Biology subjects

Gonzalez, J.

Publications and source records attributed to Gonzalez, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Differential Effects of Haloperidol on Neural Oscillations During Wakefulness and Sleep

The electrical activity of the brain, characterized by its frequency components, reflects a complex interplay between periodic (oscillatory) and aperiodic components. These components are associated with various neurophysiological processes, such as the excitation-inhibition balance (aperiodic activity) or interregional communication (oscillatory activity). However, we do not fully understand whether these components are truly independent or if different neuromodulators modulate them in different ways. The dopaminergic system has a critical role for cognition and motivation, being a potential modulator of these power spectrum components. To improve our understanding of these questions, we investigated the differential effects of this system on these components using electrocorticogram recordings in cats, which show clear oscillations and aperiodic 1/f activity. Specifically, we focused on the effects of haloperidol (a D2 receptor antagonist) on oscillatory and aperiodic dynamics during wakefulness and sleep. By parameterizing the power spectrum into these two components, our findings reveal a state-dependent modulation of oscillatory activity by the D2 receptor across the brain. Surprisingly, aperiodic activity was not significantly affected and exhibited inconsistent changes across the brain. This suggests a nuanced interplay between neuromodulation and the distinct components of brain oscillations, providing insights into the selective regulation of oscillatory dynamics in awake states.

neuroscience↗

bioRxiv2024

Communication subspace dynamics of the canonical olfactory pathway

Understanding how different brain areas communicate is crucial for elucidating the mechanisms underlying cognition. A possible way for neural populations to interact is through a communication subspace, a specific region in the state-space enabling the transmission of behaviorally-relevant spiking patterns. In the olfactory system, it remains unclear if different populations employ such a mechanism. Our study reveals that neuronal ensembles in the main olfactory pathway (olfactory bulb to olfactory cortex) interact through a communication subspace, which is driven by nasal respiration and allows feedforward and feedback transmission to occur segregated along the sniffing cycle. Moreover, our results demonstrate that subspace communication depends causally on the activity of both areas, is hindered during anesthesia, and transmits a low-dimensional representation of odor.

neuroscience↗

bioRxiv2024

Transposable elements in a cold-tolerant fly species, Drosophila montana: a link to adaptation to the harsh cold environments

BackgroundSubstantial discoveries during the past century have revealed that transposable elements (TEs) can play a crucial role in genome evolution by affecting gene expression and inducing genetic rearrangements, among other molecular and structural effects. Yet, our knowledge on the role of TEs in adaptation to extreme climates is still at its infancy. The availability of long-read sequencing has opened up the possibility to identify and study potential functional effects of TEs with higher precision. In this work, we used Drosophila montana as a model for cold-adapted organisms to study the association between TEs and adaptation to harsh climates. ResultsUsing the PacBio long-read sequencing technique, we de novo identified and manually curated TE sequences in five Drosophila montana genomes from eco-geographical distinct populations. We identified 489 new TE consensus sequences which represented 92% of the total TE consensus in D. montana. Overall, 11-13% of the D. montana genome is occupied by TEs, which as expected are non-randomly distributed across the genome. We identified five potentially active TE families, most of them from the retrotransposon class of TEs. Additionally, we found TEs present in the five analyzed genomes that were located nearby previously identified cold tolerant genes. Some of these TEs contain promoter elements and transcription binding sites. Finally, we detected TEs nearby fixed and polymorphic inversion breakpoints. ConclusionsOur research revealed a significant number of newly identified TE consensus sequences in the genome of D. montana, suggesting that non-model species should be studied to get a comprehensive view of the TE repertoire in Drosophila species and beyond. Genome annotations with the new D. montana library allowed us to identify TEs located nearby cold tolerant genes, and present at high population frequencies, that contain regulatory regions and are thus good candidates to play a role in D. montana cold stress response. Finally, our annotations also allow us to identify for the first time TEs present in the breakpoints of three D. montana inversions.

genomics↗

bioRxiv2024

Transposable elements identify previously overlooked regions undergoing parallel evolution in response to diverse selective pressures

