Biology subjects

Herrera, N.

Publications and source records attributed to Herrera, N..

10 recordsLinked to original sources

bioRxiv2026

Mitochondrial perturbation adapts the proteome from early to advanced immune responses

Dysregulated immunity, a hallmark of many human diseases, co-occurs with mitochondrial dysfunction and is commonly associated with misprimed primary immune signaling. While transcriptionally well-characterized, the impact of mitochondria on the host response at the protein level is less clear. Using in vitro and in vivo approaches including proteotranscriptomics, our data suggest that OXPHOS promotes expression of early, cell autonomous immune proteins whereas mitochondrial perturbation favors mediators of cell extrinsic responses like inflammation. This response is independent of immune cues, time-dependent, conserved, and occurs across tissues in mouse models of mitochondrial dysfunction. These data illustrate unappreciated roles for mitochondrial state in adapting host responses at the protein level, which have implications for complex disease etiology and the ancestral origins for eukaryotic immune sensing.

immunology↗

bioRxiv2026

An integrated design strategy for developing and validating microalgal formulations in common bean and rainfed rice

Microalgae and cyanobacteria have emerged as promising resources for sustainable agriculture; however, integrated methodologies for the rational design of crop-specific agricultural formulations remain scarce. This study proposes an integrated framework that combines biomass production, species characterization, nutrient characterization, mixture design, nutrient profile estimation, biological validation, and statistical optimization for the rational development of agricultural formulations based on microalgae and cyanobacteria. As a proof of concept, the proposed framework was applied to formulate consortia composed of C. vulgaris, Scenedesmus sp., and A. platensis using common bean (Phaseolus vulgaris L., ecotype Sangre Toro) and rainfed rice (Oryza sativa L., cv. Fedearroz 2020) as model crops. The experimentally determined nutrient composition of the individual biomasses was integrated into a simplex-lattice mixture design coupled with response surface methodology and desirability analysis to identify crop-specific optimal formulations and estimate their nutrient profiles. The cubic model provided the best fit (P < 0.05), showing high predictive performance and a non-significant lack of fit. The optimal bean formulation consisted of 31.6% C. vulgaris and 68.4% Scenedesmus sp., whereas the optimal rice formulation comprised 62.3% A. platensis and 37.7% C. vulgaris, demonstrating distinct crop- specific responses. The optimized bean formulation exhibited higher estimated concentrations of calcium, phosphorus, iron, and zinc, whereas the rice formulation showed higher estimated potassium and Kjeldahl nitrogen contents. These findings demonstrate the feasibility of developing crop-specific microalgal formulations and highlight that different crops may require distinct formulations rather than a universal approach. The proposed approach offers a reproducible, integrated framework for the development and optimization of next-generation agricultural formulations for sustainable crop production.

microbiology↗

bioRxiv2025

Enhancing microalgal productivity through bioactive substances, light, and CO2

Microalgae play a crucial role in ecosystems, from oxygen production to sustaining food webs and offering valuable applications in industry and environmental management. Increasing their productivity in terms of biomass yield, cultivation time, and nutritional or metabolite quality remains a major challenge. This study assessed the effects of 10 bioactive substances (including lactones, phytohormones, and natural extracts), four light wavelengths, and four CO2 injection regimes on Arthrospira platensis, Chlorella vulgaris, Ankistrodesmus falcatus, and Tetradesmus dimorphus, using linear modeling and LSD (Least Significant Difference) post hoc tests. N-butyryl-DL-homoserine lactone significantly enhanced A. platensis growth (94.4%), while naphthaleneacetic acid and indole-3-butyric acid promoted T. dimorphus growth (138.1% and 115.5%, respectively). More accessible alternatives, such as Aloe vera and coconut water, also stimulated growth: A. platensis, C. vulgaris, and A. falcatus increased by 85.3%, 69.2%, and 87.7% with Aloe vera, while T. dimorphus increased 80.5% with coconut water. Regarding light quality, red light (600-700 nm) benefited A. platensis and A. falcatus (49.2% and 20.8%, respectively), whereas blue light (400-490 nm) favored C. vulgaris and T. dimorphus (57.7% and 31.5%, respectively). CO2 injection further enhanced biomass production and carbon fixation, particularly in C. vulgaris and A. falcatus (73.5% and 53.5%, respectively). However, combined treatments did not produce additive effects, suggesting complex interactions. Overall, these findings demonstrate the potential of bioactive substances and environmental conditions to improve microalgal performance and highlight the importance of investigating synergistic effects and scalability for large-scale production.

