Biology subjects

Berry, S. P.

Publications and source records attributed to Berry, S. P..

7 recordsLinked to original sources

bioRxiv2026

Determinants of metal import and specificity in a bacterial transporter

Membrane transporters have evolved finely tuned substrate specificity within a limited repertoire of structural superfamilies, but the biophysical origins of transporter specificity remain unclear. We have systematically investigated the determinants of import and specificity in the model Deinococcus radiodurans (Dra)Nramp metal importer by testing targeted structure- and evolution-guided libraries of sequence variants in new high-throughput assays for import of the native substrate Mn2+ and the chemically similar but excluded metal Mg2+. The effects of most combinatorial mutations on Mn2+ import fit a simple global epistasis model, but many additional unexplained long-range epistatic interactions cluster at a set of structural hotspots at the inner and outer vestibules of the transporter. By contrast, mutations enabling Mg2+ import have non-additive effects and generally fall into two categories: a few core specificity positions in the first two shells around the metal are sufficient to allow DraNramp to import Mg2+, and additional modulator mutations can finetune specificity when combined with core-position mutations. The modulator mutations overlap considerably with key epistatic mutations, and we use this insight to propose a new biochemical model for how mutations that alter conformational balance in transporters can lead both to long-range epistasis and specificity modulation.

biophysics↗

bioRxiv2026

Dissecting genetic variance structure and evaluating genomic prediction models for single-cross hybrids derived from Stiff Stalk and Non-Stiff Stalk maize heterotic groups

The early 20th-century discovery of heterosis and the establishment of heterotic groups transformed maize (Zea mays L.) into a keystone of global agriculture. However, maize breeding faces two significant challenges: the gradual decline of general combining ability (GCA) variance within heterotic groups and the impracticality of testing all possible single crosses in the early stages of a breeding program. Here, we developed genomic best linear unbiased prediction (GBLUP)-based multi-kernel models, using additive and two alternative non-additive genomic relationship matrices, to estimate the variance components associated with the GCA of Stiff Stalk (SS) and Non-Stiff Stalk (NSS) heterotic groups and the specific combining ability (SCA) arising from their crosses. We further applied these models to predict the performance of untested single-cross combinations under varying levels of parental information. We showed that the SS and NSS groups retained significant GCA variance across traits in both early- and late-maturity groups. The SS group, in contrast, exhibited no detectable GCA variance in grain yield for the intermediate-flowering subset of hybrids, highlighting a limitation for future genetic improvement. Furthermore, our results showed that GBLUP-based multi-kernel models effectively identified superior hybrids when parental information was available. In the absence of this information, however, these models underperformed compared to covariance-based approaches. Both types of non-additive matrices produced similar results, affirming the robustness of the inferred genetic architecture. Overall, this study sheds light on the future use of US maize commercial germplasm and demonstrates how GBLUP-based multi-kernel models can improve the efficiency of hybrid breeding programs.

genetics↗

bioRxiv2026

Structural and functional basis of proton-independent transition metal import by a canonical bacterial Nramp transporter

Natural resistance-associated macrophage proteins (Nramps) are divalent transition metal transporters found in most organisms, typically coupling metal uptake to proton co-transport. How this coupling evolved, however, remains unclear. We present structural, functional, and evolutionary analyses of a clade B Nramp from the gut bacterium Bacteroides fragilis (BfraNramp). Phylogenetic reconstruction positions clade B as the most basal group of canonical Nramps, retaining conserved metal-binding motifs while lacking most residues that form the canonical proton pathway. We show that BfraNramp efficiently transports Mn{superscript 2} and Cd{superscript 2} with high apparent affinity but without proton co-transport or dependence on membrane potential or pH. Structures of metal-free and Mn{superscript 2}-bound BfraNramp reveal an inward-open conformation and a distinct metal coordination geometry involving a conserved glutamate on transmembrane helix 3. Together, these results identify clade B Nramps as proton-independent transition metal uniporters and suggest that proton coupling emerged later in Nramp evolution, following establishment of the metal-binding site.

biochemistry↗

bioRxiv2025

Genomic insights and breeding strategies for nixtamalization moisture content in hybrid maize