Evolve and Resequence (E&R) studies have contributed to closing the gap between adaptive phenotypic traits and their underlying genomic basis. Unlike other popular approaches, E&R studies provide a unique opportunity to understand the degree of repeatability and constraints of the evolutionary process. Still, one of the major challenges is to accurately identify the genetic variants targeted by selection. Traditionally, E&R studies have only explored part of the variation present in the genomes, SNPs, thus neglecting other sources of adaptive variation such as transposable elements (TEs). In this work, we analyzed the Pool-seq data of five published Drosophila melanogaster E&R studies in the context of TEs. We found some candidate TEs inserted in the same or nearby regions to significant SNPs/genes. As such, these TEs should be added to the set of possible targets of selection. However, we also found a subset of significant TEs that were not associated with previously identified significant SNPs/genes. Most of these TEs are inserted within or flanked by genes related to the trait of interest and thus they are the only potential targets of selection identified in these regions. Functional enrichment analysis of the genes located nearby all candidate adaptive TEs allowed to identify new relevant biological functions. Finally, the replicability of candidate TEs was similar or higher than that reported for SNPs. We argue that TE variants should also be considered as candidate targets of selection in E&R studies and we also provide guidelines to improve the detection of TEs as targets of selection.

evolutionary biology↗

bioRxiv2024

YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response.

Cells have evolved a robust and highly regulated DNA damage response to preserve their genomic integrity. Although increasing evidence highlights the relevance of RNA regulation, our understanding of its impact on a fully efficient DNA damage response remains limited. Here, through a targeted CRISPR-knockout screen, we identified RNA binding proteins and modifiers that participate in mediating the p53 response. Among the top hits, m6A reader YTHDC1 was identified as a master regulator of p53 expression. YTHDC1 binds to the transcription start sites of TP53 and other genes involved in DNA damage response, promoting their transcriptional elongation. YTHDC1 deficiency leads to reduced TP53 expression, and also retention of introns leading to aberrant protein production of key DNA damage factors. While intron retention is dependent on m6A, YTHDC1 favors TP53 transcriptional pause-release independently of m6A. Depletion of YTHDC1 causes genomic instability and aberrant cancer cell proliferation mediated by genes regulated by YTHDC1. Our results uncover YTHDC1 as an orchestrator of the DNA damage response through distinct mechanisms of co-transcriptional mRNA regulation.

cancer biology↗

bioRxiv2024

A senescence-specific lncRNA controls metabolic rewiring of senescent cells

Despite the classical view of senescence as passive growth arrest, senescent cells remain metabolically active to be able to cope with the energetic demand of the senescence program. However, the mechanisms underlying this metabolic reprogramming remain poorly understood. We have identified sin-lncRNA, a previously uncharacterized lncRNA, that plays a pivotal role in this response. Sin-lncRNA is only expressed by senescent cells, induced by the senescence master regulator C/EBP{beta}. While strongly activated in senescence, sin-lncRNA loss reinforces the senescence program by altering oxidative phosphorylation and rewiring mitochondrial metabolism. By interacting with the TCA enzyme dihydrolipoamide S-succinyltransferase (DLST) it facilitates its localization to the mitochondria. On the other hand, sin-lncRNA depletion results in DLST nuclear translocation linked to DLST-dependent transcriptional alteration of OXPHOS genes. While in highly proliferative cancer cells, sin-lncRNA expression remains undetected, it is strongly induced upon cisplatin-induced senescence. Depletion of sin-lncRNA in ovarian cancer cells results in deficient oxygen consumption and increased extracellular acidification, sensitizing the cells to cisplatin treatment. Altogether, these results indicate that sin-lncRNA is specifically induced in cellular senescence to maintain metabolic homeostasis. Our findings reveal a new regulatory mechanism in which a lncRNA contributes to the adaptive metabolic changes in senescent cells, unveiling the existence of an RNA-dependent metabolic rewiring specific to senescent cells.

cell biology↗

bioRxiv2023

Seasonally increasing parasite load is associated with microbiome dysbiosis in wild bumblebees

The microbiome is increasingly recognized for its complex relationship with host fitness. Bumblebees are host to a characteristic gut microbiome community that is derived and reinforced through social contact between individuals. The bumblebee microbiome is species-poor, and primarily composed from a small number of core taxa that are associated with the greater tribe of corbiculate bees. Experimental findings support a role for the core bumblebee microbiome in resistance to severe infections by a common trypanosomal parasite, Crithidia bombi. However, most studies have been small in scale, often considering just one or two bumblebee species, or making use of commercially-reared bees. To better understand the microbiome diversity of wild populations, we have deeply sampled field populations of ten sympatric species found throughout central and down east Maine in a three-year microbiome field survey. We have used 16S amplicon sequencing to produce microbiome community profiles, and qPCR to screen samples for infections by Crithidia bombi. The breadth of our dataset has enabled us to test for seasonal and interspecific trends in the microbiome community. Controlling for these external sources of variation, we have identified microbial factors associated with infection and parasite load that support the role of the core microbiome in resistance to severe infection.

