Biology subjects

Munoz-Gomez, S. A.

Publications and source records attributed to Munoz-Gomez, S. A..

9 recordsLinked to original sources

bioRxiv2026

Green algal symbionts are stably retained and provisioned in the dark despite a clear physiological cost

Photosymbioses, or associations between heterotrophs and photoautotrophs, are widespread and indispensable in today's ecosystems. The chloroplasts of algae and land plants, which are at the heart of most of earth's primary production, stem from ancient photosymbioses. Photosymbioses often combine heterotrophy and autotrophy and must thus efficiently allocate resources between these two costly cellular processes. We currently lack a clear picture of how photosymbioses allocate their valuable cellular resources in response to environmental change. In this study, we combine growth assays, automated fluorescence microscopy, transmission electron microscopy, and mass spectrometry-based proteomics to explore the physiology and cellular resource allocation of the ciliate-green alga photosymbiosis of Paramecium bursaria. In nutrient-rich environments that resemble P. bursaria's natural habitat, the maximum growth rate attained saturates regardless of light intensity. The green algae thus do not provide a benefit in nutrient-replete conditions, and the photosymbiosis primarily functions heterotrophically. The green algae occupy a remarkably similar and constant volume fractions across contrasting light environments despite displaying clear photo-physiological adaptation. This is true regardless of a clear physiological cost of the photosymbionts; aposymbiotic hosts always display higher growth rates in the dark. The host does not decrease 'symbiont load' in environments where green algae are not beneficial. Moreover, in the dark, the green algae are fully dependent on their hosts and take up a larger proteome mass fraction that increases with prey abundance. Differential protein expression analyses suggest that acetate and amino acids are the preferred sources of carbon and nitrogen for the green algae in the dark. The stable persistence and higher resource uptake by the photosymbionts in the dark argue against a view where hosts have full control over and selfishly exploit their symbionts.

physiology↗

bioRxiv2025

The phylogenetic context for the origin of a unique purple-green photosymbiosis

Symbioses are widespread in nature and have been the source of much evolutionary innovation. While some types of symbioses evolved multiple times across space and time (e.g., oxygenic photosymbioses or chemosymbioses), others are extremely rare. Purple photosymbioses are an example of such rare associations. Only two purple photosymbioses between heterotrophic eukaryotes and intracellular purple bacteria have been documented. This is in stark contrast to very common oxygenic photosymbioses and poses the question of what factors prevent the more frequent establishment of purple photosymbioses. To shed light on this question, we investigated the evolutionary history of the purple-green ciliate Pseudoblepharisma tenue (Spirostomidae) using a phylogenetic and comparative approach. We sampled about 30 new isolates of spirostomid ciliates, inferred a comprehensive and well-supported phylogenomic tree, and resolved the sister relationship between Pseudoblepharisma and Spirostomum. Furthermore, we characterized P. tenues sister species, here renamed Pseudoblepharisma chlorelligera, and revealed that it constitutes a quadripartite symbiosis between a ciliate, a green alga, and two different non-photosynthetic bacteria. In addition, we discovered three colorless, non-photosymbiotic Pseudoblepharisma species, which branch as sister to the photosymbiotic P. tenue and P. chlorelligera. Our phylogenetic and comparative genomic analyses suggest that the green algal symbionts of P. tenue predated the acquisition of purple bacterial symbionts, and that the ancestor of the extant Pseudoblepharisma species was non-photosymbiotic and facultatively anaerobic. These data allowed us to hypothesize on the evolutionary steps that led to the origin of P. tenue and thus bring us closer to explaining the conditions that led to the evolutionary emergence of a unique purple-green symbiosis.

evolutionary biology↗

bioRxiv2024

A robustly rooted tree of eukaryotes reveals their excavate ancestry.

