..

10 recordsLinked to original sources

bioRxiv2026

Inter-Individual Variability in Cycling Biomechanics During Experimentally Induced Movement-Evoked Knee Pain

Knee pain can alter lower-limb loading and contribute to inter-limb asymmetry, affecting movement mechanics and rehabilitation. Although cycling is frequently prescribed during rehabilitation, the effects of pain on bilateral cycling biomechanics remain poorly understood. This study investigated experimentally induced movement-evoked knee pain on bilateral torque and power output, inter-limb asymmetry, and inter-individual motor responses during cycling. Twenty-three healthy adults (14M and 9F) completed an incremental cycling test followed by eight randomized constant-load trials under pain and no-pain conditions at two intensities. A custom closed-loop torque-dependent electrical stimulation system induced movement-evoked knee pain during the downstroke while bilateral biomechanics were recorded. At higher intensities, movement-evoked knee pain reduced torque (p=0.026, d=0.566) and power (p=0.010, d=0.657) production in the painful limb and altered the normalized symmetry index (NSI) for power (p=0.005, d=0.659), and torque (p<0.001, d=0.754). At lower intensity, pain-leg power (p=0.154) and torque (p=0.104) did not differ significantly between conditions, although torque NSI indicated greater reliance on the non-pain leg (p=0.017, d=0.538). Despite these group-level responses, substantial inter-individual variability was observed ranging from pronounced unloading to increased pain-leg contribution. These findings demonstrate that movement-evoked knee pain alters cycling mechanical output toward the non-painful limb, with substantial heterogeneity in individual motor responses.

neuroscience↗

bioRxiv2025

Magnetosome organelles are organized through interactions between McaA and McaB that alter the dynamics of the bacterial actin-like protein MamK

Magnetotactic bacteria (MTB) are a group of Gram-negative species that produce a lipid-bounded organelle, the magnetosome, in which a magnetic crystal is biomineralized. MTB use magnetosomes to align with the geomagnetic field for improved navigation of their environment. To optimize this alignment, these species organize their magnetosomes in a linear fashion using a handful of factors including the bacterial actin-like protein MamK. Despite these shared features, there is a broad diversity of species-specific linear magnetosome chain arrangements within MTB, but the molecular mechanisms behind these phenotypic variations are unclear. Recently, genetic analyses showed that two proteins McaA and McaB interface with the chain organization machinery of Magnetospirillum magneticum AMB-to arrange magnetite crystals in a series of subchains rather than the single cohesive chains found in closely related MTB. Here, we use in vivo co-immunoprecipitation in AMB-1 to demonstrate protein-protein interactions between McaA, McaB, and MamK. Experiments with McaA truncation mutants and conditional control of McaB localization determined that McaA-McaB interactions are dependent on amino acids 530-665 of McaA and McaB localization to the magnetosome chain. We further show that disrupting the McaA-McaB interaction alters the spatial dynamics of MamK in vivo We present a model in which protein-protein interactions between McaA, McaB, and MamK drive changes in MamK behavior to establish AMB-1s magnetosome chain organization. IMPORTANCEMagnetosomes model for understanding the cell biology of bacterial organelles and the mechanisms of bacterial cell organization. MamK, one of the best-studied bacterial actins, is a notable player in magnetosome chain assembly. This work explores how MamK dynamics are altered by two potential bacterial actin binding proteins, McaA and McaB. This system illustrates how changes in bacterial cytoskeleton regulation result in different organization of subcellular compartments. The conclusions from this research also have implications for understanding the broader evolutionary strategies for regulation of actin-like proteins and compartment organization diversification in bacteria.

microbiology↗

bioRxiv2025

A network of coiled-coil and actin-like proteins controls the cellular organization of magnetosome organelles in deep-branching magnetotactic bacteria

Magnetotactic Bacteria (MTB) are a diverse group of microorganisms that use magnetosomes, organelles composed of magnetite or greigite, to navigate along geomagnetic fields. While MTB span several phyla and exhibit diverse phenotypes, magnetosome formation has been mechanistically studied in only two species of Alphaproteobacteria. Here, we use Desulfovibrio magneticus RS-1 to uncover the mechanisms behind tooth-shaped magnetosome assembly in deep-branching MTB. Our findings show that magnetic particles in RS-1 initially form randomly within the cell before localizing to the positive cell curvature. Genetic and proteomic analyses indicate that early biomineralization involves membrane-associated proteins found in all MTB, while later stages depend on coiled-coil (Mad20, 23, 25, and 26) and actin-like (MamK and Mad28) proteins, most of which are unique to deep-branching MTB. These findings suggest that while biomineralization originates from a common ancestor, magnetosome chain organization has distinct evolutionarily origins among different MTB lineages.

