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Stuart SH, Ahmed ACC, Kilikevicius L, Robinson GE. Effects of microRNA-305 knockdown on brain gene expression associated with division of labor in honey bee colonies (Apis mellifera). J Exp Biol 2024; 227:jeb246785. [PMID: 38517067 PMCID: PMC11112348 DOI: 10.1242/jeb.246785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 03/13/2024] [Indexed: 03/23/2024]
Abstract
Division of labor in honey bee colonies is based on the behavioral maturation of adult workers that involves a transition from working in the hive to foraging. This behavioral maturation is associated with distinct task-related transcriptomic profiles in the brain and abdominal fat body that are related to multiple regulatory factors including juvenile hormone (JH) and queen mandibular pheromone (QMP). A prominent physiological feature associated with behavioral maturation is a loss of abdominal lipid mass as bees transition to foraging. We used transcriptomic and physiological analyses to study whether microRNAs (miRNAs) are involved in the regulation of division of labor. We first identified two miRNAs that showed patterns of expression associated with behavioral maturation, ame-miR-305-5p and ame-miR-375-3p. We then downregulated the expression of these two miRNAs with sequence-specific antagomirs. Neither ame-miR-305-5p nor ame-miR-375-3p knockdown in the abdomen affected abdominal lipid mass on their own. Similarly, knockdown of ame-miR-305-5p in combination with JH or QMP also did not affect lipid mass. By contrast, ame-miR-305-5p knockdown in the abdomen caused substantial changes in gene expression in the brain. Brain gene expression changes included genes encoding transcription factors previously implicated in behavioral maturation. The results of these functional genomic experiments extend previous correlative associations of microRNAs with honey bee division of labor and point to specific roles for ame-miR-305-5p.
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Affiliation(s)
- Sarai H. Stuart
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Amy C. Cash Ahmed
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Laura Kilikevicius
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Gene E. Robinson
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Entomology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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2
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Pyenson BC, Rehan SM. Gene regulation supporting sociality shared across lineages and variation in complexity. Genome 2024; 67:99-108. [PMID: 38096504 DOI: 10.1139/gen-2023-0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Across evolutionary lineages, insects vary in social complexity, from those that exhibit extended parental care to those with elaborate divisions of labor. Here, we synthesize the sociogenomic resources from hundreds of species to describe common gene regulatory mechanisms in insects that regulate social organization across phylogeny and levels of social complexity. Different social phenotypes expressed by insects can be linked to the organization of co-expressing gene networks and features of the epigenetic landscape. Insect sociality also stems from processes like the emergence of parental care and the decoupling of ancestral genetic programs. One underexplored avenue is how variation in a group's social environment affects the gene expression of individuals. Additionally, an experimental reduction of gene expression would demonstrate how the activity of specific genes contributes to insect social phenotypes. While tissue specificity provides greater localization of the gene expression underlying social complexity, emerging transcriptomic analysis of insect brains at the cellular level provides even greater resolution to understand the molecular basis of social insect evolution.
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Affiliation(s)
| | - Sandra M Rehan
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada
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3
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Nassar AH, Abou Alaiwi S, Baca SC, Adib E, Corona RI, Seo JH, Fonseca MAS, Spisak S, El Zarif T, Tisza V, Braun DA, Du H, He M, Flaifel A, Alchoueiry M, Denize T, Matar SG, Acosta A, Shukla S, Hou Y, Steinharter J, Bouchard G, Berchuck JE, O'Connor E, Bell C, Nuzzo PV, Mary Lee GS, Signoretti S, Hirsch MS, Pomerantz M, Henske E, Gusev A, Lawrenson K, Choueiri TK, Kwiatkowski DJ, Freedman ML. Epigenomic charting and functional annotation of risk loci in renal cell carcinoma. Nat Commun 2023; 14:346. [PMID: 36681680 PMCID: PMC9867739 DOI: 10.1038/s41467-023-35833-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/04/2023] [Indexed: 01/22/2023] Open
Abstract
While the mutational and transcriptional landscapes of renal cell carcinoma (RCC) are well-known, the epigenome is poorly understood. We characterize the epigenome of clear cell (ccRCC), papillary (pRCC), and chromophobe RCC (chRCC) by using ChIP-seq, ATAC-Seq, RNA-seq, and SNP arrays. We integrate 153 individual data sets from 42 patients and nominate 50 histology-specific master transcription factors (MTF) to define RCC histologic subtypes, including EPAS1 and ETS-1 in ccRCC, HNF1B in pRCC, and FOXI1 in chRCC. We confirm histology-specific MTFs via immunohistochemistry including a ccRCC-specific TF, BHLHE41. FOXI1 overexpression with knock-down of EPAS1 in the 786-O ccRCC cell line induces transcriptional upregulation of chRCC-specific genes, TFCP2L1, ATP6V0D2, KIT, and INSRR, implicating FOXI1 as a MTF for chRCC. Integrating RCC GWAS risk SNPs with H3K27ac ChIP-seq and ATAC-seq data reveals that risk-variants are significantly enriched in allelically-imbalanced peaks. This epigenomic atlas in primary human samples provides a resource for future investigation.
