Biology subjects

McCutcheon, J.

Publications and source records attributed to McCutcheon, J..

11 recordsLinked to original sources

bioRxiv2026

A mitochondrion-like ribosome in an insect endosymbiont

Understanding how the mitochondrion evolved from a bacterial endosymbiont to an organelle is obscured by time and a lack of comparative examples. It is clear that mitochondrial ribosomes are derived from bacterial ribosomes, but it is unclear whether the baroque and idiosyncratic structural changes seen in mitochondrial ribosomes are specifically driven by mitochondrial evolution or simply reflect the syndrome of being a long-term endosymbiont. Here we show that two of the most characteristic features of mitochondrial ribosomes--the acquisition of host proteins and alterations to specific structural regions--are shared by Hodgkinia, an ancient bacterial endosymbiont of cicadas. These results imply that many of the striking changes observed in mitochondrial ribosomes result from their common ancestry as bacterial endosymbionts rather than their uniqueness as mitochondria.

evolutionary biology↗

bioRxiv2026

The transcriptional and translational outcomes for pseudogenes in bacterial endosymbionts

Intracellular bacteria in the early stages of host adaptation often show extraordinarily disrupted genomes, where up to half of their ancestral genes are found in a pseudogenized state. The mealybug Pseudococcus longispinus hosts two bacterial endosymbionts with high pseudogene loads, Symbiopectobacterium endolongispinus and Sodalis endolongispinus. Here, we measure transcript abundance, ribosome-associated RNA, and protein abundance in these bacterial symbionts to understand how bacteria avoid (or fail to avoid) accumulating large amounts of non-functional RNAs and proteins from these pseudogenes. Consistent with previous work, we show that pseudogene transcripts remain detectable, but at lower levels compared to those from intact and functional genes, and that relatively few pseudogenes yield detectable proteins in proteomic data. However, we find that many pseudogene transcripts still bind to Symbiopectobacterium ribosomes, and uncover a possible role for the tmRNA ribosome rescue system in the targeting of pseudogene proteins for degradation. Our results suggest a possible mechanism by which bacterial endosymbionts remove aberrant pseudogene-derived proteins during the critical time when many pseudogenes have formed but not enough time has passed for sequence evolution to erode ribosome binding sites from pseudogene transcripts. SignificanceBacteria transitioning from free-living to host-dependent lifestyles often go through a transitory period where large numbers of genes are broken but not yet deleted. How cells navigate this period without producing useless or toxic gene products remains poorly understood. By combining transcriptomic, proteomic, and ribosomal profiling data from two bacterial endosymbionts, we uncover a possible mechanism that cells use to mitigate the presence of thousands of newly formed pseudogenes. We show that pseudogenes are still widely represented in the transcriptome and are often associated with ribosomes, but rarely yield measurable protein products. RNA sequencing from purified ribosomes suggests that the tmRNA ribosome rescue system may act as a short-term quality control mechanism during early stages of genome reduction. These findings provide a mechanistic glimpse into how endosymbionts survive the unstable phase between gene inactivation and gene deletion, a fleeting but critical window in the evolution of endosymbiosis.

evolutionary biology↗

bioRxiv2025

Expression of four mitochondrial tRNAs from only two loci

Transfer RNAs (tRNAs) are among the few genes retained in animal mitochondrial genomes after more than a billion years of gene loss. These ancient bacterial vestiges are often structurally aberrant and less stable than their bacterial or cytosolic tRNA counterparts. In some lineages, mitochondrial tRNAs (mt-tRNAs) have become so truncated that the loss of one or both arms has expanded our understanding of what constitutes a functional tRNA. Here, we report another radical departure from canonical tRNA gene architecture: two overlapping tRNAs produced from opposite strands of the same locus. These mirror tRNA pairs eliminate the need to retain separate loci for all tRNA genes, as a single locus can produce tRNAs to decode two different amino acids. We show that these mirror tRNAs are aminoacylated and demonstrate their presence in mitoribosomes. Furthermore, mirror tRNAs display strand-specific patterns of nucleotide modification and RNA editing, reflecting specific post-transcriptional maturation that depends on transcriptional orientation. To our knowledge, this demonstration of functional, bidirectional tRNA expression is a first for any genome or organism and reveals an unexpected strategy by which mitochondrial genomes maintain a complete set of tRNAs in the face of unrelenting gene loss. The discovery of mirror tRNAs has broad implications for the evolution of tRNA-interacting enzymes, mitochondrial biology, and even the origins of the protein synthesis machinery itself.