The eukaryote Tree of Life (eToL) depicts the relationships among all eukaryotic organisms; its root represents the last eukaryotic common ancestor (LECA) from which all extant complex lifeforms are descended. Locating this root is crucial for reconstructing the features of LECA, both as the endpoint of eukaryogenesis and the start-point for the evolution of the myriad complex traits underpinning the diversification of living eukaryotes. However, the position of the root remains contentious due to pervasive phylogenetic artefacts stemming from inadequate evolutionary models, poor taxon sampling, and limited phylogenetic signal. Here, we estimate the root of the eToL with unprecedented resolution based on a new, much larger, dataset of mitochondrial proteins which includes all known eukaryotic supergroups. Our comprehensive analyses with state-of-the-art phylogenetic models reveal that the eukaryotic root lies between two multi-supergroup assemblages: Opimoda+ and Diphoda+. Compellingly, this position is consistently supported across different models and robustness analyses. Notably, groups containing typical excavates are placed on both sides of the root, suggesting the complex features of the excavate cell architecture trace back to LECA. This study is the most comprehensive phylogenetic investigation of the eukaryote root to date, shedding light on the ancestral cells from which extant eukaryotes arose and providing a crucial framework for investigating the origin and evolution of canonical eukaryotic features.

evolutionary biology↗

bioRxiv2024

Phylogeny and species delimitation of ciliates in the genus Spirostomum (Class, Heterotrichea) using single-cell transcriptomes

Ciliates are single-celled microbial eukaryotes that diverged from other eukaryotic lineages over a billion years ago. The extensive evolutionary timespan of ciliate has led to enormous genetic and phenotypic changes, contributing significantly to their high level of diversity. Recent analyses based on molecular data have revealed numerous cases of cryptic species complexes in different ciliate lineages, demonstrating the need for a robust approach to delimit species boundaries and elucidate phylogenetic relationships. Heterotrich ciliate species of the genus Spirostomum are abundant in freshwater and brackish environments and are commonly used as biological indicators for assessing water quality. However, some Spirostomum species are difficult to identify due to a lack of distinguishable morphological characteristics, and the existence of cryptic species in this genus remains largely unexplored. Previous phylogenetic studies have focused on only a few loci, namely the ribosomal RNA genes, alpha-tubulin, and mitochondrial CO1. In this study, we obtained single-cell transcriptome of 25 Spirostomum species populations (representing six morphospecies) sampled from South Korea and the USA, and used concatenation- and coalescent-based methods for species tree inference and delimitation. Phylogenomic analysis of 37 Spirostomum populations and 265 protein-coding genes provided a robustious insight into the evolutionary relationships among Spirostomum species and confirmed that species with moniliform and compact macronucleus each form a distinct monophyletic lineage. Furthermore, the multispecies coalescent (MSC) model suggests that there are at least nine cryptic species in the Spirostomum genus, three in S. minus, two in S. ambiguum, S. subtilis, and S. teres each. Overall, our fine sampling of closely related Spirostomum populations and wide scRNA-seq allowed us to demonstrate the hidden crypticity of species within the genus Spirostomum, and to resolve and provide much stronger support than hitherto to the phylogeny of this important ciliate genus.

evolutionary biology↗

bioRxiv2024

Nucleomorph phylogenomics suggests a deep and ancient origin of cryptophyte plastids within Rhodophyta

The evolutionary origin of red algae-derived complex plastids remains obscure. Cryptophyta, one of four eukaryotic lineages harboring these plastids, still contain nucleomorphs, which are highly reduced remnants of red algal nuclei. The genes present on nucleomorph genomes can be used for phylogenomic reconstruction in order to unravel the evolutionary origin of all red complex plastids and provide data independent from previously analyzed plastid-encoded proteins. Here, we leverage these genes in a first attempt at pinpointing the position of cryptophyte nucleomorphs within a comprehensive diversity of Rhodophyta, including new sequence representatives from seven deep-branching red algae. Our analysis, supported by a series of rigorous topology tests, places cryptophyte nucleomorphs as sister to the extremophilic, freshwater subphylum Cyanidiophytina. This conflicts with previously published analyses based on plastidial genes that placed red complex plastids closer to the mesophilic Rhodophytina. Regardless of exact placement, our results reject a nucleomorph origin within any known subgroup of Rhodophyta, instead suggesting an ancient origin of complex red plastids among the deepest branches of the red algal tree of life.