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Affiliation(s)
- Amin H Nassar
- Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT, 06510, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sarah Abou Alaiwi
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sylvan C Baca
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Elio Adib
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Rosario I Corona
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Marcos A S Fonseca
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - Talal El Zarif
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Viktoria Tisza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - David A Braun
- Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT, 06510, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - Heng Du
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Monica He
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Abdallah Flaifel
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Michel Alchoueiry
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Thomas Denize
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sayed G Matar
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Andres Acosta
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sachet Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yue Hou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John Steinharter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Gabrielle Bouchard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jacob E Berchuck
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Pier Vitale Nuzzo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Mark Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Elizabeth Henske
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- McGraw/Patterson Center for Population Sciences, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Kate Lawrenson
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Toni K Choueiri
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - David J Kwiatkowski
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA.
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Abstract
The question of the heritability of behavior has been of long fascination to scientists and the broader public. It is now widely accepted that most behavioral variation has a genetic component, although the degree of genetic influence differs widely across behaviors. Starting with Mendel's remarkable discovery of "inheritance factors," it has become increasingly clear that specific genetic variants that influence behavior can be identified. This goal is not without its challenges: Unlike pea morphology, most natural behavioral variation has a complex genetic architecture. However, we can now apply powerful genome-wide approaches to connect variation in DNA to variation in behavior as well as analyses of behaviorally related variation in brain gene expression, which together have provided insights into both the genetic mechanisms underlying behavior and the dynamic relationship between genes and behavior, respectively, in a wide range of species and for a diversity of behaviors. Here, we focus on two systems to illustrate both of these approaches: the genetic basis of burrowing in deer mice and transcriptomic analyses of division of labor in honey bees. Finally, we discuss the troubled relationship between the field of behavioral genetics and eugenics, which reminds us that we must be cautious about how we discuss and contextualize the connections between genes and behavior, especially in humans.
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Affiliation(s)
- Hopi E. Hoekstra
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
- HHMI, Harvard University, Cambridge, MA 02138
| | - Gene E. Robinson
- Department of Entomology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Neuroscience Program, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
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5
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Fang F, Zhou H, Feng X, Chen X, Wang Z, Zhao S, Li X. Gene expression and chromatin conformation differs between worker bees performing different tasks. Genomics 2022; 114:110362. [PMID: 35398245 DOI: 10.1016/j.ygeno.2022.110362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 02/16/2022] [Accepted: 04/02/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND Revealing the effect of transcriptomic regulation on behavioral differences is a fundamental goal in biology, but the relationship between gene regulatory networks and individual behavior differences remains largely unknown. Honey bees are considered as good models for studying the mechanisms underlying gene expression changes and behavioral differences since they exhibit strong and obvious differences in tasks between individuals. The cis-regulatory regions usually contain the binding sites of diverse transcription factor (TFs) influencing bee behavior. Thus, the identification of cis-regulatory elements in the brains across different behavioral states is important for understanding how genomic and transcriptomic variations affect different tasks in honeybees. METHODS In this study, we employed transcriptome and genome-wide chromatin accessibility assays to analyze brain tissues of honey bees in different behavioral states for examining the relationship between individual behavior differences and brain gene expression changes. We also used the obtained open chromatin regions to identify cis-motifs associating differentially expressed TFs and genes in order to reveal the transcriptional regulatory mechanism related to the different tasks. RESULTS We identified genetic regulatory modules regulating different tasks that contained key TFs (CTCF, Trl and schlank) associated with open chromatin regions enriched for DNA sequence motifs belonging to the family of the corresponding TFs. The most prominent transcriptomic changes, which correlated with chromatin accessibility modifications within their proximal promoter regions, occurred in nervous system development, and were associated with behavior switch. CONCLUSIONS Our results revealed the regulatory landscape among three behavioral stages in honeybees and identified interactive molecular networks regulating different tasks. These results provide a comprehensive insight into behavioral differences of honeybees, which offers reference for future study.