microbiology↗

bioRxiv2024

Intrinsic and extrinsic determinants of conditional localization of Mms6 to magnetosome organelles in Magnetospirillum magneticum AMB-1

Magnetotactic bacteria are a diverse group of microbes that use magnetic particles housed within intracellular lipid-bounded magnetosome organelles to guide navigation along geomagnetic fields. Development of magnetosomes and their magnetic crystals in Magnetospirillum magneticum AMB-1 requires the coordinated action of numerous proteins. Most proteins are thought to localize to magnetosomes during the initial stages of organelle biogenesis regardless of environmental conditions. However, magnetite-shaping protein Mms6 is only found in magnetosomes that contain magnetic particles, suggesting that it might conditionally localize after the formation of magnetosome membranes. The mechanisms for this unusual mode of localization to magnetosomes are unclear. Here, using pulse-chase labeling, we show that Mms6 translated under non-biomineralization conditions translocates to pre-formed magnetosomes when cells are shifted to biomineralizing conditions. Genes essential for magnetite production, namely mamE, mamM, and mamO are necessary for Mms6 localization, whereas mamN inhibits Mms6 localization. MamD localization is also investigated and found to be controlled by similar cellular factors. The membrane localization of Mms6 is dependent on a glycine-leucine repeat region, while the N-terminal domain of Mms6 is necessary for retention in the cytosol and impacts conditional localization to magnetosomes. The N-terminal domain is also sufficient to impart conditional magnetosome localization to MmsF, altering its native constitutive magnetosome localization. Our work illuminates an alternative mode of protein localization to magnetosomes in which Mms6 and MamD are kept in the cytosol by MamN until biomineralization initiates, whereupon they translocate into magnetosome membranes to control the development of growing magnetite crystals. ImportanceMagnetotactic bacteria (MTB) are a diverse group of bacteria that form magnetic nanoparticles surrounded by membranous organelles. MTB are widespread and serve as a model for bacterial organelle formation and biomineralization. Magnetosomes require a specific cohort of proteins to enable magnetite formation, but how those proteins are localized to magnetosome membranes is unclear. Here, we investigate protein localization using pulse-chase microscopy and find a system of protein coordination dependent on biomineralization permissible conditions. In addition, our findings highlight a protein domain that alters the localization behavior of magnetosome proteins. Utilization of this protein domain may provide a synthetic route for conditional functionalization of magnetosomes for biotechnological applications.

cell biology↗

bioRxiv2022

McaA and McaB control the dynamic positioning of a bacterial magnetic organelle

Magnetotactic bacteria (MTB) are a diverse group of microorganisms that use intracellular chains of ferrimagnetic nanocrystals, produced within their magnetosome organelles, to align and navigate along the geomagnetic field. The cell biological and biochemical properties of magnetosomes make them a powerful model for studying the molecular mechanisms of biomineralization and compartmentalization in bacteria. While several conserved magnetosome formation genes have been described, the evolutionary strategies for their species-specific diversification remain unknown. Here, we demonstrate that the fragmented nature of magnetosome chains in Magnetospirillum magneticum AMB-1 is controlled by two genes named mcaA and mcaB. McaA recognizes the positive curvature of the inner cell membrane while McaB localises to magnetosomes. Along with the MamK actin-like cytoskeleton, they create space for addition of new magnetosomes in between pre-existing magnetosomes. Phylogenetic analyses suggest that McaAB homologs are widespread and may represent an ancient strategy for organelle positioning in MTB.

microbiology↗

bioRxiv2021

Mapping the genetic landscape of biomineralization in Magnetospirillum magneticum AMB-1 with RB-Tnseq

Magnetotactic bacteria (MTB) are a phylogenetically diverse group of bacteria remarkable for their ability to biomineralize magnetite (Fe3O4) or greigite (Fe3S4) in organelles called magnetosomes. The majority of genes required for magnetosome formation are encoded by a magnetosome gene island (MAI). Most previous genetic studies in MTB have focused on the MAI, using screens to identify key MAI genes or targeted genetics to isolate specific genes and their function in one specific growth condition. Here, we conducted random barcoded transposon mutagenesis (RB-TnSeq) in Magnetospirillum magneticum AMB-1 to identify the global genetic requirements for magnetosome formation under different growth conditions. We generated a library of 184,710 unique strains in a wild-type background, generating ~34 mutant strains for each gene. RB-TnSeq also allowed us to determine the essential gene set of AMB-1 under standard laboratory growth conditions. To pinpoint novel genes that are important for magnetosome formation, we subjected the library to magnetic selection screens in varied growth conditions. We compared biomineralization in standard growth conditions to biomineralization in high iron and anaerobic conditions, respectively. Strains with transposon insertions in the MAI gene mamT had an exacerbated biomineralization defect under both high iron and anerobic conditions compared to standard conditions, adding to our knowledge of the role of MamT in magnetosome formation. Mutants in amb4151, a gene outside of the MAI, are more magnetic than wild-type cells under anaerobic conditions. All three of these phenotypes were validated by creating a markerless deletion strain of the gene and evaluating with TEM imaging. Overall, our results indicate that growth conditions affect which genes are required for biomineralization and that some MAI genes may have more nuanced functions than was previously understood.