microbiology↗

bioRxiv2023

A DRP-like pseudoenzyme coordinates with MICOS to promote cristae architecture

Mitochondrial cristae architecture is crucial for optimal respiratory function of the organelle. Cristae shape is maintained in part by the mitochondrial inner membrane-localized MICOS complex. While MICOS is required for normal cristae morphology, the precise mechanistic role of each of the seven human MICOS subunits, and how the complex coordinates with other cristae shaping factors, has not been fully determined. Here, we examine the MICOS complex in Schizosaccharomyces pombe, a minimal model whose genome only encodes for four core subunits. Using an unbiased proteomics approach, we identify a poorly characterized inner mitochondrial membrane protein that interacts with MICOS and is required to maintain cristae morphology, which we name Mmc1. We demonstrate that Mmc1 works in concert with MICOS complexes to promote normal mitochondrial morphology and respiratory function. Bioinformatic analyses reveal that Mmc1 is a distant relative of the Dynamin-Related Protein (DRP) family of GTPases, which are well established to shape and remodel membranes. We find that, like DRPs, Mmc1 self-associates and forms high molecular weight assemblies. Interestingly, however, Mmc1 is a pseudoenzyme that lacks key residues required for GTP binding and hydrolysis, suggesting it does not dynamically remodel membranes. These data are consistent with a model in which Mmc1 stabilizes cristae architecture by acting as a scaffold to support cristae ultrastructure on the matrix side of the inner membrane. Our study reveals a new class of proteins that evolved early in fungal phylogeny and is required for the maintenance of cristae architecture. This highlights the possibility that functionally analogous proteins work with MICOS to establish cristae morphology in metazoans.

cell biology↗

bioRxiv2023

Single-cell genomics reveals the divergent mitochondrial genomes of Retaria (Foraminifera and Radiolaria)

Mitochondria originated from an ancient bacterial endosymbiont that underwent reductive evolution by gene loss and endosymbiont gene transfer to the nuclear genome. The diversity of mitochondrial genomes published to date has revealed that gene loss and transfer processes are ongoing in many lineages. Most well-studied eukaryotic lineages are represented in mitochondrial genome databases, except for the superphylum Retaria--the lineage comprising Foraminifera and Radiolaria. Using single-cell approaches, we present two complete mitochondrial genomes of Foraminifera and two near-complete mitochondrial genomes of radiolarians. We report the complete coding content of an additional 14 foram species. We show that foraminiferan and radiolarian mitochondrial genomes encode a nearly fully overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. In contrast to animals and fungi, many protists encode a diverse set of proteins on their mitochondrial genomes, including several ribosomal genes; however, some aerobic eukaryotic lineages (euglenids, myzozoans, and chlamydomonas-like algae) have reduced mitochondrial gene content and lack all ribosomal genes. Similar to these reduced outliers, we show that retarian mitochondrial genomes lack ribosomal protein and tRNA genes, contain truncated and divergent small and large rRNA genes, and encode only 14-15 protein-coding genes, including nad1, 3, 4, 4L, 5, 7, cob, cox1, 2, 3, atp1, 6, and 9, with forams and radiolarians additionally encoding nad2 and nad6, respectively. In radiolarian mitogenomes, a non-canonical genetic code was identified in which all three stop codons encode amino acids. Collectively, these results add to our understanding of mitochondrial genome evolution and fill in one of the last major gaps in mitochondrial sequence databases.

genomics↗

bioRxiv2022

The development of intracytoplasmic membranes in alphaproteobacteria involves the conserved mitochondrial crista-developing Mic60 protein