molecular biology↗

bioRxiv2025

Swainson's thrushes vary song structure and singing behavior across ambient noise gradients and rapidly adjust songs in response to experimental traffic noise

Anthropogenic noise pollution has a variety of negative consequences for animals, with observed effects ranging from physiological processes to community structures. Sound waves from anthropogenic noise can mask animal signals, creating challenges for animal communication. Songbirds have been observed to combat noise pollution by changing their song rate, duration, frequency, or amplitude, with different species employing different strategies. We examined whether Swainsons thrushes (Catharus usulatus) adjust their song structure under different traffic noise regimens using both population level surveys and individual level noise playback experiments. Swainsons thrushes song frequency varied with background traffic noise levels across the surveyed population, but other song parameters did not. When confronted with realistic levels of experimental traffic noise playback, individual thrushes rapidly changed their song structure, increasing both the duration and the minimum frequency of their songs, before quickly returning towards baseline levels after the noise playback ended. Together, these results suggest that Swainsons thrushes are adjusting their singing to reduce acoustic masking in noisy areas and further indicate that some songbirds might continually assess ambient noise levels and only adjust their signals when necessary.

animal behavior and cognition↗

bioRxiv2023

No Transcriptional Compensation for Extreme Gene Dosage Imbalance in Fragmented Bacterial Endosymbionts of Cicadas

Bacteria that form long-term intracellular associations with host cells lose many genes, a process that often results in tiny, gene-dense, and stable genomes. Paradoxically, the same evolutionary processes that drive genome reduction and simplification may also sometimes cause genome expansion and complexification. A bacterial endosymbiont of cicadas, Hodgkinia cicadicola, exemplifies this paradox. In many cicada species, a single Hodgkinia lineage with a tiny, gene-dense genome has split into several interdependent cell and genome lineages. Each new Hodgkinia lineage encodes a unique subset of the ancestral unsplit genome in a complementary way, such that the collective gene contents of all lineages sum to the total found in the ancestral single genome. This splitting process creates genetically distinct Hodgkinia cells that must function together to carry out basic cellular processes, but also creates a gene dosage problem where some genes are encoded by only a small fraction of cells while others are much more abundant. Here, by sequencing DNA and RNA of Hodgkinia from different cicada species with different amounts of splitting - along with those of its structurally stable, unsplit partner endosymbiont Sulcia muelleri - we show that Hodgkinia does not transcriptionally compensate to rescue the wildly unbalanced gene and genome ratios that result from lineage splitting. We also find evidence that Hodgkinia has a reduced capacity for basic transcriptional control independent of the splitting process. Collectively, these findings reveal another layer of degeneration that further pushes the limits of canonical molecular and cell biology in Hodgkinia, and may in part explain its propensity to go extinct through symbiont replacement. SignificanceMany cicadas host two bacterial endosymbionts, Hodgkinia and Sulcia, which produce essential amino acids missing from the insects xylem sap diet. Following 100+ million years of strict host association, both bacteria have lost many genes and posses extremely tiny genomes. In some cicadas, Hodgkinia has split into multiple cell lineages, distributing its genes, with little respect to their function, among separate lineages present at (sometimes wildly) different abundances. We find no transcriptional response to this in Hodgkinia, resulting in similarly imbalanced mRNA abundances. We also find less control of transcription in Hodgkinia compared to Sulcia. Hodgkinias transcriptome embodies an extreme, even relative to other highly-reduced endosymbionts, and raises questions about how cell biology in multi-lineage Hodgkinia can function at all.

