Biology subjects

Martin, E. C.

Publications and source records attributed to Martin, E. C..

7 recordsLinked to original sources

bioRxiv2025

The impact of carotenoid energy levels on the exciton dynamics and singlet-triplet annihilation in the bacterial Light-Harvesting 2 complex

The light-harvesting 2 (LH2) complex of purple phototrophic bacteria plays a critical role in absorbing solar energy and distributing excitation energy. Exciton dynamics within LH2 complexes are controlled by the structural arrangement and energy levels of the bacteriochlorophyll (BChl) and carotenoid (Car) pigments. However, there is still debate over the competing light-harvesting versus energy-dissipation pathways. In this work, we compared five variants of the LH2 complex from genetically modified strains of Rhodobacter sphaeroides, all containing the same BChls but different Cars with increasing conjugation: zeta-carotene (N=7; LH2Zeta), neurosporene (N=9; LH2Neu), spheroidene (N=10; LH2Spher), lycopene (N=11; LH2Lyco), and spirilloxanthin (N=13; LH2Spir). Absorption measurements confirmed that Car excited state energy decreased with increasing conjugation. Similarly, fluorescence spectra showed that the B850 BChl emission peak had an increasing red shift from LH2Zeta[->](LH2Neu/LH2Spher)[->]LH2Lyco[->]LH2Spir. In contrast, time-resolved fluorescence and ultrafast transient absorption (fs-TA) revealed similar excited state lifetimes ([~]1 ns) for all complexes except LH2Spir ([~]0.7 ns). From fs-TA analysis, an additional [~]7 ps non-radiative dissipation step from B850 BChl was observed for LH2Zeta. Further, singlet-singlet and singlet-triplet annihilation studies showed a [~]50% average fluorescence lifetime reduction in LH2Zeta at high laser power and high repetition rate, compared to [~]10-15% reductions in LH2Neu/LH2Spher/LH2Lyco and minimal lifetime change in LH2Spir. In LH2Zeta, the fastest decay component (<50 ps) became prominent at high repetition rates, consistent with strong singlet-triplet annihilation. Nanosecond TA measurements revealed long-lived (>40 s) BChl triplet states in LH2Zeta and signs of damage caused by singlet oxygen, whereas other LH2s showed faster triplet quenching ([~]18 ns) by Cars. These findings highlight a key design principle of LH2 complexes: the Car triplet energy must be significantly lower than the BChl triplet energy to efficiently quench BChl triplets that otherwise act as potent "trap states" causing exciton annihilation in laser-based experiments or photo-damage in native membranes.

biophysics↗

bioRxiv2024

Sulfoquinovosyl diacylglycerol is required for dimerization of the Rhodobacter sphaeroides RC-LH1 core complex

The reaction centre-light harvesting 1 (RC-LH1) core complex is indispensable for anoxygenic photosynthesis. In the purple bacterium Rhodobacter (Rba.) sphaeroides RC-LH1 is produced both as a monomer in which 14 LH1 subunits form a crescent-shaped antenna around one RC, and as a dimer, where 28 LH1 subunits form an S-shaped antenna surrounding two RCs. The PufX polypeptide augments the five RC and LH subunits, and in addition to providing an interface for dimerization, PufX also prevents LH1 ring closure, introducing a channel for quinone exchange that is essential for photoheterotrophic growth. Structures of Rba. sphaeroides RC-LH1 complexes revealed several new components; protein-Y, which helps to form a quinone channel; protein-Z, of unknown function but which is unique to dimers; and a tightly bound sulfoquinovosyl diacylglycerol (SQDG) lipid that interacts with two PufX arginines. This lipid lies at the dimer interface alongside weak density for a second molecule, previously proposed to be an ornithine lipid. In this work we have generated strains of Rba. sphaeroides lacking protein-Y, protein-Z, SQDG or ornithine lipids to assess the roles of these previously unknown components in the assembly and activity of RC-LH1. We show that whilst the removal of either protein-Y, protein-Z or ornithine lipids has only subtle effects, SQDG is essential for the formation of RC-LH1 dimers but its absence has no functional effect on the monomeric complex.

biochemistry↗

bioRxiv2023

How do life history traits influence the environment's effect on population synchrony? Insights from European birds and insects