Mitochondrial cristae expand the surface area of respiratory membranes and ultimately allow for the evolutionary scaling of respiration with cell volume across eukaryotes. The discovery of Mic60 homologs among alphaproteobacteria, the closest extant relatives of mitochondria, suggested that cristae might have evolved from bacterial intracytoplasmic membranes (ICMs). Here, we investigated the predicted structure and function of alphaproteobacterial Mic60, and a protein encoded by an adjacent gene Orf52, in two distantly related purple alphaproteobacteria, Rhodobacter sphaeroides and Rhodopseudomonas palustris. In addition, we assessed the potential physical interactors of Mic60 and Orf52 in R. sphaeroides. We show that the three -helices of mitochondrial Mic60s mitofilin domain, as well as its adjacent membrane-binding amphipathic helix, are present in alphaproteobacterial Mic60. The disruption of Mic60 and Orf52 caused photoheterotrophic growth defects, which are most severe under low light conditions, and both their disruption and overexpression led to enlarged ICMs in both studied alphaproteobacteria. We also found that alphaproteobacterial Mic60 physically interacts with BamA, the homolog of Sam50, one of the main physical interactors of eukaryotic Mic60. This interaction, responsible for making contact sites at mitochondrial envelopes, has been conserved in modern alphaproteobacteria despite more than a billion years of evolutionary divergence. Our results suggest a role for Mic60 in photosynthetic ICM development and contact site formation at alphaproteobacterial envelopes. Overall, we provide support for the hypothesis that mitochondrial cristae evolved from alphaproteobacterial ICMs, and therefore have improved our understanding of the nature of the mitochondrial ancestor.

evolutionary biology↗

bioRxiv2021

The role of mitochondrial energetics in the origin and diversification of eukaryotes

The origin of eukaryotic cell size and complexity is thought by some to have required an energy excess provided by mitochondria, whereas others claim that mitochondria provide no energetic boost to eukaryotes. Recent observations show that energy demand scales continuously and linearly with cell volume across both prokaryotes and eukaryotes, and thus suggest that eukaryotes do not have an increased energetic capacity over prokaryotes. However, amounts of respiratory membranes and ATP synthases scale super-linearly with cell surface area. Furthermore, the energetic consequences of the contrasting genomic architectures between prokaryotes and eukaryotes have yet to be precisely quantified. Here, we investigated (1) potential factors that affect the cell volumes at which prokaryotes become surface area-constrained, (2) the amount of energy that is divested to increasing amounts of DNA due to the contrasting genomic architectures of prokaryotes and eukaryotes, and (3) the costs and benefits of respiring symbionts for a host cell. Our analyses suggest that prokaryotes are not necessarily constrained by their cell surfaces at cell volumes of 100-103 m3, and that the genomic architecture of eukaryotes is only slightly advantageous at genomes sizes of 106-107 bp. This suggests that eukaryotes may have first evolved without the need for mitochondria as these ranges hypothetically encompass the Last Eukaryote Common Ancestor and its proto-eukaryotic ancestors. At these slightly larger cell volumes, a host cell may also have derived a greater advantage (lower cost) from harboring a population of ATP-producing symbionts. However, our analyses also show that increasingly larger and fast-dividing prokaryotes would have a shortage of surface area devoted to respiration and would disproportionally divest more energy to DNA synthesis at larger genome sizes. We thus argue that, even though mitochondria may not have been required by the first eukaryotes, the successful diversification of eukaryotes into larger and faster-growing cells was ultimately contingent upon the origin of mitochondria. SignificanceThere has been a lot of theorizing about the evolution of eukaryotes from prokaryotes, but no consensus seems to be on the horizon. Our quantitative analyses on the required amount of respiratory membrane, and the amount of energy diverted to DNA synthesis, by both prokaryotes and eukaryotes, suggest that mitochondria provided rather small advantages to the first eukaryotes, but were advantageous for the macro-evolutionary diversification of eukaryotes. This conclusion provides a middle road in the debate between those that claim that the origin of eukaryotes required a massive energy boost provided by mitochondria, and those that argue that the origin of mitochondria did not represent a quantum leap in energetic advantages to eukaryotes.

evolutionary biology↗