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Bhatia P, Bickle M, Agrawal AA, Truss B, Nikolaidi A, Brockmann K, Reinhardt L, Vogel S, Szegoe EM, Pal A, Hermann A, Mikicic I, Yun M, Falkenburger B, Sterneckert J. Axonal Lysosomal Assays for Characterizing the Effects of LRRK2 G2019S. Biology (Basel) 2024; 13:58. [PMID: 38275734 PMCID: PMC10813644 DOI: 10.3390/biology13010058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
The degeneration of axon terminals before the soma, referred to as "dying back", is a feature of Parkinson's disease (PD). Axonal assays are needed to model early PD pathogenesis as well as identify protective therapeutics. We hypothesized that defects in axon lysosomal trafficking as well as injury repair might be important contributing factors to "dying back" pathology in PD. Since primary human PD neurons are inaccessible, we developed assays to quantify axonal trafficking and injury repair using induced pluripotent stem cell (iPSC)-derived neurons with LRRK2 G2019S, which is one of the most common known PD mutations, and isogenic controls. We observed a subtle axonal trafficking phenotype that was partially rescued by a LRRK2 inhibitor. Mutant LRRK2 neurons showed increased phosphorylated Rab10-positive lysosomes, and lysosomal membrane damage increased LRRK2-dependent Rab10 phosphorylation. Neurons with mutant LRRK2 showed a transient increase in lysosomes at axotomy injury sites. This was a pilot study that used two patient-derived lines to develop its methodology; we observed subtle phenotypes that might correlate with heterogeneity in LRRK2-PD patients. Further analysis using additional iPSC lines is needed. Therefore, our axonal lysosomal assays can potentially be used to characterize early PD pathogenesis and test possible therapeutics.
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Affiliation(s)
- Priyanka Bhatia
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany; (P.B.)
| | - Marc Bickle
- Roche Institute of Human Biology, 4070 Basel, Switzerland
| | - Amay A. Agrawal
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany; (P.B.)
| | - Buster Truss
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany; (P.B.)
| | - Aikaterina Nikolaidi
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany; (P.B.)
| | - Kathrin Brockmann
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
| | - Lydia Reinhardt
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany; (P.B.)
| | - Stefanie Vogel
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany; (P.B.)
| | - Eva M. Szegoe
- Department of Neurology, Technische Universität Dresden, 01307 Dresden, Germany
| | - Arun Pal
- Department of Neurology, Technische Universität Dresden, 01307 Dresden, Germany
| | - Andreas Hermann
- Department of Neurology, Technische Universität Dresden, 01307 Dresden, Germany
- Translational Neurodegeneration Section “Albrecht Kossel”, Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany
- Center for Transdisciplinary Neurosciences Rostock (CTNR), University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald, 18147 Rostock, Germany
| | - Ivan Mikicic
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany; (P.B.)
| | - Maximina Yun
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany; (P.B.)
- Max Planck Institute of Molecular Cellular Biology and Genetics, 01307 Dresden, Germany
- Physics of Life Excellence Cluster, 01307 Dresden, Germany
| | - Björn Falkenburger
- Department of Neurology, Technische Universität Dresden, 01307 Dresden, Germany
| | - Jared Sterneckert
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany; (P.B.)
- Medical Faculty Carl Gustav Carus of TU Dresden, 01307 Dresden, Germany
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Malekian N, Agrawal AA, Berendonk TU, Al-Fatlawi A, Schroeder M. A genome-wide scan of wastewater E. coli for genes under positive selection: focusing on mechanisms of antibiotic resistance. Sci Rep 2022; 12:8037. [PMID: 35577863 PMCID: PMC9110714 DOI: 10.1038/s41598-022-11432-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/07/2022] [Indexed: 11/30/2022] Open
Abstract
Antibiotic resistance is a global health threat and consequently, there is a need to understand the mechanisms driving its emergence. Here, we hypothesize that genes and mutations under positive selection may contribute to antibiotic resistance. We explored wastewater E. coli, whose genomes are highly diverse. We subjected 92 genomes to a statistical analysis for positively selected genes. We obtained 75 genes under positive selection and explored their potential for antibiotic resistance. We found that eight genes have functions relating to antibiotic resistance, such as biofilm formation, membrane permeability, and bacterial persistence. Finally, we correlated the presence/absence of non-synonymous mutations in positively selected sites of the genes with a function in resistance against 20 most prescribed antibiotics. We identified mutations associated with antibiotic resistance in two genes: the porin ompC and the bacterial persistence gene hipA. These mutations are located at the surface of the proteins and may hence have a direct effect on structure and function. For hipA, we hypothesize that the mutations influence its interaction with hipB and that they enhance the capacity for dormancy as a strategy to evade antibiotics. Overall, genomic data and positive selection analyses uncover novel insights into mechanisms driving antibiotic resistance.