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Affiliation(s)
- Fang Fang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, PR China; National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong Agricultural University, Wuhan, PR China
| | - Huanhuan Zhou
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, PR China
| | - Xiaojuan Feng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, PR China; National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong Agricultural University, Wuhan, PR China
| | - Xiasang Chen
- Department of Honeybee Protection and Biosafety, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhen Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, PR China; National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong Agricultural University, Wuhan, PR China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, PR China; Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, PR China
| | - Xiang Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, PR China; National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong Agricultural University, Wuhan, PR China.
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6
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Shell WA, Rehan SM. Social divergence: molecular pathways underlying castes and longevity in a facultatively eusocial small carpenter bee. Proc Biol Sci 2022; 289:20212663. [PMID: 35317677 PMCID: PMC8941392 DOI: 10.1098/rspb.2021.2663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Unravelling the evolutionary origins of eusocial life is a longstanding endeavour in the field of evolutionary-developmental biology. Descended from solitary ancestors, eusocial insects such as honeybees have evolved ontogenetic division of labour in which short-lived workers perform age-associated tasks, while a long-lived queen produces brood. It is hypothesized that (i) eusocial caste systems evolved through the co-option of deeply conserved genes and (ii) longevity may be tied to oxidative damage mitigation capacity. To date, however, these hypotheses have been examined primarily among only obligately eusocial corbiculate bees. We present brain transcriptomic data from a Japanese small carpenter bee, Ceratina japonica (Apidae: Xylocopinae), which demonstrates both solitary and eusocial nesting in sympatry and lives 2 or more years in the wild. Our dataset captures gene expression patterns underlying first- and second-year solitary females, queens and workers, providing an unprecedented opportunity to explore the molecular mechanisms underlying caste-antecedent phenotypes in a long-lived and facultatively eusocial bee. We find that C. japonica's queens and workers are underpinned by divergent gene regulatory pathways, involving many differentially expressed genes well-conserved among other primitively eusocial bee lineages. We also find support for oxidative damage reduction as a proximate mechanism of longevity in C. japonica.
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Affiliation(s)
- Wyatt A. Shell
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
| | - Sandra M. Rehan
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
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7
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Page RE. Societies to genes: can we get there from here? Genetics 2021; 219:iyab104. [PMID: 34849914 PMCID: PMC8633090 DOI: 10.1093/genetics/iyab104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/01/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the organization and evolution of social complexity is a major task because it requires building an understanding of mechanisms operating at different levels of biological organization from genes to social interactions. I discuss here, a unique forward genetic approach spanning more than 30 years beginning with human-assisted colony-level selection for a single social trait, the amount of pollen honey bees (Apis mellifera L.) store. The goal was to understand a complex social trait from the social phenotype to genes responsible for observed trait variation. The approach combined the results of colony-level selection with detailed studies of individual behavior and physiology resulting in a mapped, integrated phenotypic architecture composed of correlative relationships between traits spanning anatomy, physiology, sensory response systems, and individual behavior that affect individual foraging decisions. Colony-level selection reverse engineered the architecture of an integrated phenotype of individuals resulting in changes in the social trait. Quantitative trait locus (QTL) studies combined with an exceptionally high recombination rate (60 kb/cM), and a phenotypic map, provided a genotype-phenotype map of high complexity demonstrating broad QTL pleiotropy, epistasis, and epistatic pleiotropy suggesting that gene pleiotropy or tight linkage of genes within QTL integrated the phenotype. Gene expression and knockdown of identified positional candidates revealed genes affecting foraging behavior and confirmed one pleiotropic gene, a tyramine receptor, as a target for colony-level selection that was under selection in two different tissues in two different life stages. The approach presented here has resulted in a comprehensive understanding of the structure and evolution of honey bee social organization.