evolutionary biology↗

bioRxiv2021

Pseudofinder: detection of pseudogenes in prokaryotic genomes

Prokaryotic genomes are generally gene dense and encode relatively few pseudogenes, or nonfunctional/inactivated remnants of genes. However, in certain contexts, such as recent ecological shifts or extreme population bottlenecks (such as those experienced by symbionts and pathogens), pseudogenes can quickly accumulate and form a substantial fraction of the genome. Identification of pseudogenes is, thus, a critical step for understanding the evolutionary forces acting upon, and the functional potential encoded within, prokaryotic genomes. Here, we present Pseudofinder, an open-source software dedicated to pseudogene identification and analysis. With Pseudofinders multi-pronged, reference-based approach, we demonstrate its capacity to detect a wide variety of pseudogenes, including those that are highly degraded and typically missed by gene-calling pipelines, as well newly formed pseudogenes, which can have only one or a few inactivating mutations. Additionally, Pseudofinder can detect intact genes undergoing relaxed selection, which may indicate incipient pseudogene formation. Implementation of Pseudofinder in annotation pipelines will not only clarify the functional potential of sequenced microbes, but will also generate novel insights and hypotheses regarding the evolutionary dynamics of bacterial and archaeal genomes.

bioinformatics↗

bioRxiv2021

Large differences in carbohydrate degradation and transport potential in the genomes of lichen fungal symbionts

Lichen symbioses are generally thought to be stabilized by the transfer of fixed carbon compounds from a photosynthesizing unicellular symbiont to a fungus. In other fungal symbioses, carbohydrate subsidies correlate with genomic reductions in the number of genes for plant cell wall-degrading enzymes (PCWDEs), but whether this is the case with lichen fungal symbionts (LFSs) is unknown. We predicted genes encoding carbohydrate-active enzymes (CAZymes) and sugar transporters in 17 existing and 29 newly sequenced genomes from across the class Lecanoromycetes, the largest extant clade of LFSs. Despite possessing lower mean numbers of PCWDE genes compared to non-symbiont Ascomycota, all LFS genomes possessed a robust suite of predicted PCWDEs. The largest CAZyme gene numbers, on par with model species such as Penicillium, were retained in genomes from the subclass Ostropomycetidae, which are found in crust lichens with highly specific ecologies. The lowest numbers were in the subclass Lecanoromycetidae, which are symbionts of many generalist macrolichens. Our results suggest that association with phototroph symbionts does not in itself result in functional loss of PCWDEs and that PCWDE losses may have been driven by adaptive processes within the evolution of specific LFS lineages. The inferred capability of some LFSs to access a wide range of carbohydrates suggests that some lichen symbioses may augment fixed CO2 with carbon from external sources. SignificanceLichen symbioses are considered self-contained autotrophic systems in which the total carbon economy is the sum of phototroph-fixed CO2, supplied to a fungus as sugars. In other fungal-plant symbioses, such as mycorrhizae, plant-derived sugar subsidies are associated with loss of plant cell wall-degrading enzymes (PCWDEs). We compared PCWDE inventories in 46 genomes from the largest group of lichen fungal symbionts (LFSs) with non-symbionts from across Ascomycota. We found that despite lower overall gene numbers, all LFSs retain PCWDEs, and some possess gene numbers and functional diversity on par with non-symbionts. Our results suggest that association with a phototroph does not necessarily result in PCWDE loss, and some lichens may obtain carbon from sources other than CO2 fixation.

genomics↗

bioRxiv2021

Lichen fungi do not depend on the alga for ATP production

Lichen fungi live in a symbiotic association with unicellular phototrophs and have no known aposymbiotic stage. A recent study postulated that some of them have lost mitochondrial oxidative phosphorylation and rely on their algal partners for ATP. This claim originated from an apparent lack of ATP9, a gene encoding one subunit of ATP synthase, from a few mitochondrial genomes. Here we show that while these fungi indeed have lost the mitochondrial ATP9, each retain a nuclear copy of this gene. Our analysis reaffirms that lichen fungi produce their own ATP.