Populations closer together in space are more likely to experience shared environmental fluctuations. This correlation in experienced environmental conditions is the main driver of spatial population synchrony, defined as the tendency for geographically separate populations of the same species to exhibit parallel fluctuations in abundance over time. Morans theorem states that spatially distinct populations are expected to show the same synchrony in their population dynamics as the synchrony in their environment. However, this is rarely the case in the wild, and the population synchrony of different species inhabiting the same area is rarely similar. These species-specific differences in how the environment synchronizes populations can be due to life history traits that make some species more susceptible to environmental stochasticity, such as reduced mobility or faster pace of life. In this study, we compiled long-term annual abundance datasets on European birds and insects (Lepidoptera sp. and Bombus sp.) to identify how environmental synchrony (i.e., positively spatially correlated fluctuations in the environment, also called the Moran effect) affects species population synchrony. As expected, the environment synchronized populations of both birds and insects. Populations experiencing correlated fluctuations in precipitation or temperature had higher synchrony in annual population growth rates. Birds were more strongly synchronized by temperature, while precipitation was a stronger driver of synchrony in insects. In birds, species with short generation times had a stronger synchronizing effect of the environment compared to species with long generation times. Moreover, in birds the effects of synchrony in the environment also depended on movement propensity, with a positive impact for resident and short-distance migration species. In insects, annual population synchrony was affected by species movement propensity and dietary niche breadth, but these traits did not modify the effects of environmental synchrony. Our study provides empirical support for the prediction that spatial correlation in population dynamics is more influenced by environmental stochasticity for life histories with lower mobility and faster pace of life, but only in birds. By quantifying spatial population synchrony across different levels of environmental synchrony and life history traits, our study improves the understanding of the Moran effect as well as factors that drive population persistence in the face of environmental change.

ecology↗

bioRxiv2023

Insights into RAG evolution from the identification of "missing link" family A RAGL transposons

A series of "molecular domestication" events are thought to have converted an invertebrate RAG-like (RAGL) transposase into the RAG1-RAG2 (RAG) recombinase, a critical enzyme for adaptive immunity in jawed vertebrates. The timing and order of these events is not well understood, in part because of a dearth of information regarding the invertebrate RAGL-A transposon family. In contrast to the abundant and divergent RAGL-B transposon family, RAGL-A most closely resembles RAG and is represented by a single orphan RAG1-like (RAG1L) gene in the genome of the hemichordate Ptychodera flava (PflRAG1L-A). Here, we provide evidence for the existence of complete RAGL-A transposons in the genomes of P. flava and several echinoderms. The predicted RAG1L-A and RAG2L-A proteins encoded by these transposons intermingle sequence features of jawed vertebrate RAG and RAGL-B transposases, leading to a prediction of DNA binding, catalytic, and transposition activities that are a hybrid of RAG and RAGL-B. Similarly, the terminal inverted repeats (TIRs) of the RAGL-A transposons combine features of both RAGL-B transposon TIRs and RAG recombination signal sequences. Unlike all previously described RAG2L proteins, PflRAG2L-A and echinoderm RAG2L-A contain an acidic hinge region, which we demonstrate is capable of efficiently inhibiting RAG-mediated transposition. Our findings provide evidence for a critical intermediate in RAG evolution and argue that certain adaptations thought to be specific to jawed vertebrates (e.g., the RAG2 acidic hinge) actually arose in invertebrates, thereby focusing attention on other adaptations as the pivotal steps in the completion of RAG domestication in jawed vertebrates.

evolutionary biology↗

bioRxiv2023

Generation time and seasonal migration explain variation in spatial population synchrony across European bird species