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Affiliation(s)
- Robert E Page
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
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8
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Sociality sculpts similar patterns of molecular evolution in two independently evolved lineages of eusocial bees. Commun Biol 2021; 4:253. [PMID: 33637860 PMCID: PMC7977082 DOI: 10.1038/s42003-021-01770-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/28/2021] [Indexed: 12/19/2022] Open
Abstract
While it is well known that the genome can affect social behavior, recent models posit that social lifestyles can, in turn, influence genome evolution. Here, we perform the most phylogenetically comprehensive comparative analysis of 16 bee genomes to date: incorporating two published and four new carpenter bee genomes (Apidae: Xylocopinae) for a first-ever genomic comparison with a monophyletic clade containing solitary through advanced eusocial taxa. We find that eusocial lineages have undergone more gene family expansions, feature more signatures of positive selection, and have higher counts of taxonomically restricted genes than solitary and weakly social lineages. Transcriptomic data reveal that caste-affiliated genes are deeply-conserved; gene regulatory and functional elements are more closely tied to social phenotype than phylogenetic lineage; and regulatory complexity increases steadily with social complexity. Overall, our study provides robust empirical evidence that social evolution can act as a major and surprisingly consistent driver of macroevolutionary genomic change.
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9
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Rey S, Jin X, Damsgård B, Bégout ML, Mackenzie S. Analysis across diverse fish species highlights no conserved transcriptome signature for proactive behaviour. BMC Genomics 2021; 22:33. [PMID: 33413108 PMCID: PMC7792025 DOI: 10.1186/s12864-020-07317-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023] Open
Abstract
Background Consistent individual differences in behaviour, known as animal personalities, have been demonstrated within and across species. In fish, studies applying an animal personality approach have been used to resolve variation in physiological and molecular data suggesting a linkage, genotype-phenotype, between behaviour and transcriptome regulation. In this study, using three fish species (zebrafish; Danio rerio, Atlantic salmon; Salmo salar and European sea bass; Dicentrarchus labrax), we firstly address whether personality-specific mRNA transcript abundances are transferrable across distantly-related fish species and secondly whether a proactive transcriptome signature is conserved across all three species. Results Previous zebrafish transcriptome data was used as a foundation to produce a curated list of mRNA transcripts related to animal personality across all three species. mRNA transcript copy numbers for selected gene targets show that differential mRNA transcript abundance in the brain appears to be partially conserved across species relative to personality type. Secondly, we performed RNA-Seq using whole brains from S. salar and D. labrax scoring positively for both behavioural and molecular assays for proactive behaviour. We further enriched this dataset by incorporating a zebrafish brain transcriptome dataset specific to the proactive phenotype. Our results indicate that cross-species molecular signatures related to proactive behaviour are functionally conserved where shared functional pathways suggest that evolutionary convergence may be more important than individual mRNAs. Conclusions Our data supports the proposition that highly polygenic clusters of genes, with small additive effects, likely support the underpinning molecular variation related to the animal personalities in the fish used in this study. The polygenic nature of the proactive brain transcriptome across all three species questions the existence of specific molecular signatures for proactive behaviour, at least at the granularity of specific regulatory gene modules, level of genes, gene networks and molecular functions. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07317-z.
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Affiliation(s)
- Sonia Rey
- Institute of Aquaculture, University of Stirling, Stirlingshire, FK9 4LA, UK
| | - Xingkun Jin
- Institute of Aquaculture, University of Stirling, Stirlingshire, FK9 4LA, UK.,Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, NO-0316, Oslo, Norway.,Institute of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Børge Damsgård
- Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | | | - Simon Mackenzie
- Institute of Aquaculture, University of Stirling, Stirlingshire, FK9 4LA, UK.
