Biology subjects

Vanegas, J.

Publications and source records attributed to Vanegas, J..

4 recordsLinked to original sources

bioRxiv2026

Genomic architecture and adaptive plasticity of Enterococcus lactis strains isolated from extreme Semi-arid environments

The presence of Enterococcus lactis in semi-arid "resource islands" the remarkable ecological plasticity of a species often associated with host-related environments. Characterizing the genomic mechanisms that facilitate its persistence in extreme edaphic niches is crucial for exploring its biotechnological potential in arid agriculture. This study characterized the genomic architecture, abiotic stress tolerance, and plant growth-promoting (PGP) capabilities of six E. lactis strains isolated from the rhizosphere of Pithecellobium dulce and Haematoxylum brasiletto in La Guajira, Colombia. We compared the pangenomes of the isolates with clinical and environmental reference strains. Genomic predictions were validated through in vitro assays for thermal, saline, and pH stress, PGP traits, and biosafety (hemolysis, biofilm formation). Analysis revealed a pangenome with a conserved 2,113-gene core and a highly plastic 3,134-gene accessory genome. The core genome encodes robust machinery for osmotic stress (e.g., opuA-C operons) and DNA repair (uvrC), while the accessory genome is heavily shaped by Horizontal Gene Transfer, containing abundant Mobile Genetic Elements (6.3%-16.4%). Phenotypically, strains exhibited high resilience to heat (50{degrees}C), salinity (5% NaCl), and alkalinity (pH 12). Adaptation in these isolates favors metabolic parsimony: rather than complex phytohormone synthesis, the strains prioritize inorganic phosphate solubilization (conserved pst system) and harbor a complete 2,3-butanediol cluster for volatile-mediated plant interaction. Notably, strain IS_B39 produced siderophores and carried a specific RiPP-like biosynthetic cluster, indicating niche-specific functional diversification. Genomic and phenotypic screening confirmed a safe profile, lacking key virulence factors. These findings define a robust, low-risk genomic toolkit, supporting the potential of E. lactis as a tailored bioinoculant for sustainable agriculture in extreme, water-limited environments. ImportanceEnterococcus species are traditionally studied as clinical pathogens or dairy-associated bacteria, leaving their ecological role in natural, non-host environments largely overlooked. This study challenges conventional paradigms by exploring Enterococcus lactis strains naturally persisting in the extreme, water-limited soils of semi-arid "resource islands" in La Guajira, Colombia. Through functional genomics and laboratory validation, we demonstrated how these bacteria utilize a specialized genetic toolkit to withstand extreme heat and alkalinity, while actively promoting plant resilience. Rather than relying on complex hormone production, they optimize vital nutrient uptake like phosphorus. These findings significantly advance environmental microbiology by uncovering the hidden survival strategies of lactic acid bacteria in arid lands, showcasing their immense potential as sustainable bioinoculants to support global dryland agriculture under climate change stress.

microbiology↗

bioRxiv2026

Genome-resolved metagenomics reveals abundant novel, non-methanogenic lineages in tropical alpine paramo soils

Wetlands are the largest natural source of atmospheric methane, and tropical wetlands are projected to drive the greatest increase in emissions under climate change, yet high-altitude tropical systems remain largely absent from global frameworks predicting this response. Here, we investigated soil metagenomes from the paramo ecosystem in Chingaza National Natural Park, Colombia, across three ecosites. Microbial community composition differed significantly among ecosites, with peatland soils exhibiting the highest diversity. Genome-resolved metagenomics recovered 109 high-quality metagenome-assembled genomes (MAGs); 8.3% (9 MAGs) could not be assigned to any described genus, representing phylogenetically novel lineages, while 37.6% (41 MAGs) were absent from the wetland-specific MUCC database but present in GTDB. Functional analyses revealed widespread Wood-Ljungdahl pathway potential, complemented by the bacterial reductive glycine pathway and reverse tricarboxylic acid cycle. No methanogenesis marker (mcrABG) was detected in any high- or medium-quality genomes or assembled contigs, identifying the genomically resolved community as non-methanogenic. A read-level search nonetheless recovered a low-abundance methanogen signal concentrated in peatland and affiliated with hydrogenotrophic lineages typical of acidic peatlands, indicating that methanogenesis is present but minor. Metabolic potential instead supported acetogenic carbon fixation and sulfate reduction, suggesting a carbon-cycling regime distinct from canonical methane-dominated wetlands. Together, these findings establish tropical alpine paramos as overlooked reservoirs of phylogenetically novel microbial diversity with metabolic potential distinct from other wetlands. Public release of these MAGs expands genomic representation of tropical alpine ecosystems and provides a foundation for improving predictions of carbon cycling in high-altitude ecosystems.