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Elias JD, Agrawal AA. A private channel of nitrogen alleviates interspecific competition for an annual legume. Ecology 2021; 102:e03449. [PMID: 34166532 DOI: 10.1002/ecy.3449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/29/2021] [Accepted: 05/14/2021] [Indexed: 11/08/2022]
Abstract
The way resource availability predictably alters interspecific interactions and may favor one resource-acquisition strategy over another is critical for understanding context dependency. The ubiquity of nitrogen (N) limitation across terrestrial environments is a driver of plant competition and the association of some plants with N-fixing bacteria (rhizobia) may alleviate competition with nonfixing plants. Conversely, when available soil N is elevated, competitive advantages imparted by rhizobia are hypothesized to decline because nonfixing species are able to acquire those nutrients readily. We manipulated competition, soil N, and soil microbial inoculation, employing the ground bean Amphicarpaea bracteata, a native annual N-fixing legume, and jewelweed Impatiens capensis, a native co-occurring nonfixing annual. We found that legume performance was negatively impacted by interspecific competition, but less so under lower soil N in both the greenhouse and field. The legume invested a greater proportion of resources in rhizobia when competing, but only under low N. Also consistent with predictions, a competition-by-microbial-inoculation interaction demonstrated that negative effects of competition were alleviated by rhizobia. Finally, we detected an interaction between inoculation and fertilization, whereby N addition resulted in increased performance for uninoculated legumes, but a small decline in performance for inoculated plants, the latter likely representing a cost of mutualism. Thus, several lines of evidence point to the legume-rhizobia mutualism being more beneficial under competition and limited soil N. Competing I. capensis, in contrast, benefited from N addition regardless of the addition of soil microbes. In a survey of natural populations, legume and rhizobia growth were positively correlated at population edges (where interspecific competition is expected to be higher, the mutualism is stronger), whereas at population centers we found no association. Isotopic evidence confirmed a higher degree of rhizobial N-fixation at population edges compared to centers. Taken together, our results demonstrate an important role for the largely private channel of nitrogen in legume competitive performance, but with the benefits imparted by rhizobia being predictably weaker at higher soil fertility. We speculate that alleviation of competitive impacts through resource partitioning is an important and yet largely overlooked aspect of the evolutionary ecology of legume-rhizobia interactions.
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Affiliation(s)
- J D Elias
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853, USA
| | - A A Agrawal
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853, USA
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Mupo A, Seiler M, Sathiaseelan V, Pance A, Yang Y, Agrawal AA, Iorio F, Bautista R, Pacharne S, Tzelepis K, Manes N, Wright P, Papaemmanuil E, Kent DG, Campbell PC, Buonamici S, Bolli N, Vassiliou GS. Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts. Leukemia 2017; 31:720-727. [PMID: 27604819 PMCID: PMC5336192 DOI: 10.1038/leu.2016.251] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 08/19/2016] [Indexed: 02/06/2023]
Abstract
Heterozygous somatic mutations affecting the spliceosome gene SF3B1 drive age-related clonal hematopoiesis, myelodysplastic syndromes (MDS) and other neoplasms. To study their role in such disorders, we generated knock-in mice with hematopoietic-specific expression of Sf3b1-K700E, the commonest type of SF3B1 mutation in MDS. Sf3b1K700E/+ animals had impaired erythropoiesis and progressive anemia without ringed sideroblasts, as well as reduced hematopoietic stem cell numbers and host-repopulating fitness. To understand the molecular basis of these observations, we analyzed global RNA splicing in Sf3b1K700E/+ hematopoietic cells. Aberrant splicing was associated with the usage of cryptic 3' splice and branchpoint sites, as described for human SF3B1 mutants. However, we found a little overlap between aberrantly spliced mRNAs in mouse versus human, suggesting that anemia may be a consequence of globally disrupted splicing. Furthermore, the murine orthologues of genes associated with ring sideroblasts in human MDS, including Abcb7 and Tmem14c, were not aberrantly spliced in Sf3b1K700E/+ mice. Our findings demonstrate that, despite significant differences in affected transcripts, there is overlap in the phenotypes associated with SF3B1-K700E between human and mouse. Future studies should focus on understanding the basis of these similarities and differences as a means of deciphering the consequences of spliceosome gene mutations in MDS.