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10
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Guzman-Novoa E, Morfin N, De la Mora A, Macías-Macías JO, Tapia-González JM, Contreras-Escareño F, Medina-Flores CA, Correa-Benítez A, Quezada-Euán JJG. The Process and Outcome of the Africanization of Honey Bees in Mexico: Lessons and Future Directions. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.608091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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11
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Shih SR, Huntsman EM, Flores ME, Snow JW. Reproductive potential does not cause loss of heat shock response performance in honey bees. Sci Rep 2020; 10:19610. [PMID: 33184302 PMCID: PMC7661715 DOI: 10.1038/s41598-020-74456-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 09/28/2020] [Indexed: 12/21/2022] Open
Abstract
In other species characterized to date, aging, as a function of reproductive potential, results in the breakdown of proteaostasis and a decreased capacity to mount responses by the heat shock response (HSR) and other proteostatic network pathways. Our understanding of the maintenance of stress pathways, such as the HSR, in honey bees, and in the reproductive queen in particular, is incomplete. Based on the findings in other species showing an inverse relationship between reproductive potential and HSR function, one might predict that that HSR function would be lost in the reproductive queens. However, as queens possess an atypical uncoupling of the reproduction-maintenance trade-off typically found in solitary organisms, HSR maintenance might also be expected. Here we demonstrate that reproductive potential does not cause loss of HSR performance in honey bees as queens induce target gene expression to levels comparable to those induced in attendant worker bees. Maintenance of HSR function with advent of reproductive potential is unique among invertebrates studied to date and provides a potential model for examining the molecular mechanisms regulating the uncoupling of the reproduction-maintenance trade-off in queen bees, with important consequences for understanding how stresses impact different types of individuals in honey bee colonies.
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Affiliation(s)
- S R Shih
- Biology Department, Barnard College, New York, NY, 10027, USA
| | - E M Huntsman
- Biology Department, Barnard College, New York, NY, 10027, USA
| | - M E Flores
- Biology Department, Barnard College, New York, NY, 10027, USA
| | - J W Snow
- Biology Department, Barnard College, New York, NY, 10027, USA.
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12
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Novikova DD, Cherenkov PA, Sizentsova YG, Mironova VV. metaRE R Package for Meta-Analysis of Transcriptome Data to Identify the cis-Regulatory Code behind the Transcriptional Reprogramming. Genes (Basel) 2020; 11:genes11060634. [PMID: 32526881 PMCID: PMC7348973 DOI: 10.3390/genes11060634] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/01/2020] [Accepted: 06/05/2020] [Indexed: 12/17/2022] Open
Abstract
At the molecular level, response to an external factor or an internal condition causes reprogramming of temporal and spatial transcription. When an organism undergoes physiological and/or morphological changes, several signaling pathways are activated simultaneously. Examples of such complex reactions are the response to temperature changes, dehydration, various biologically active substances, and others. A significant part of the regulatory ensemble in such complex reactions remains unidentified. We developed metaRE, an R package for the systematic search for cis-regulatory elements enriched in the promoters of the genes significantly changed their transcription in a complex reaction. metaRE mines multiple expression profiling datasets generated to test the same organism’s response and identifies simple and composite cis-regulatory elements systematically associated with differential expression of genes. Here, we showed metaRE performance for the identification of low-temperature-responsive cis-regulatory code in Arabidopsis thaliana and Danio rerio. MetaRE identified potential binding sites for known as well as unknown cold response regulators. A notable part of cis-elements was found in both searches discovering great conservation in low-temperature responses between plants and animals.
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Affiliation(s)
- Daria D. Novikova
- Institute of Cytology and Genetics, Lavrentyeva avenue 10, 630090 Novosibirsk, Russia; (D.D.N.); (Y.G.S.)
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Pavel A. Cherenkov
- Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia;
| | - Yana G. Sizentsova
- Institute of Cytology and Genetics, Lavrentyeva avenue 10, 630090 Novosibirsk, Russia; (D.D.N.); (Y.G.S.)
| | - Victoria V. Mironova
- Institute of Cytology and Genetics, Lavrentyeva avenue 10, 630090 Novosibirsk, Russia; (D.D.N.); (Y.G.S.)
- Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia;
- Correspondence:
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13
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Adames TR, Rondeau NC, Kabir MT, Johnston BA, Truong H, Snow JW. The IRE1 pathway regulates honey bee Unfolded Protein Response gene expression. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 121:103368. [PMID: 32229172 DOI: 10.1016/j.ibmb.2020.103368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 03/05/2020] [Accepted: 03/24/2020] [Indexed: 06/10/2023]
Abstract
Our molecular understanding of honey bee cellular stress responses is incomplete. Previously, we sought to identify and began functional characterization of the components of the Unfolded Protein Response (UPR) in honey bees. We observed that UPR stimulation resulted in induction of target genes upon IRE1 pathway activation, as assessed by splicing of Xbp1 mRNA. However, we were not able to determine the relative role of the various UPR pathways in gene activation. Our understanding of honey bee signal transduction and transcriptional regulation has been hampered by a lack of tools. After using RNA-seq to expand the known UPR targets in the honey bee, we used the Drosophila melanogaster S2 cell line and honey bee trans and cis elements to investigate the role of the IRE1 pathway in the transcriptional activation of one of these targets, the honey bee Hsc70-3 gene. Using a luciferase reporter, we show that honey bee Hsc70 promoter activity is inducible by UPR activation. In addition, we show that this activation is IRE1-dependent and relies on specific cis regulatory elements. Experiments using exogenous honey bee or fruit fly XBP1S proteins demonstrate that both factors can activate the Hsc70-3 promoter and further support a role for the IRE1 pathway in control of Hsc70-3 expression in the honey bee. By providing foundational knowledge about the UPR in the honey bee and demonstrating the usefulness of a heterologous cell line for molecular characterization of honey bee pathways, this work stands to improve our understanding of this critical species.
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Affiliation(s)
| | | | | | - Brittany A Johnston
- Biology Department, The City College of New York - CUNY, New York, NY, 10031, USA
| | - Henry Truong
- Biology Department, Barnard College, New York, NY, 10027, USA
| | - Jonathan W Snow
- Biology Department, Barnard College, New York, NY, 10027, USA.
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14
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Cunningham CB. Functional genomics of parental care of insects. Horm Behav 2020; 122:104756. [PMID: 32353447 DOI: 10.1016/j.yhbeh.2020.104756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 04/01/2020] [Accepted: 04/06/2020] [Indexed: 12/19/2022]
Abstract
Parental care was likely the first step most lineages made towards sociality. However, the molecular mechanisms that generate parental care are not broadly characterized. Insects are important as an evolutionary independent group from classic models of parental care, such as, house mice. They provide an opportunity to test the generality of our understanding. With this review, I survey the functional genomics of parental care of insects, summarize several recent advances in the broader framework for studying and understanding parental care, and finish with suggested priorities for further research. Although there are too few studies to draw definitive conclusions, I argue that natural selection appears to be rewiring existing gene networks to produce parental care, that the epigenetic mechanisms influencing parental care are not well understood, and, as an interesting early consensus, that genes strongly associated with carer/offspring interactions appear biased towards proteins that are secreted. I summarize the studies that have functionally validate candidate genes and highlight the increasing need to perform this work. I finish with arguments for both conceptual and practical changes moving forward. I argue that future work can increase the use of predictive frameworks, broaden its definition of conservation of mechanism to gene networks rather than single genes, and increase the use of more established comparative methods. I further highlight the practical considerations of standardizing analyses and reporting, increasing the sampling of both carers and offspring, better characterizing gene regulatory networks, better characterizing taxonomically restricted genes and any consistent role they have underpinning parental care, and using factorial designs to disentangle the influence of multiple variables on the expression of parental care.