microbiology↗

bioRxiv2023

The epigenetics effects of transposable elements are context dependent and not restricted to gene silencing

Transposable elements (TEs) represent a threat to genome integrity due to their proliferation capacity. Eukaryotic cells silence TEs through different epigenetic mechanisms, including the deposition of repressive histone marks. Previous studies have shown that repressive marks can spread to neighboring sequences. However, evidence for this spreading affecting nearby gene expression remains limited. Similarly, whether TEs induce changes in the enrichment of active histone marks genome-wide, and its potential impact on gene expression have not been widely studied. In this work, we performed a comprehensive study of the epigenetic effects of 2,235 TEs and their potential effects on nearby gene expression on D. melanogaster head, gut and ovary. While most of the TEs (816) induce the enrichment of the H3K9me3 repressive mark, with stronger epigenetic effects in the ovary, a substantial number (345 TEs) induce the enrichment of the H3K27ac active mark, particularly in the gut. We found that 70% of the H3K9me3 enriched TEs induced gene down-regulation, and 50% of the H3K27ac enriched TEs induced gene up-regulation. These changes in expression affect specific regulatory networks in head and gut while in ovary, genes were not enriched for any biological functions. Furthermore, TE epigenetic effects on gene expression are genomic context dependent. Finally, we found that TEs also affect gene expression by disrupting regions enriched for histone marks. Overall, our results show that TEs do generate regulatory novelty through epigenetic changes, with these epigenetic effects not restricted to gene silencing and being context dependent. Significance statementTransposable elements (TEs) are repetitive DNA sequences found in nearly all studied organisms that have the capacity to move within the genome. To prevent their proliferation, eukaryotic cells target TEs with repressive histone marks, an epigenetic signal that blocks their expression. While these repressive marks can spread to neighboring genes, the evidence of how this impacts gene expression is limited. Similarly, whether TEs also influence the enrichment and depletion of active histone marks and their genome-wide impact is not understood. In this work, we studied the histone mark enrichment of 2,235 polymorphic TEs across three body parts of D. melanogaster. Our results provide evidence for the genome-wide role of TEs in the generation of regulatory novelty through epigenetic changes.

evolutionary biology↗

bioRxiv2023

Fast and efficient root phenotyping via pose estimation

Image segmentation is commonly used to estimate the location and shape of plants and their external structures. Segmentation masks are then used to localize landmarks of interest and compute other geometric features that correspond to the plants phenotype. Despite its prevalence, segmentation-based approaches are laborious (requiring extensive annotation to train), and error-prone (derived geometric features are sensitive to instance mask integrity). Here we present a segmentation-free approach which leverages deep learning-based landmark detection and grouping, also known as pose estimation. We use a tool originally developed for animal motion capture called SLEAP (Social LEAP Estimates Animal Poses) to automate the detection of distinct morphological landmarks on plant roots. Using a gel cylinder imaging system across multiple species, we show that our approach can reliably and efficiently recover root system topology at high accuracy, few annotated samples, and faster speed than segmentation-based approaches. In order to make use of this landmark-based representation for root phenotyping, we developed a Python library (sleap-roots) for trait extraction directly comparable to existing segmentation-based analysis software. We show that landmark-derived root traits are highly accurate and can be used for common downstream tasks including genotype classification and unsupervised trait mapping. Altogether, this work establishes the validity and advantages of pose estimation-based plant phenotyping. To facilitate adoption of this easy-to-use tool and to encourage further development, we make sleap-roots, all training data, models, and trait extraction code available at: https://github.com/talmolab/sleap-roots and https://osf.io/k7j9g/.

plant biology↗

bioRxiv2023

ZNF397 Loss Triggers TET2-driven Epigenetic Rewiring, Lineage Plasticity, and AR-targeted Therapy Resistance in AR-dependent Cancers