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Affiliation(s)
- A Mupo
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - M Seiler
- H3 Biomedicine, Inc., Cambridge, MA, USA
| | | | - A Pance
- Malaria Programme, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Y Yang
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | - F Iorio
- European Bioinformatics, Institute, Hinxton, Cambridge, UK
| | - R Bautista
- LIMS Compute and Infrastructure, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - S Pacharne
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - K Tzelepis
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - N Manes
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - P Wright
- Department of Pathology, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | - E Papaemmanuil
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - D G Kent
- Cambridge Stem Cell Institute, Cambridge, UK
| | - P C Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | - N Bolli
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Dipartimento di Oncologia ed Onco-Ematologia, Universita' degli Studi di Milano, Milano, Italy
- Dipartimento di Ematologia ed Onco-Ematologia Pediatrica, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - G S Vassiliou
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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Johnson MTJ, Agrawal AA, Maron JL, Salminen JP. Heritability, covariation and natural selection on 24 traits of common evening primrose (Oenothera biennis) from a field experiment. J Evol Biol 2009; 22:1295-307. [PMID: 19490388 DOI: 10.1111/j.1420-9101.2009.01747.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study explored genetic variation and co-variation in multiple functional plant traits. Our goal was to characterize selection, heritabilities and genetic correlations among different types of traits to gain insight into the evolutionary ecology of plant populations and their interactions with insect herbivores. In a field experiment, we detected significant heritable variation for each of 24 traits of Oenothera biennis and extensive genetic covariance among traits. Traits with diverse functions formed several distinct groups that exhibited positive genetic covariation with each other. Genetic variation in life-history traits and secondary chemistry together explained a large proportion of variation in herbivory (r(2) = 0.73). At the same time, selection acted on lifetime biomass, life-history traits and two secondary compounds of O. biennis, explaining over 95% of the variation in relative fitness among genotypes. The combination of genetic covariances and directional selection acting on multiple traits suggests that adaptive evolution of particular traits is constrained, and that correlated evolution of groups of traits will occur, which is expected to drive the evolution of increased herbivore susceptibility. As a whole, our study indicates that an examination of genetic variation and covariation among many different types of traits can provide greater insight into the evolutionary ecology of plant populations and plant-herbivore interactions.
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Affiliation(s)
- M T J Johnson
- Department of Plant Biology, North Carolina State University, Raleigh, NC 27695, USA.
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Abstract
Coexistence of host-specific herbivores on plants is believed to be governed by interspecific interactions, but few empirical studies have systematically unraveled these dynamics. We investigated the role of several factors in promoting coexistence among the aphids Aphis nerii, Aphis asclepiadis, and Myzocallis asclepiadis that all specialize on common milkweed (Asclepias syriaca). Competitive exclusion is thought to occur when interspecific competition is stronger than intraspecific competition. Consequently, we investigated whether predators, mutualists, or resource quality affected the strength of intra- vs. interspecific competition among aphids in factorial manipulations of competition with exposure to predation, ants, and variable plant genotypes in three separate experiments. In the predation x competition experiment, predators reduced aphid per capita growth by 66%, but the strength of intra- and interspecific competition did not depend on predators. In the ants x competition experiment, ants reduced per capita growth of A. nerii and M. asclepiadis (neither of which were mutualists with ants) by approximately one-half. In so doing, ants ameliorated the negative effects of these competitors on ant-tended A. asclepiadis by two-thirds, representing a novel benefit of ant-aphid mutualism. Nevertheless, ants alone did not explain the persistence of competitively inferior A. asclepiadis as, even in the presence of ants, interspecific competition remained stronger than intraspecific competition. In the plant genotype x competition experiment, both A. asclepiadis and M. asclepiadis were competitively inferior to A. nerii, with the strength of interspecific competition exceeding that of intraspecific competition by 83% and 23%, respectively. Yet these effects differed among milkweed genotypes, and there were one or more plant genotypes for each aphid species where coexistence was predicted. A synthesis of our results shows that predators play little or no role in preferentially suppressing competitively dominant A. nerii. Nonetheless, A. asclepiadis benefits from ants, and A. asclepiadis and M. asclepiadis may escape competitive exclusion by A. nerii on select milkweed genotypes. Taken as a whole, the coexistence of three host-specific aphid species sharing the same resource was promoted by the dual action of ants as antagonists and mutualists and by genetic diversity in the plant population itself.