microbiology↗

bioRxiv2025

Ferlin C2A-C2B linkers are alternatively spliced, intrinsically disordered, and interact with negatively charged membranes

Ferlins are vesicle trafficking proteins composed of folded C2 domains conjugated by linkers which are largely disordered. Although a role for the for the C2 domains as calcium sensors has been established it remains unclear whether the linkers function beyond acting as passive spacers. We examined the C2A-C2B linker of vertebrate ferlins and found both putative AP2 and SH3 binding short linear motifs (SLiMs) as well as membrane binding sequences for members of the protein family. Specifically for otoferlin we identified an arginine-rich region proximal to a AP2 binding dileucine motif which interacts with negatively charged lipid membranes. Further, the linker region dominated the liposome binding properties of a larger C2A-C2B two-C2 domain segment of otoferlin, suggesting a dominant role in mediating the membrane binding property of the N-terminus. We also found that alternative splicing of the otoferlin C2A-C2B linker adds and additional membrane binding segment and alters the affinity and kinetics of membrane binding. By contrast alternative splicing of the dysferlin linker is not predicted to alter membrane binding but rather alters the number of predicted short linear motifs (SLiMs). In addition we found the otoferlin linker-membrane interaction was sensitive to ionic strength, and simulations suggest positively charged residues including an arginine-rich region mediates binding. We conclude that the C2A-C2B linker of vertebrate ferlins encode both SLiMs which recruit endocytic proteins as well as membrane binding regions that would place the endocytic binding motif proximal to the membrane surface to facilitate endocytosis and synaptic vesicle resupply.

molecular biology↗

bioRxiv2024

Structural basis of bulk lipid transfer by bridge-like lipid transfer protein LPD-3

Bridge-like lipid transport proteins (BLTPs) are an evolutionarily conserved family of proteins that localize to membrane contact sites and are thought to mediate the bulk transfer of lipids from a donor membrane, typically the endoplasmic reticulum (ER), to an acceptor membrane, such as a that of the cell or an organelle 1. Despite the fundamental importance of BLTPs for cellular function, the architecture, composition, and lipid transfer mechanisms remain poorly characterized. Here, we present the subunit composition and the cryo-electron microscopy structure of the native LPD-3 BLTP complex isolated from transgenic C. elegans. LPD-3 folds into an elongated, rod-shaped tunnel whose interior is filled with ordered lipid molecules that are coordinated by a track of ionizable residues that line one side of the tunnel. LPD-3 forms a complex with two previously uncharacterized proteins, here named "Intake" and "Spigot", both of which interact with the N-terminal end of LPD-3 where lipids enter the tunnel. Intake has three transmembrane helices, one of which borders the entrance to the tunnel; Spigot has one transmembrane helix and extends 80 [A] along the cytosolic surface of LPD-3. Experiments in multiple model systems indicate that Spigot plays a conserved role in ER-PM contact site formation. Our LPD-3 complex structural data, together with molecular dynamics simulations of the transmembrane region in a lipid bilayer, reveal protein-lipid interactions that suggest a model for how the native LPD-3-complex mediates bulk lipid transport and provide a foundation for mechanistic studies of BLTPs.

biochemistry↗