O_LISpatial population synchrony is common among populations of the same species and is an important predictor of extinction risk. Despite the potential consequences for metapopulation persistence, we still largely lack understanding of what makes one species more likely to be synchronized than another given the same environmental conditions. C_LIO_LIGenerally, environmental conditions on a shared environment or a species sensitivity to the environment can explain the extent of synchrony. Populations that are closer together experience more similar fluctuations in their environments than those populations that are further apart and are therefore more synchronized. The relative importance of environmental and demographic stochasticity for population dynamics is strongly linked to species life history traits, such as pace of life, why may impact population synchrony. For populations that migrate, there may be multiple environmental conditions at different locations driving synchrony. However, the importance of life history and migration strategies in determining patterns of spatial population synchrony have rarely been explored empirically. We therefore hypothesize that generation time, a proxy for pace of life, and migration play an important role in determining spatial population synchrony. C_LIO_LIWe used population abundance data on breeding birds from four countries to investigate patterns of spatial population synchrony in growth rate and abundance. We investigated differences in synchrony across a gradient of generation times in resident, short-distance migrant, and long-distance migrant bird species. C_LIO_LISpecies with shorter generation times were more synchronized than species with longer generation times. Short-distance migrants were more synchronized than long-distance migrants and resident birds. C_LIO_LIOur results provide novel empirical links between spatial population synchrony and species traits known to be of key importance for population dynamics, generation time and migration characteristics. We show how these different mechanisms can be combined to understand species-specific causes of spatial population synchrony. Understanding these specific drivers of spatial population synchrony is important in the face of increasingly severe threats to biodiversity and could be key for successful future conservation outcomes. C_LI

ecology↗

bioRxiv2022

intSDM: A reproducible framework for integrated species distribution models

1O_LIThere has been an exponential increase in quantity and type of biodiversity data in recent years, including presence-absence, counts, and presence-only citizen science data. Species Distribution Models (SDMs) have typically been used in ecology to estimate current and future ranges of species, and are a common tool used when making conservation prioritisation decisions. However integration of these data in a model-based framework is needed to address many of the current large-scale threats to biodiversity. C_LIO_LICurrent SDM practice typically underutilizes the large amount of publicly available biodi-versity data and does not follow a set of standard best practices. Integrating different data types with open-source tools and reproducible workflows saves time, increases collaboration opportunities, and increases the power of data inference in SDMs. C_LIO_LIWe aim to address this issue by (1) proposing methods and (2) generating a reproducible workflow to integrate different available data types to increase the power of SDMs. We provide the R package intSDM, as well as guidance on how to accommodate users diverse needs and ecological questions with different data types available on the Global Biodiversity Information Facility (GBIF), the largest biodiversity data aggregator in the world. C_LIO_LIFinally, we provide a case study of the application of our proposed reproducible workflow by creating SDMs for vascular plants in Norway, integrating presence-only and presence-absence species occurrence data and climate data. C_LI

ecology↗

bioRxiv2019

Structure-function analysis of ZAR1 immune receptor reveals key molecular interactions for activity

NLR (Nucleotide-binding [NB] Leucine-rich repeat [LRR] Receptor) proteins are critical for inducing immune responses in response to pathogen proteins, and must be tightly regulated to prevent spurious activation in the absence of a pathogen. The ZAR1 NLR recognizes diverse effector proteins from Pseudomonas syringae, including HopZ1a, and Xanthomonas species. Receptor-like cytoplasmic kinases (RLCKs) such as ZED1, interact with ZAR1 and provide specificity for different effector proteins, such as HopZ1a. We previously developed a transient expression system in Nicotiana benthamiana, that allowed us to demonstrate ZAR1 function is conserved from the Brassicaceae to the Solanaceae. Here, we combined structural modeling of ZAR1, with molecular and functional assays in our transient system, to show that multiple intramolecular and intermolecular interactions regulate ZAR1 activity. We identified new determinants required for the formation of the ZARCC dimer and its activity. Lastly, we characterized new intramolecular interactions between ZAR1 subdomains that participate in keeping ZAR1 immune complexes inactive. This work identifies molecular constraints on immune receptor function and activation.\n\nOne sentence-summaryStructure-informed analyses reveal multiple finely-tuned intramolecular interactions that regulate the activity of the immune receptor ZAR1.\n\nFundingResearch on plant immunity in the Lewis laboratory was supported by the USDA ARS 2030-21000-046-00D and 2030-21000-050-00D (JDL), and the NSF Directorate for Biological Sciences IOS-1557661 (JDL). ECM and AJP acknowledge financial support from UEFISCDI grant PN-III-ID-PCE-2016-0650 and the Romanian Academy programs 1 & 2 of IBAR.

plant biology↗