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Affiliation(s)
- R A Smith
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
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Abstract
The evolutionary mechanisms underlying the maintenance of invariant traits are poorly understood, partly because the lack of variance makes these mechanisms difficult to study. Although the number of cotyledons that plant species produce is highly canalized, populations of plants frequently contain individuals with abnormal cotyledon numbers. In a garden study with 1857 wild radish plants from 75 paternal half-sibling families, 89 (almost 5%) had cotyledon numbers less or greater than two. We found evidence for direct selection on cotyledon number, but no evidence for additive genetic variation for cotyledon number. In spite of the very large sample size, our power to detect variation and selection was hampered by the small number of individuals (10) producing more than two cotyledons. Thus, our results provide support for both a lack of genetic variation and selection as reasons for the current lack of variation in wild radish cotyledon number.
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Affiliation(s)
- J K Conner
- W. K. Kellogg Biological Station, and Department of Plant Biology, Michigan State University, Hickory Corners, MI 49060, USA.
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Abstract
When individuals of two species interact, they can adjust their phenotypes in response to their respective partner, be they antagonists or mutualists. The reciprocal phenotypic change between individuals of interacting species can reflect an evolutionary response to spatial and temporal variation in species interactions and ecologically result in the structuring of food chains. The evolution of adaptive phenotypic plasticity has led to the success of organisms in novel habitats, and potentially contributes to genetic differentiation and speciation. Taken together, phenotypic responses in species interactions represent modifications that can lead to reciprocal change in ecological time, altered community patterns, and expanded evolutionary potential of species.
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Affiliation(s)
- A A Agrawal
- Department of Botany, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada.
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Affiliation(s)
- A A Agrawal
- Department of Entomology and Center for Population Biology, University of California, Davis, California 95616-8584, USA.
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Abstract
Indirect defences involve the protection of a host organism by a mutualistic partner. Threat of predation to the host organism may induce the production of rewards and/or signals that attract the mutualistic partner. In laboratory and field experiments we show that threatened lycaenid butterfly larvae (Plebejus acmon) produce more nectar rewards from their gland and were tended by protective ants twice as much as controls. Ant attendance did not affect the leaf consumption or feeding behaviour of larvae in the absence of predators. Inducible nectar production and indirect defence in this system may be a mechanism by which larvae provide rewards for services when they are needed the most. Such a system may stabilize the mutualistic association between lycaenid larvae and ants by preventing exploitation by either partner.
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Affiliation(s)
- A A Agrawal
- Department of Botany, University of Toronto, ON, Canada.
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Abstract
Recent research bridging mechanistic and ecological approaches demonstrates that plant attributes can affect herbivores, natural enemies of herbivores, and their interaction. Such effects may be genetically variable among plants and/or induced in individual plants by herbivore attack, and are mediated by primary plant attributes (i.e. nutritional quality and physical structure) and defense-related products (i.e. secondary chemicals and plant volatiles), and may be modified by human activity (e.g. by the introduction of Bacillus thuringiensis). The study of tri-trophic interactions is important in order to understand natural species interactions and to manipulate these interactions in pest control.
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Affiliation(s)
- A A Agrawal
- Department of Botany, University of Toronto, Toronto, M5S 3B2, Canada.
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Abstract
Plants that overcompensate for herbivory are relatively healthier when damaged. In this mutualistic association, the herbivore benefits from the plant, and the plant benefits from the herbivore's actions. As long as the benefit to the plant outweighs the costs imposed by browsing herbivores, this interaction should remain stable. Many apparently parasitic associations can be mutually beneficial under some environmental conditions.
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Affiliation(s)
- A A Agrawal
- Department of Botany, University of Toronto, 25 Willcocks Street, ON, Canada M5S 3B2.
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Abstract
Plant resistance to herbivores was induced in a field experiment to evaluate the consequences of induced responses for subsequent herbivory and plant fitness. Induction early in the season resulted in halving of herbivory by chewing herbivores and a reduction in the abundance of phloem-feeding aphids when compared with controls. A correlate of lifetime plant fitness, seed mass, was enhanced by over 60 percent for individuals that were induced.
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Affiliation(s)
- AA Agrawal
- Department of Entomology, and Center for Population Biology, One Shields Avenue, University of California at Davis, Davis, CA 95616-8584, USA. E-mail:
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