microbiology↗

bioRxiv2025

The phenotypic landscape of the mycobacterial cell

The Mycobacteriales are an order of diverse bacteria that thrive in many environmental and host-associated niches. Because the most notorious member of this clade, Mycobacterium tuberculosis, is a major human pathogen, research on Mycobacteriales has focused on pathogenesis, and, as a consequence, many fundamental aspects of Mycobacterial biology remain understudied. Here, we address this gap by performing a genome-wide CRISPRi chemical genomics screen using a diverse set of >35 antibiotics, detergents, and other anti-microbials predominantly targeting the cell envelope of Mycobacterium smegmatis, a saprophytic model Mycobacterium. We highlight new information derived from this screen, including the identification of novel functions for previously uncharacterized conserved and essential genes (in mycolic acid and arabinogalactan synthesis), the discovery of a new drug scaffold/protein target pair, and insights into the mechanism of action of two commonly used antibiotics. These data are also a valuable resource for the mycobacterial research community, as they provide thousands of novel phenotypes for uncharacterized genes and meaningful phenotypic correlations between annotated and uncharacterized genes.

microbiology↗

bioRxiv2025

Archaeal SegAB forms a bipolar structure that promotes chromosome segregation in spherical cells

Archaeal segAB operons are thought to promote chromosome segregation, but their mechanism remains unknown. We employ comparative genomics, structural biology, genetic knockouts, and quantitative cell biology to investigate how SegA and SegB proteins work together to segregate chromosomes in the thermophilic archaeon Sulfolobus acidocaldarius. In vitro, SegB binds a centromeric DNA sequence adjacent to the segAB operon, and in vivo forms a distinct focus on each segregating chromosome. SegA, a ParA-like ATPase, binds DNA non-specifically in vitro and promotes chromosome compaction and segregation in vivo. During division, SegA shifts from chromosome-associated puncta to form a single, elongated figure that runs between separating SegB foci. Late in division, SegA retreats to regions surrounding separated SegB foci. Elongated SegA figures appear in segB knockout cells but no longer lie perpendicular to the division plane. We propose that SegA and SegB interact to form a bipolar, DNA-segregating structure radically different from bacterial ParABS systems.

cell biology↗

bioRxiv2023

Three bacterial DedA subfamilies with distinct functions and phylogenetic distribution

Recent studies in bacteria suggested that the broadly conserved but enigmatic DedA proteins function as undecaprenyl-phosphate (UndP) flippases, recycling this essential lipid carrier. To determine whether all DedA proteins have UndP flippase activity, we performed a phylogenetic analysis and correlated it to previously published experimental results and predicted structures. We uncovered three major DedA subfamilies: one contains UndP flippases, the second contains putative phospholipid flippases and is associated with aerobic metabolism, and the third is found only in specific Gram-negative phyla. IMPORTANCEDedA-family proteins are highly conserved and nearly ubiquitous integral membrane proteins found in Archaea, Bacteria, and Eukaryotes. Recent work revealed that eukaryotic DedA proteins are phospholipid scramblases and some bacterial DedA proteins are undecaprenyl phosphate flippases. We perform a phylogenetic analysis of this protein family in Bacteria revealing 3 DedA subfamilies with distinct phylogenetic distributions, genomic contexts, and putative functions. Our analysis lays the groundwork for a deeper understanding of DedA proteins and their role in maintaining and modifying the membrane.

molecular biology↗

bioRxiv2021

The ESX-1 secretion system senses bacterial contact and prepares mycobacteria for environmental adaptation

The ESX-1 system (6-kDa early secretory antigenic target (ESAT-6) secretion system-1) is essential for Mycobacterium tuberculosis pathogenesis and conjugal transfer in Mycobacterium smegmatis, yet little is known about how its function is regulated. Live-cell fluorescence microscopy showed natively expressed ESX-1 was organized into distinct foci predominantly observed at cell-cell contacts. These foci formed when two cells touched and required a fully assembled ESX-1 system in both bacteria, suggesting the generation of an ESX-1 megacomplex across multiple membranes. The emergence of ESX-1 foci and ESX-1 secretion was environmentally dependent: foci formed in low nitrogen environments in which secretion was suppressed, yet with increasing concentrations of nitrogen, ESX-1 systems diffused along the plasma membrane and secretion was activated. Genome-wide transcriptional profiling revealed ESX-1 dependent induction of genes required for the SOS response and error prone DNA replication in high nitrogen. Based on these findings, we propose a new model of ESX-1 function where ESX-1 localization and secretion are responsive to nitrogen levels and form an integral node in the mycobacterial response to neighboring cells and environmental adaptation.

microbiology↗

bioRxiv2021

Cbp1, a rapidly evolving fungal virulence factor, forms an effector complex that drives macrophage lysis