microbiology↗

bioRxiv2020

Magnetotactic bacteria accumulate a large pool of iron distinct from their magnetite crystals

Magnetotactic bacteria (MTB) are ubiquitous aquatic microorganisms that form intracellular nanoparticles of magnetite (Fe3O4) or greigite (Fe3S4) in a genetically controlled manner. Magnetite and greigite synthesis requires MTB to transport a large amount of iron from the environment which is subsequently concentrated in organelles called magnetosomes for crystal precipitation and maturation. X-ray absorption analysis of MTB suggests that the intracellular iron is mainly contained within the crystals, thus preventing potential toxic effects of free iron. In contrast, recent mass spectrometry studies suggest that MTB may contain a large amount of iron that is not precipitated in crystals. Here, we attempt to resolve these descrepancies by performing chemical and magnetic assays to quantify the different iron pools in the magnetite-forming strain Magnetospirillum magneticum AMB-1 cultivated at varying iron concentrations. AMB-1 mutants showing defects in crystal precipitation were also characterized following the same approach. All results show that magnetite represents at most 30 % of the total intracellular iron under our experimental conditions. We further examined the iron speciation and subcellular localization in AMB-1 using the fluorescent indicator FIP-1 that is designed for detection of labile Fe(II). Staining with this probe suggests that unmineralized reduced iron is found in the cytoplasm and associated with magnetosomes. Our results demonstrate that, under our experimental conditions, AMB-1 is able to accumulate a large pool of iron distinct from magnetite. Finally, we discuss the biochemical and geochemical implications of these results. ImportanceMagnetotactic bacteria (MTB) are a group of microorganisms producing iron-based intracellular magnetic crystals. They represent a model system for studying iron homeostasis and biomineralization in bacteria. MTB contain an important mass of iron, about 10 to 100 higher than other bacterial model such as Escherichia coli, suggesting efficient iron uptake and storage systems. Accordingly, MTB have been proposed to significantly impact the iron biogeochemical cycle in sequestering a large amount of soluble iron into crystals. Recently, several studies proposed that MTB could also accumulate iron in a reservoir distinct from their crystals. Here, we present a chemical and magnetic methodology for quantifying the fraction of the total cellular iron contained in the magnetic crystals of the magnetotactic strain Magnetospirillum magneticum AMB-1. Comparison of the mass of iron contained in the different cellular pools showed that most of the bacterial iron is not contained in AMB-1 crystals. We then adapted protocols for the fluorescent detection of Fe(II) in bacteria, and showed that iron could be detected outside of crystals using fluorescence assays. This work suggests a more complex picture for iron homeostasis in MTB than previously thought. Because iron speciation controls its solubility, our results also provide important insights into the geochemical impact of MTB. A large pool of unmineralized iron in MTB could be more easily released in the environment than magnetite, thus limiting iron sequestration into MTB crystals.

microbiology↗

bioRxiv2020

Ferrosomes are iron storage organelles formed by broadly conserved gene clusters in bacteria and archaea

Cellular iron homeostasis is vital and maintained through tight regulation of iron import, efflux, storage, and detoxification1-3. The most common modes of iron storage employ proteinaceous compartments that are composed of ferritin or related proteins4,5. While lipid-bounded iron compartments have also been described, the basis for their formation and function remains unknown. Here, we focus on one such compartment, the ferrosome, which had been previously observed in the anaerobic bacterium Desulfovibrio magneticus6. We identify three ferrosome-associated (Fez) proteins, encoded by a putative operon, that are associated with and responsible for forming ferrosomes in D. magneticus. Fez proteins include FezB, a P1B-6-ATPase found in phylogenetically and metabolically diverse species of bacteria and archaea with anaerobic lifestyles. In the majority of these species, two to ten genes define a cluster that encodes FezB. We show that two other species, Rhodopseudomonas palustris and Shewanella putrefaciens, make ferrosomes in anaerobic conditions through the action of their six-gene fez operon. Additionally, we find that the S. putrefaciens fez operon is sufficient for ferrosome formation in Escherichia coli. Using S. putrefaciens as a model, we find that ferrosomes likely play a role in the anaerobic adaptation to iron starvation. Overall, this work establishes ferrosomes as a new class of lipid-bounded iron storage organelles and sets the stage for studying ferrosome formation and structure in diverse microorganisms.