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15
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Rago A, Werren JH, Colbourne JK. Sex biased expression and co-expression networks in development, using the hymenopteran Nasonia vitripennis. PLoS Genet 2020; 16:e1008518. [PMID: 31986136 PMCID: PMC7004391 DOI: 10.1371/journal.pgen.1008518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 02/06/2020] [Accepted: 11/13/2019] [Indexed: 12/17/2022] Open
Abstract
Sexual dimorphism requires regulation of gene expression in developing organisms. These developmental differences are caused by differential expression of genes and isoforms. The effect of expressing a gene is also influenced by which other genes are simultaneously expressed (functional interactions). However, few studies have described how these processes change across development. We compare the dynamics of differential expression, isoform switching and functional interactions in the sexual development of the model parasitoid wasp Nasonia vitripennis, a system that permits genome wide analysis of sex bias from early embryos to adults. We find relatively little sex-bias in embryos and larvae at the gene level, but several sub-networks show sex-biased functional interactions in early developmental stages. These networks provide new candidates for hymenopteran sex determination, including histone modification. In contrast, sex-bias in pupae and adults is driven by the differential expression of genes. We observe sex-biased isoform switching consistently across development, but mostly in genes that are already differentially expressed. Finally, we discover that sex-biased networks are enriched by genes specific to the Nasonia clade, and that those genes possess the topological properties of key regulators. These findings suggest that regulators in sex-biased networks evolve more rapidly than regulators of other developmental networks.
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Affiliation(s)
- Alfredo Rago
- School of Biosciences, The University of Birmingham, Birmingham, United Kingdom
| | - John H. Werren
- Department of Biology, University of Rochester, Rochester, NY, United States of America
| | - John K. Colbourne
- School of Biosciences, The University of Birmingham, Birmingham, United Kingdom
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16
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Shell WA, Rehan SM. Social modularity: conserved genes and regulatory elements underlie caste-antecedent behavioural states in an incipiently social bee. Proc Biol Sci 2019; 286:20191815. [PMID: 31771475 PMCID: PMC6939254 DOI: 10.1098/rspb.2019.1815] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/29/2019] [Indexed: 12/15/2022] Open
Abstract
The evolutionary origins of advanced eusociality, one of the most complex forms of phenotypic plasticity in nature, have long been a focus within the field of sociobiology. Although eusocial insects are known to have evolved from solitary ancestors, sociogenomic research among incipiently social taxa has only recently provided empirical evidence supporting theories that modular regulation and deeply conserved genes may play important roles in both the evolutionary emergence and elaboration of insect sociality. There remains, however, a paucity of data to further test the biological reality of these and other evolutionary theories among taxa in the earliest stages of social evolution. Here, we present brain transcriptomic data from the incipiently social small carpenter bee, Ceratina calcarata, which captures patterns of cis-regulation and gene expression associated with female maturation, and underlying two well-defined behavioural states, foraging and guarding, concurrently demonstrated by mothers and daughters during early autumn. We find that an incipiently social nest environment may dramatically affect gene expression. We further reveal foraging and guarding behaviours to be putatively caste-antecedent states in C. calcarata, and offer strong empirical support for the operation of modular regulation, involving deeply conserved and differentially expressed genes in the expression of early social forms.
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Affiliation(s)
- Wyatt A. Shell
- Department of Biological Sciences, University of New Hampshire, 38 Academic Way, Durham, NH 03824, USA
| | - Sandra M. Rehan
- Department of Biological Sciences, University of New Hampshire, 38 Academic Way, Durham, NH 03824, USA
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, CanadaM3 J 1P3
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17
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Hamilton AR, Traniello IM, Ray AM, Caldwell AS, Wickline SA, Robinson GE. Division of labor in honey bees is associated with transcriptional regulatory plasticity in the brain. J Exp Biol 2019; 222:jeb200196. [PMID: 31138635 PMCID: PMC6679348 DOI: 10.1242/jeb.200196] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/16/2019] [Indexed: 12/19/2022]
Abstract
Studies in evolutionary and developmental biology show that relationships between transcription factors (TFs) and their target genes can be altered to result in novel regulatory relationships that generate phenotypic plasticity. We hypothesized that context-dependent shifts in the nervous system associated with behavior may also be linked to changes in TF-target relationships over physiological time scales. We tested this hypothesis using honey bee (Apis mellifera) division of labor as a model system by performing bioinformatic analyses of previously published brain transcriptomic profiles together with new RNAi and behavioral experiments. The bioinformatic analyses identified five TFs that exhibited strong signatures of regulatory plasticity as a function of division of labor. RNAi targeting of one of these TFs (broad complex) and a related TF that did not exhibit plasticity (fushi tarazu transcription factor 1) was administered in conjunction with automated analyses of foraging behavior in the field, laboratory assays of aggression and brood care behavior, and endocrine treatments. The results showed that changes in the regulatory relationships of these TFs were associated with behavioral state, social context and endocrine state. These findings provide the first empirical evidence that TF-target relationships in the brain are altered in conjunction with behavior and social context. They also suggest that one mechanism for this plasticity involves pleiotropic TFs high up in regulatory hierarchies producing behavior-specific transcriptional responses by activating different downstream TFs to induce discrete context-dependent transcriptional cascades. These findings provide new insights into the dynamic nature of the transcriptional regulatory architecture underlying behavior in the brain.