genomics↗

bioRxiv2019

Protein appetite drives neural activity in the ventral tegmental area

Control of protein intake is essential for numerous biological processes as several amino acids cannot be synthesized de novo, however, its neurobiological substrates are still poorly understood. In the present study, we combined in vivo fiber photometry with nutrient-conditioned flavor in a rat model of protein appetite to record neuronal activity in the ventral tegmental area (VTA), a central brain region for the control of food-related processes. In adult male rats, protein restriction increased preference for casein (protein) over maltodextrin (carbohydrate). Moreover, protein consumption was associated with a greater VTA response relative to carbohydrate. After initial nutrient preference, a switch from a normal balanced diet to protein restriction induced rapid development of protein preference but required extensive exposure to macronutrient solutions to induce greater VTA responses to casein. Furthermore, prior protein restriction induced long-lasting food preference and VTA responses. This study reveals that VTA circuits are involved in protein appetite in times of need, a crucial process for all animals to acquire an adequate amount of protein in their diet. Significance StatementAcquiring insufficient protein in ones diet has severe consequences for health and ultimately will lead to death. In addition, a low level of dietary protein has been proposed as a driver of obesity as it can leverage up intake of fat and carbohydrate. However, much remains unknown about the role of the brain in ensuring adequate intake of protein. Here, we show that in a state of protein restriction a key node in brain reward circuitry, the ventral tegmental area, is activated more strongly during consumption of protein than carbohydrate. Moreover, although rats behavior changed to reflect new protein status, patterns of neural activity were more persistent and only loosely linked to protein status.

neuroscience↗

bioRxiv2018

Cicada endosymbionts have tRNAs that are correctly processed despite having genomes that do not encode all of the tRNA processing machinery

Gene loss and genome reduction are defining characteristics of nutritional endosymbiotic bacteria. In extreme cases, even essential genes related to core cellular processes such as replication, transcription, and translation are lost from endosymbiont genomes. Computational predictions on the genomes of the two bacterial symbionts of the cicada Diceroprocta semicincta, \"Candidatus Hodgkinia cicadicola\" (Alphaproteobacteria) and \"Ca. Sulcia muelleri\" (Betaproteobacteria), find only 26 and 16 tRNA, and 15 and 10 aminoacyl tRNA synthetase genes, respectively. Furthermore, the original \"Ca. Hodgkinia\" genome annotation is missing several essential genes involved in tRNA processing, such as RNase P and CCA tRNA nucleotidyltransferase, as well as several RNA editing enzymes required for tRNA maturation. How \"Ca. Sulcia\" and \"Ca. Hodgkinia\" preform basic translation-related processes without these genes remains unknown. Here, by sequencing eukaryotic mRNA and total small RNA, we show that the limited tRNA set predicted by computational annotation of \"Ca. Sulcia\" and \"Ca. Hodgkinia\" is likely correct. Furthermore, we show that despite the absence of genes encoding tRNA processing activities in the symbiont genomes, symbiont tRNAs have correctly processed 5 and 3 ends, and seem to undergo nucleotide modification. Surprisingly, we find that most \"Ca. Hodgkinia\"and \"Ca. Sulcia\" tRNAs exist as tRNA halves. Finally, and in contrast with other related insects, we show that cicadas have experienced little horizontal gene transfer that might complement the activities missing from the endosymbiont genomes. We conclude that \"Ca. Sulcia\" and \"Ca. Hodgkinia\" tRNAs likely function in bacterial translation, but require host-encoded enzymes to do so.

evolutionary biology↗

bioRxiv2017

Mode Of Sucrose Delivery Alters Reward-Related Phasic Dopamine Signals In Nucleus Accumbens

In studies of appetitive Pavlovian conditioning, rewards are often delivered to subjects in a manner that confounds several processes. For example, delivery of a sugar pellet to a rodent requires movement to collect the pellet and is associated with sensory stimuli such as the sight and sound of the pellet arrival. Thus, any neurochemical events occurring in proximity to the reward may be related to multiple coincident phenomena. We used fast-scan cyclic voltammetry in rats to compare nucleus accumbens dopamine responses to two different modes of delivery: sucrose pellets, which require goal-directed action for their collection and are associated with sensory stimuli, and intraoral infusions of sucrose, which are passively received and not associated with external stimuli. We found that when rewards were unpredicted both pellets and infusions evoked similar dopamine release. However, when rewards were predicted by distinct cues, greater dopamine release was evoked by pellet cues than infusion cues. Thus, dopamine responses to pellets, infusions as well as predictive cues suggest a nuanced role for dopamine in both reward seeking and reward evaluation.

neuroscience↗