microbiology↗

bioRxiv2019

Single-cell determination of iron content in magnetotactic bacteria: implications for the iron biogeochemical cycle

Magnetotactic bacteria (MTB) are ubiquitous aquatic microorganisms that biomineralize dissolved iron from the environment into intracellular nanoparticles of magnetite [Fe(II)Fe(III)2O4] or greigite [Fe(II)Fe(III)2S4] in a genetically controlled manner. After cell death, these magnetite and greigite crystals are trapped into sediments which effectively removes iron from the soluble pool. MTB may significantly impact the iron biogeochemical cycle, especially in the ocean where dissolved iron limits nitrogen fixation and primary productivity. Although MTB are ubiquitous in the environment, their impact on the biogeochemical cycling of metallic elements is still poorly constrained. A thorough assessment of the mass of iron incorporated by MTB has been hampered by a lack of methodology to accurately measure the amount of, and variability in, their intracellular iron content. Here, we quantify the mass of iron contained in single MTB cells of the model organism, Magnetospirillum magneticum sp. AMB-1, using a time-resolved mass spectrometry methodology. Bacterial iron content depends on the external iron concentration, and reaches a maximum value of 10-6 ng of iron per cell when bacteria are cultivated with initial iron concentrations of 100 M or higher. From our experimental results, we calculated the flux of dissolved iron incorporation into natural MTB populations and conclude that MTB may mineralize a significant fraction of environmental dissolved iron into crystals.

microbiology↗

bioRxiv2018

A method for genome editing in the anaerobic magnetotactic bacterium Desulfovibrio magneticus RS-1

ABSTRACTMagnetosomes are complex bacterial organelles that serve as model systems for studying cell biology, biomineralization, and global iron cycling. Magnetosome biogenesis is primarily studied in two closely related Alphaproteobacterial Magnetospirillum spp. that form cubooctahedral-shaped magnetite crystals within a lipid membrane. However, chemically and structurally distinct magnetic particles have also been found in physiologically and phylogenetically diverse bacteria. Due to a lack of molecular genetic tools, the mechanistic diversity of magnetosome formation remains poorly understood. Desulfovibrio magneticus RS-1 is an anaerobic sulfate-reducing Deltaproteobacterium that forms bullet-shaped magnetite crystals. A recent forward genetic screen identified ten genes in the conserved magnetosome gene island of D. magneticus that are essential for its magnetic phenotype. However, this screen likely missed many interesting mutants with defects in crystal size, shape, and arrangement. Reverse genetics to target the remaining putative magnetosome genes using standard genetic methods of suicide vector integration has not been feasible due to low transconjugation efficiency. Here, we present a reverse genetic method for targeted mutagenesis in D. magneticus using a replicative plasmid. To test this method, we generated a mutant resistant to 5-fluorouracil by making a markerless deletion of the upp gene that encodes uracil phosphoribosyltransferase. We also used this method for targeted marker exchange mutagenesis by replacing kupM, a gene identified in our previous screen as a magnetosome formation factor, with a streptomycin resistance cassette. Overall, our results show that targeted mutagenesis using a replicative plasmid is effective in D. magneticus and may also be applied to other genetically recalcitrant bacteria.\n\nIMPORTANCEMagnetotactic bacteria (MTB) are a group of organisms that form small, intracellular magnetic crystals though a complex process involving lipid and protein scaffolds. These magnetic crystals and their lipid membrane, termed magnetosomes, are model systems for studying bacterial cell biology and biomineralization as well as potential platforms for biotechnological applications. Due to a lack of genetic tools and unculturable representatives, the mechanisms of magnetosome formation in phylogenetically deeply-branching MTB remain unknown. These MTB contain elongated bullet-/tooth-shaped magnetite and greigite crystals that likely form in a manner distinct from the cubooctahedral-shaped magnetite crystals of the genetically tractable Alphaproteobacteria MTB. Here, we present a method for genome editing in the anaerobic Deltaproteobacterium Desulfovibrio magneticus RS-1, the first cultured representative of the deeply-branching MTB. This marks a crucial step in developing D. magneticus as a model for studying diverse mechanisms of magnetic particle formation by MTB.

microbiology↗