CORE IDEASO_LINixtamalization moisture content can be selected early in breeding programs using NIR spectroscopy. C_LIO_LIYield does not significantly correlate with nixtamalization moisture content in diverse or elite populations. C_LIO_LIAdditive and dominance gene action impact nixtamalization moisture content in hybrid maize. C_LIO_LIGenomic prediction can be used to assess nixtamalization moisture content early in hybrid maize breeding. C_LI Nixtamalization moisture content, a measure of the quantity of water absorbed during the nixtamalization of a grain such as maize, has a large impact on the end-quality of masa-based products. An application to predict nixtamalization moisture content from raw inbred and hybrid maize grain was recently developed, but its utility in a breeding context has not been assessed. Important breeding considerations for nixtamalization moisture content were assessed in diverse maize hybrids, modern commercial hybrids, and historically high-acreage hybrids grown in up to three environments across two years. This study demonstrated that nixtamalization moisture content is heavily influenced by growing conditions, but sufficient genetic variance is present to allow breeders to make gains from selection. Contrary to prior theory, there was no substantial correlation between nixtamalization moisture content and yield suggesting breeders can select for both traits without negatively impacting either trait. Both additive and dominant genetic action was observed and genomic prediction was able to predict nixtamalization moisture content in hybrids with an average Spearmans rank correlation coefficient greater than 0.441 and a root mean square error below 0.006. The findings here suggest that nixtamalization moisture content can be selected for early in breeding cycles, allowing breeders to develop improved food-grade maize germplasm without negatively impacting important traits such as yield. PLAIN LANGUAGE SUMMARYPlant breeders need to understand the biological mechanisms underlying a trait of interest to maximize the efficiency of their efforts. Nixtamalization moisture content is a highly complex trait that is determined by both genetic and environmental factors. In this study, nixtamalization moisture content was assessed in a diverse set of hybrid and inbred maize to understand the biological mechanisms underlying nixtamalization moisture content. The relationship between nixtamalization moisture content and yield was assessed, the genetic architecture and mode of gene action underlying nixtamalization moisture content were evaluated, and the efficacy of genomic prediction in assessing nixtamalization moisture content was determined. The findings of this study will allow breeders to create optimized breeding strategies for nixtamalization moisture content, thus improving the raw materials that are used to produce globally consumed products such as tortillas and tortilla chips.

plant biology↗

bioRxiv2024

They all rock: A systematic comparison of conformational movements in LeuT-fold transporters

Many membrane transporters share the LeuT fold--two five-helix repeats inverted across the membrane plane. Despite hundreds of structures, whether distinct conformational mechanisms are supported by the LeuT fold has not been systematically determined. After annotating published LeuT-fold structures, we analyzed distance difference matrices (DDMs) for nine proteins with multiple available conformations. We identified rigid bodies and relative movements of transmembrane helices (TMs) during distinct steps of the transport cycle. In all transporters the bundle (first two TMs of each repeat) rotates relative to the hash (third and fourth TMs). Motions of the arms (fifth TM) to close or open the intracellular and outer vestibules are common, as is a TM1a swing, with notable variations in the opening-closing motions of the outer vestibule. Our analyses suggest that LeuT-fold transporters layer distinct motions on a common bundle-hash rock and demonstrate that systematic analyses can provide new insights into large structural datasets.

biophysics↗

bioRxiv2023

GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway

The orphan G protein-coupled receptor (GPCR) GPR161 is enriched in primary cilia, where it plays a central role in suppressing Hedgehog signaling1. GPR161 mutations lead to developmental defects and cancers2,3,4. The fundamental basis of how GPR161 is activated, including potential endogenous activators and pathway-relevant signal transducers, remains unclear. To elucidate GPR161 function, we determined a cryogenic-electron microscopy structure of active GPR161 bound to the heterotrimeric G protein complex Gs. This structure revealed an extracellular loop 2 that occupies the canonical GPCR orthosteric ligand pocket. Furthermore, we identify a sterol that binds to a conserved extrahelical site adjacent to transmembrane helices 6 and 7 and stabilizes a GPR161 conformation required for Gs coupling. Mutations that prevent sterol binding to GPR161 suppress cAMP pathway activation. Surprisingly, these mutants retain the ability to suppress GLI2 transcription factor accumulation in cilia, a key function of ciliary GPR161 in Hedgehog pathway suppression. By contrast, a protein kinase A-binding site in the GPR161 C-terminus is critical in suppressing GLI2 ciliary accumulation. Our work highlights how unique structural features of GPR161 interface with the Hedgehog pathway and sets a foundation to understand the broader role of GPR161 function in other signaling pathways.

biochemistry↗

bioRxiv2022

High-resolution structures map the metal import pathway in an Nramp transporter

Transporters of the Nramp (Natural resistance-associated macrophage protein) family import divalent transition metal ions into cells of most organisms. By supporting metal homeostasis, Nramps prevent disorders related to metal insufficiency or overload. Previous studies revealed that Nramps take on a LeuT fold and identified the metal-binding site. We present high- resolution structures of Deinococcus radiodurans Nramp in three stable conformations of the transport cycle revealing that global conformational changes are supported by distinct coordination geometries of its physiological substrate, Mn2+, across conformations and conserved networks of polar residues lining the inner and outer gates. A Cd2+-bound structure highlights differences in coordination geometry for Mn2+ and Cd2+. Measurements of metal binding using isothermal titration calorimetry indicate that the thermodynamic landscape for binding and transporting physiological metals like Mn2+ is different and more robust to perturbation than for transporting the toxic Cd2+ metal.

biochemistry↗