Biology subjects

Michie, K. A.

Publications and source records attributed to Michie, K. A..

8 recordsLinked to original sources

bioRxiv2026

Viruses, Proviruses and Satellites from Asgard Archaea Enrichments Reveal Complex Microbial Interactions

Asgard archaea are the closest known relatives of eukaryotes and are central to models of eukaryogenesis involving archaeal bacterial symbiosis, yet the contribution of viruses remains unexplored. Here, for the first time, we visualised unique viruses associated with Asgard archaeal cells. Additionally, we identified the first putative Asgard-archaeal virus satellite, which exhibited genomic interactions involving a bacterium, Stromatodesulfovibrio nilemahensis, providing evidence of a virus-mediated interaction between an Asgard archaeon and a bacterium. Additionally, novel proviruses of S. nilemahensis displayed distinct genomic features where predictions of alternate recombination sites suggested the acquisition of horizontally acquired genes associated with biofilm formation. Further, we comprehensively characterise (pro)viruses associated with this co-culture using high resolution cryo-electron tomography, proximity ligation (Hi-C), and metagenomics. Together, these findings expand the known diversity of Asgard archaeal viruses and establish a foundation for investigating the role of viruses in microbial symbiosis relevant to the emergence of eukaryotic life.

microbiology↗

bioRxiv2025

LMI4Boltz: Optimizing VRAM utilization to predict large macromolecular complexes with consumer grade hardware

AlphaFold2 has revolutionised structural biology by enabling the prediction of protein structures approaching experimental quality. AlphaFold3 extends this framework to support modelling broad biomolecular classes while also reducing the computational cost of prediction. However, AlphaFold3 is distributed with licence conditions which restrict general purpose use. Boltz is a permissive, open-source re-implementation of AlphaFold3, but it is bottlenecked by increased VRAM requirements and requires high-end GPU hardware to model large molecular systems. Here we introduce Low Memory Inference for Boltz (LMI4Boltz) which reduces VRAM requirements using in-place updates, offloading tensors to host memory, careful management of functional scope and aggressive chunking of key operations. Using these strategies, LMI4Boltz increases the token size limit of Boltz-2 by 66.7% without sacrificing prediction accuracy. These optimisations improve the accessibility of Boltz using consumer grade hardware and unlock the ability to model large molecular systems. LMI4Boltz is available at https://github.com/tlitfin/lmi4boltz.

bioinformatics↗

bioRxiv2025

The prokaryotic origins of the COMMD protein family involved in eukaryotic membrane trafficking

The ten eukaryotic COMMD proteins are core components of the Commander complex, with central roles in endosomal membrane trafficking and signalling. Each protein has an -helical N-terminal (HN) domain with a C-terminal copper metabolism gene MURR1 (COMM) domain. These ten family members assemble into a heterodecameric ring composed of five specific heterodimers. In this work we have combined structural homology searches with genome-wide predicted structures to identify ancestral COMMD-like proteins that exist as single genes in Bacteria and Archaea. Although there is limited sequence similarity to the eukaryotic proteins the bacterial and archaeal COMMD-like proteins are predicted to form homomeric ring-shaped assemblies like their eukaryotic counterparts. Our biophysical studies, crystal and cryo-EM structures confirm COMMD-like proteins readily form homooligomeric rings composed of eight or ten subunits assembled from core dimeric building blocks and inter-dimer interactions that are analogous to the heterodecameric core structure of the eukaryotic Commander complex. Phylogenetic analyses using amino acid sequences and FoldSeek structural alphabet (3Di) infer that the closest identified relatives to the eukaryotic COMMD proteins are found in Myxococcota bacteria. These findings indicate that COMMD genes emerged early in eukaryotic evolution through multiple rounds of duplication from a single ancestral gene likely acquired from bacteria.

biochemistry↗

bioRxiv2025

An Asgard archaeon from a modern analog of ancient microbial mats

It has been proposed that eukaryotic cells evolved via symbiosis between sulfate-reducing bacteria and hydrogen-producing archaea. Here we describe a highly enriched culture of a novel Asgard archaeon, Nerearchaeum marumarumayae, with a bacterium Stromatodesulfovibrio nilemahensis from a stromatolite-associated microbial mat. The N. marumarumayae genome indicates it produces H2, acetate, formate, and sulfite, while S. nilemahensis synthesizes amino acids and vitamins, which can be exchanged in a syntrophic partnership. Electron cryotomography revealed N. marumarumayae cells produce chains of budded envelope vesicles attached to the coccoid cell body by extracellular fibers, and intracellular tube- and cage-like structures. Furthermore, the two species were observed interacting via intercellular nanotubes assembled by the bacterium. These characteristics and interactions may reflect an early step in the symbiotic evolution of eukaryotic cells.

microbiology↗

bioRxiv2024

Assessing the Validity of Leucine Zipper Constructs Predicted in AlphaFold2.