Intracellular pathogens secrete effectors to manipulate their host cells. Histoplasma capsulatum (Hc) is a fungal intracellular pathogen of humans that grows in a yeast form in the host. Hc yeasts are phagocytosed by macrophages, where fungal intracellular replication precedes macrophage lysis. The most abundant virulence factor secreted by Hc yeast cells is Calcium Binding Protein 1 (Cbp1), which is absolutely required for macrophage lysis. Here we take an evolutionary, structural, and cell biological approach to understand Cbp1 function. We find that Cbp1 is present only in the genomes of closely related dimorphic fungal species of the Ajellomycetaceae family that lead primarily intracellular lifestyles in their mammalian hosts (Histoplasma, Paracoccidioides, and Emergomyces), but not conserved in the extracellular fungal pathogen Blastomyces dermatitidis. We determine the de novo structures of Hc H88 Cbp1 and the Paracoccidioides americana (Pb03) Cbp1, revealing a novel "binocular" fold consisting of a helical dimer arrangement wherein two helices from each monomer contribute to a four-helix bundle. In contrast to Pb03 Cbp1, we show that Emergomyces Cbp1 orthologs are unable to stimulate macrophage lysis when expressed in the Hc cbp1 mutant. Consistent with this result, we find that wild-type Emergomyces africanus yeast are able to grow within primary macrophages but are incapable of lysing them. Finally, we use subcellular fractionation of infected macrophages and indirect immunofluorescence to show that Cbp1 localizes to the macrophage cytosol during Hc infection, making this the first instance of a phagosomal human fungal pathogen directing an effector into the cytosol of the host cell. We additionally show that Cbp1 forms a complex with Yps-3, another known Hc virulence factor that accesses the cytosol. Taken together, these data imply that Cbp1 is a rapidly evolving fungal virulence factor that localizes to the cytosol to trigger host cell lysis. Author SummaryThe members of the Ajellomycetaceae fungal family are human pathogens that are responsible for a rising number of mycoses around the world. Calcium binding protein 1 (Cbp1) is a rapidly evolving virulence factor that is present in the genomes of the Ajellomycetaceae species that lead primarily intracellular lifestyles, including Histoplasma, Paracoccidioides, and Emergomyces but not Blastomyces, which remains largely extracellular during infection. Both Paracoccidioides and Histoplasma Cbp1 homologs are able to cause lysis of macrophages whereas Emergomyces homologs cannot. This result is consistent with Emergomyces africanus natural infection of macrophages, during which the yeast cells can replicate but cannot actively lyse the host cell. Despite divergence of the primary sequence of Histoplasma and Paracoccidioides Cbp1 homologs, their protein structures are remarkably similar and reveal a novel fold. During infection, Cbp1 enters the cytosol of the host macrophage, making it the first known virulence factor from an intracellular human fungal pathogen that localizes to the cytosol of the host cell. We also show that Cbp1 forms a complex with another cytosolic virulence factor, Yps-3. Taken together, these studies significantly advance our understanding of Histoplasma virulence.

microbiology↗

bioRxiv2021

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic model for full-length Nsp2 obtained by combining cryo-electron microscopy with deep learning-based structure prediction from AlphaFold2. The resulting structure reveals a highly-conserved zinc ion-binding site, suggesting a role for Nsp2 in RNA binding. Mapping emerging mutations from variants of SARS-CoV-2 on the resulting structure shows potential host-Nsp2 interaction regions. Using structural analysis together with affinity tagged purification mass spectrometry experiments, we identify Nsp2 mutants that are unable to interact with the actin-nucleation-promoting WASH protein complex or with GIGYF2, an inhibitor of translation initiation and modulator of ribosome-associated quality control. Our work suggests a potential role of Nsp2 in linking viral transcription within the viral replication-transcription complexes (RTC) to the translation initiation of the viral message. Collectively, the structure reported here, combined with mutant interaction mapping, provides a foundation for functional studies of this evolutionary conserved coronavirus protein and may assist future drug design.

biophysics↗

bioRxiv2020

Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

The SARS-CoV-2 macrodomain (Mac1) within the non-structural protein 3 (Nsp3) counteracts host-mediated antiviral ADP-ribosylation signalling. This enzyme is a promising antiviral target because catalytic mutations render viruses non-pathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of diverse fragment libraries resulted in 214 unique macrodomain-binding fragments, out of 2,683 screened. An additional 60 molecules were selected from docking over 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several crystallographic and docking fragment hits were validated for solution binding using three biophysical techniques (DSF, HTRF, ITC). Overall, the 234 fragment structures presented explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.

biochemistry↗