Cancer cells exhibit phenotypical plasticity and epigenetic reprogramming, which allows them to evade lineage-dependent targeted treatments by adopting lineage plasticity. The underlying mechanisms by which cancer cells exploit the epigenetic regulatory machinery to acquire lineage plasticity and therapy resistance remain poorly understood. We identified Zinc Finger Protein 397 (ZNF397) as a bona fide co-activator of the androgen receptor (AR), essential for the transcriptional program governing AR-driven luminal lineage. ZNF397 deficiency facilitates the transition of cancer cell from an AR-driven luminal lineage to a Ten-Eleven Translocation 2 (TET2)-driven lineage plastic state, ultimately promoting resistance to therapies inhibiting AR signaling. Intriguingly, our findings indicate that TET2 inhibitor can eliminate the AR targeted therapies resistance in ZNF397-deficient tumors. These insights uncover a novel mechanism through which prostate and breast cancers acquire lineage plasticity via epigenetic rewiring and offer promising implications for clinical interventions designed to overcome therapy resistance dictated by lineage plasticity. Statement of SignificanceThis study reveals a novel epigenetic mechanism regulating tumor lineage plasticity and therapy response, enhances understanding of drug resistance and unveils a new therapeutic strategy for prostate cancer and other malignancies. Our findings also illuminate TET2s oncogenic role and mechanistically connect TET2-driven epigenetic rewiring to lineage plasticity and therapy resistance.

cancer biology↗

bioRxiv2023

MCHelper automatically curates transposable element libraries across species

The number of species with high quality genome sequences continues to increase, in part due to scaling up of multiple large scale biodiversity sequencing projects. While the need to annotate genic sequences in these genomes is widely acknowledged, the parallel need to annotate transposable element sequences that have been shown to alter genome architecture, rewire gene regulatory networks, and contribute to the evolution of host traits is becoming ever more evident. However, accurate genome-wide annotation of transposable element sequences is still technically challenging. Several de novo transposable element identification tools are now available, but manual curation of the libraries produced by these tools is needed to generate high quality genome annotations. Manual curation is time-consuming, and thus impractical for large-scale genomic studies, and lacks reproducibility. In this work, we present the Manual Curator Helper tool MCHelper, which automates the TE library curation process. By leveraging MCHelpers fully automated mode with the outputs from three de novo transposable element identification tools, RepeatModeler2, EDTA and REPET, in fruit fly, rice, hooded crow, zebrafish, maize, and human, we show a substantial improvement in the quality of the transposable element libraries and genome annotations. MCHelper libraries are less redundant, with up to 65% reduction in the number of consensus sequences, have up to 11.4% fewer false positive sequences, and up to [~]48% fewer "unclassified/unknown" transposable element consensus sequences. Genome-wide transposable element annotations were also improved, including larger unfragmented insertions. Moreover, MCHelper is an easy to install and easy to use tool.

genomics↗

bioRxiv2023

Noribogaine effects on wakefulness and sleep

Ibogaine is a potent atypical psychedelic that has gained considerable attention due to its antiaddictive and antidepressant properties in preclinical and clinical studies. Previous research from our group showed that ibogaine suppresses sleep and produces an altered wakefulness state which resembles natural REM sleep. However, after systemic administration, ibogaine is rapidly metabolized to noribogaine, which also shows antiaddictive effects and a distinct pharmacological profile, making this drug a promising therapeutic candidate. Therefore, whether the sleep/wake alterations depend on ibogaine or its principal metabolite noribogaine remains unknown. To answer this question, we conducted polysomnographic recordings in rats following the administration of pure noribogaine. Our results show that noribogaine promotes wakefulness while reducing slow-wave sleep and blocking REM sleep. Thus, like ibogaine, noribogaine significantly alters the sleep-wake architecture, highlighting the possible role of serotonin reuptake inhibition as a likely candidate underlying the wake-promoting and REM sleep-suppressing effects.

neuroscience↗

bioRxiv2023

Piroplasm parasites (Apicomplexa: Piroplasmida) in northeastern populations of the invasive Asian longhorned tick, Haemaphysalis longicornis Neumann (Ixodida: Ixodidae), in the United States

Piroplasms, which include the agents of cattle fever and human and dog babesiosis, are a diverse group of blood parasites of significant veterinary and medical importance. The invasive Asian longhorned tick, Haemaphysalis longicornis, is a known vector of piroplasms in its native range in east Asia and invasive range in Australasia. In the US state of Virginia, H. longicornis has been associated with Theileria orientalis Ikeda outbreaks that caused cattle mortality. We examined 667 H. longicornis collected in 2021 from three sites in New Brunswick, New Jersey, the US state where established populations of this species were first detected in 2017. We used primers targeting the 18S small subunit rRNA and the cytochrome b oxidase loci and unveiled the presence of DNA from an unidentified Theileria species (in 1 nymph) and Theileria cervi type F (1 adult, 5 nymphs). In addition, we sequenced a 130 bp fragment of the cytochrome oxidase b locus from Odocoileus virginianus, the white-tailed deer, in a partially engorged questing H. longicornis, supporting the association of this tick species with deer. We also detected DNA from an undescribed Babesia sensu stricto ( true Babesia, 2 adults, 2 nymphs) as well as Babesia sp. Coco (1 adult, 1 nymph). Finally, we detected DNA from Babesia microti S837 (1 adult, 4 nymphs). Babesia microti S837 has been sequenced from striped skunks, Mephitis mephitis, and is closely related to the human pathogen B. microti US-type. The five parasites we are associating with H. longicornis represent a diverse assemblage spanning three clades in the piroplasm phylogeny, two undescribed, raising concerns of transmission amplification of veterinary pathogens as well as spillover of pathogens from wildlife to humans.