AP-1 transcription factors are a network of cellular regulators, that combine in different dimer pairs to control a range of pathways involved in differentiation, growth, and cell death. They dimerise via leucine zipper coiled-coil domains, that are preceded by a basic DNA binding domain. Depending on which AP-1 transcription factors dimerise, different DNA sequences will be recognised resulting in differential gene expression. The affinity of AP-1 transcription factors for each other dictates which dimers form. The relative concentration of AP-1 transcription factors varies with tissue type and environment, adding another layer of control to this integral network of cellular regulation. The development of artificial intelligence (AI) protein structure prediction programs gives us a new technique to investigate or predict how dimerization effects combinatorial control. AlphaFold2 and AlphaFold-Multimer are AI programs that predict 3D structures of proteins using primary sequence as their only input, even if there is no homologous model available. To fully realise the potential of AI for structural biology, it is essential to understand its current capabilities and limitations. In this study we used the classical example of an AP-1 dimer: Fos and Jun, to interrogate how AlphaFold2 and AlphaFold-Multimer model leucine zipper domains, and if AlphaFold-Multimer can be used to differentiate between probable and improbable dimer interfaces. We found that AlphaFold-Multimer predicts highly confident leucine zipper dimers, even for dimer pairs, such as the FosB homodimer, for which electrostatics are known to prevent their formation in vivo. This is an important case study concerning high-confidence, but low-accuracy protein structure prediction. statementArtificial intelligence (AI) programs that predict protein structures, like AlphaFold, could transform structural biology by speeding up the experimental process. However, it is important to grasp the capabilities and limitations of these AI tools. This study examines how AlphaFold identifies structural features, specifically a leucine zipper, while not considering other factors like electrostatic interactions, using the well-studied transcription factors Fos and Jun as a case study.

bioinformatics↗

bioRxiv2024

Cell division protein A (CdpA) assembles and anchors the two FtsZ rings at midcell in haloarchaea

Many archaea appear to divide through the coordinated activities of two FtsZ homologues (FtsZ1 and FtsZ2) and another bacterial cell division homologue (SepF), which are part of the midcell division ring. Here, we identify an additional protein (HVO_0739, renamed CdpA) that is involved in cell division in Haloferax volcanii, with homologues in other Haloarchaea. CdpA localizes at the mid-cell division ring, and this requires the presence of the ring-assembly protein FtsZ1. The division constriction protein FtsZ2 also influenced the proper midcell assembly and structure of CdpA. In the absence of CdpA, cells frequently failed to divide properly, and FtsZ1 formed poorly condensed pseudo-helical structures spanning across a broad region of the cell, whereas FtsZ2 showed mispositioned foci, nano-rings, and filaments. The rate of directional movement of FtsZ1 and FtsZ2 structures around the division ring appeared minimally affected by loss of CdpA, which resulted in continual repositioning of the aberrant FtsZ structures in the cells. In contrast to the FtsZ proteins, CdpA formed relatively immobile foci around the ring. Protein domain function studies, pull-down assays, and multimer structure predictions suggest that CdpA is part of a membrane complex that tethers FtsZ2 and other division proteins to the midcell membrane. Our discovery of an archaeal FtsZ organisation and midcell anchor protein offers new insights into cell division mechanisms that are similar across the tree of life.

microbiology↗

bioRxiv2023

Molecular dissection of the soluble photosynthetic antenna from a cryptophyte alga

Cryptophyte algae have a unique phycobiliprotein light-harvesting antenna that fills a spectral gap in chlorophyll absorption, however, it is unclear how it transfers energy efficiently to photosystems. We show that the cryptophyte Hemiselmis andersenii expresses an energetically complex antenna comprising three distinct spectrotypes of phycobiliprotein with different quaternary structures arising from a diverse subunit family. The bulk of the antenna consists of open quaternary form phycobiliproteins acting as primary photon acceptors, supplemented by novel open-braced forms. The final components are closed forms with a long wavelength spectral feature due to substitution of a single chromophore. We propose that the macromolecular organization of the cryptophyte antennas consists of bulk open and open-braced forms that transfer excitations to photosystems via this bridging closed form phycobiliprotein. One-Sentence SummaryAlgae generate a rainbow of antenna proteins by combining a conserved subunit with different members of a multigene family.

molecular biology↗

bioRxiv2022

Ancestral reconstruction of the MotA stator subunit reveals that conserved residues far from the pore are required to drive flagellar motility

The bacterial flagellar motor (BFM) is a rotary nanomachine powered by the translocation of ions across the inner membrane through the stator complex. The stator complex consists of two membrane proteins: MotA and MotB (in H+ powered motors), or PomA and PomB (in Na+ powered motors). In this study we used ancestral sequence reconstruction (ASR) to probe which residues of MotA correlate with function and may have been conserved to preserve motor function. We reconstructed ten ancestral sequences of MotA and found four of them were motile in combination with contemporary E. coli MotB and in combination with our previously published functional ancestral MotBs. Sequence comparison between wild-type (WT) E. coli MotA and MotA-ASRs revealed 30 critical residues across multiple domains of MotA that were conserved among all motile stator units. These conserved residues included pore-facing, cytoplasm-facing and MotA-MotA intermolecular facing sites. Overall, this work demonstrates the role of ASR in assessing conserved variable residues in a subunit of a molecular complex.

microbiology↗