ecology↗

bioRxiv2023

Characterizing the power spectrum dynamics of the NREM to REM sleep transition

The transition from NREM to REM sleep is considered a transitional or intermediate stage (IS), characterized by high amplitude spindles in the frontal cortex and theta activity in the occipital cortex. Early reports in rats showed an IS lasting from 1 to 5 s, but recent studies suggested a longer duration of this stage. To further characterize the IS, we analyzed its spectral characteristics on electrocorticogram (ECoG) recordings of the olfactory bulb (OB), motor (M1), somato-sensory (S1) and secondary visual cortex (V2) in twelve Wistar male adult rats. By comparing the IS to consolidated NREM/REM epochs, our results reveal that the IS has specific power spectral patterns that statistically differ from both NREM and REM sleep states. Specifically, the main findings were that sigma (11-16 Hz) and beta (17-30 Hz) power in OB, M1, and S1 increased during the IS compared to NREM and REM sleep and began 55 s before REM sleep onset. Additionally, low gamma (31-48 Hz) in the OB started transitioning from NREM levels to REM ones 65 s before its onset. Finally, the high-frequency oscillations (102-198 Hz) in OB, M1, and S1 showed a power increase that began 40 s before REM sleep and reached REM sleep values 10 s after its onset. Thus, we argue that the NREM to REM transition contains its own spectral profile and is more extended than previously described.

neuroscience↗

bioRxiv2023

Cortical high-frequency oscillations ({approx} 110 Hz) in cats are state-dependent and enhanced by a subanesthetic dose of ketamine

Ketamine is an NMDA receptor antagonist that has both antidepressant and anesthetic properties. At subanesthetic doses, ketamine can cause transient psychosis in humans, and is used to model psychosis in experimental animals. In rodents, subanesthetic doses of ketamine increase the power of high-frequency oscillations (HFO, 100-180 Hz) in the electroencephalogram and field potentials, a frequency band linked to cognitive functions. However, the effects of ketamine in higher mammals, with more translatable relevance, are poorly investigated. Here, we have examined cortical HFO during wakefulness, sleep, and after administering a sub-anesthetic dose of ketamine (15 mg/kg), utilizing the cat as an animal model. Four cats were implanted with cortical electrodes for chronic polysomnographic recordings. HFO power, connectivity, information flow directionality, and their relationships with respiratory activity were analyzed. During wakefulness, but not during sleep, we found that HFO were coupled with the inspiratory phase of the respiration. After ketamine administration, HFO were enhanced significantly and remained associated with the inspiratory phase. The analysis of the information flow after ketamine suggest that HFO originate from the olfactory bulb and stream towards the prefrontal cortex. Accordingly, occluding the nostrils significantly reduced HFO power in both the olfactory bulb and prefrontal cortex. In contrast, auditory stimulation did not affect HFO. In conclusion, spontaneous cortical HFO show certain state-dependent features in cats, and enhancement of this rhythm by ketamine may disrupt cortical information processing, which could contribute to some of the neuropsychiatric manifestations associated with ketamine. HighlightsO_LIKetamine is used to model psychosis in humans and experimental animals C_LIO_LISubanesthetic doses of ketamine increase the power of high-frequency oscillations C_LIO_LIHigh-frequency oscillations are coupled with the inspiratory phase of respiration C_LIO_LIThese oscillations originate in the olfactory bulb and stream to the neocortex C_LIO_LINostril occlusion lowers high-frequency activity in the olfactory bulb and neocortex C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=69 SRC="FIGDIR/small/543142v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@e386feorg.highwire.dtl.DTLVardef@1b3c06aorg.highwire.dtl.DTLVardef@1d93ecorg.highwire.dtl.DTLVardef@1daa161_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

The Nbeta motif of NaTrxh directs secretion as an endoplasmic reticulum transit peptide and variations might result in different cellular targeting

Soluble secretory proteins with a signal peptide reach the extracellular space through the endoplasmic reticulum-Golgi conventional pathway. During translation, the signal peptide is recognised by the secretory recognition particle and results in a co-translational translocation to the endoplasmic reticulum to continue the secretory pathway. However, soluble secretory proteins lacking a signal peptide are also abundant, and several unconventional (endoplasmic reticulum/Golgi independent) pathways have been proposed and some demonstrated. This work describes new features of the secretion signal called N{beta}, originally identified in NaTrxh, a plant extracellular thioredoxin, that does not possess an orthodox signal peptide. We provide evidence that other proteins, including thioredoxins type h, with similar sequences are also signal peptide-lacking secretory proteins. To be a secretion signal, positions 5, 8 and 9 must contain neutral residues -a negative residue in position 9 in animal proteins- to maintain the N{beta} motif negatively charged and a hydrophilic profile. Moreover, our results suggest that the NaTrxh translocation to the endoplasmic reticulum occurs as a post-translational event. Finally, the N{beta} motif sequence at the N- or C-terminus could be a feature that may help to predict protein localisation, mainly in plant and animal proteins.

cell biology↗

bioRxiv2023

Dorsal and median raphe neuronal firing dynamics characterized by non-linear metrics

The dorsal (DRN) and median (MRN) raphe are the main serotonergic nuclei, being implicated in sleep and mood regulation. The DRN is mainly serotonergic, where neurons have regular spiking activity, slow firing rate (FR), and long action potential duration (APD). The MRN is divided in a median serotonergic region and a paramedian region, containing principally GABAergic neurons, resulting in more diverse neurochemical and electrophysiological features. In the present study, we aimed to enrich the characterization of the raphe nuclei neurons by using non-linear metrics. This was done by analyzing the neuronal basal firing profile in both nuclei of urethane-anesthetized rats using Ordinal Patterns (OP) Entropy, Bins Entropy, and Permutation Lempel-Ziv Complexity (PLZC). In a first step, we found that typical linear metrics - such as FR, coefficient of variation (CV), and APD - fail to distinguish between MRN and DRN neurons, while OP entropy is significantly different between these nuclei. We also found that the FR has a strong linear relationship with CV, Bins Entropy, and PLZC. Similarly, CV has a strong correlation with FR and Bins Entropy, whereas PLZC shows a strong linear fit with Bins Entropy. However, OP Entropy has either a weak or no linear relationship with the rest of the metrics tested, suggesting that OP Entropy is a good metric to differentiate neuronal firing profiles. In a second step, we studied how these metrics are affected by the oscillatory properties of the firing patterns. We found that all metrics are sensitive to rhythmicity - with the exception of OP Entropy. Again, this highlights OP Entropy as a powerful and useful quantity for the characterization of neuronal discharge patterns.

neuroscience↗

bioRxiv2023

Neo-functionalization in Saccharomyces cerevisiae: A Novel Nrg1-Rtg3 chimeric transcriptional modulator is essential to maintain mitochondrial DNA integrity

In Saccharomyces cerevisiae, the transcriptional repressor Nrg1 (Negative Regulator of Glucose-repressed genes) and the b/Zip transcription factor Rtg3 (ReTroGrade regulation) mediate glucose repression and mitochondria to nucleus signaling, respectively. Here we show a novel function for these two proteins, in which alanine promotes the formation of a chimeric Nrg1/Rtg3 regulator that represses the ALT2 gene (encoding an alanine transaminase paralogue of unknown function) expression. A NRG1/NRG2 paralogous pair, resulting from a post-wide genome, small scale duplication event, is extant in the Saccharomyces genus. Neo-functionalization of only one paralogue resulted in Nrg1, able to interact with Rtg3. Either nrg1{Delta} or rtg3{Delta} single mutant strains are unable to utilize ethanol and show a typical petite (small) phenotype on glucose. Neither of the WT genes complemented the petite phenotype, suggesting irreversible mitochondrial DNA damage in these mutants. Neither nrg1{Delta} nor rtg3{Delta} mutant strains express genes encoded by any of five polycistronic units transcribed from mitochondrial DNA in S. cerevisiae. This, and the direct measure of the mitochondrial DNA gene complement confirms that irreversible damage of the mitochondrial DNA occurred in both mutant strains and is consistent with an essential role of the chimeric Nrg1/Rtg3 regulator in mitochondrial DNA maintenance.

microbiology↗