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Affiliation(s)
- Adam R Hamilton
- Neuroscience Program, University of Illinois at Champaign-Urbana, Urbana, IL 61801, USA
| | - Ian M Traniello
- Neuroscience Program, University of Illinois at Champaign-Urbana, Urbana, IL 61801, USA
| | - Allyson M Ray
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Champaign-Urbana, Urbana, IL 61801, USA
| | - Arminius S Caldwell
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Champaign-Urbana, Urbana, IL 61801, USA
| | - Samuel A Wickline
- Department of Computation and Molecular Biophysics, School of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Gene E Robinson
- Neuroscience Program, University of Illinois at Champaign-Urbana, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Champaign-Urbana, Urbana, IL 61801, USA
- Department of Entomology, University of Illinois at Champaign-Urbana, Urbana, IL 61801, USA
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18
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Steffen MA, Rehan SM. Genetic signatures of dominance hierarchies reveal conserved cis-regulatory and brain gene expression underlying aggression in a facultatively social bee. GENES BRAIN AND BEHAVIOR 2019; 19:e12597. [PMID: 31264771 DOI: 10.1111/gbb.12597] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 11/29/2022]
Abstract
Agonistic interactions among individuals can result in the formation of dominance hierarches that can reinforce individual behavior and social status. Such dominance hierarches precede the establishment of reproductive dominance, division of labor and caste formation in highly social insect taxa. As such, deciphering the molecular basis of aggression is fundamental in understanding the mechanisms of social evolution. Assessing the proximate mechanisms of aggression in incipiently social bees can provide insights into the foundations of genomic mechanisms of social behavior. Here, we measured the effects of aggression on brain gene expression in the incipiently social bee, Ceratina australensis. We examine the brain transcriptomic differences between individuals who have experienced recurrent winning, losing, or a change in rank during repeated encounters. Using comparative analyses across taxa, we identify deeply conserved candidate genes, pathways, and regulatory networks for the formation of social hierarchies.
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Affiliation(s)
- Michael A Steffen
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire
| | - Sandra M Rehan
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire
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19
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Kasper C, Hebert FO, Aubin-Horth N, Taborsky B. Divergent brain gene expression profiles between alternative behavioural helper types in a cooperative breeder. Mol Ecol 2018; 27:4136-4151. [DOI: 10.1111/mec.14837] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 07/21/2018] [Accepted: 08/07/2018] [Indexed: 01/17/2023]
Affiliation(s)
- Claudia Kasper
- Behavioural Ecology; University of Bern; Hinterkappelen Switzerland
| | - Francois Olivier Hebert
- Département de Biologie et Institut de Biologie Intégrative et des Systèmes; Université Laval; Québec Québec Canada
| | - Nadia Aubin-Horth
- Département de Biologie et Institut de Biologie Intégrative et des Systèmes; Université Laval; Québec Québec Canada
| | - Barbara Taborsky
- Behavioural Ecology; University of Bern; Hinterkappelen Switzerland
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20
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Cervoni MS, Cardoso-Júnior CAM, Craveiro G, Souza ADO, Alberici LC, Hartfelder K. Mitochondrial capacity, oxidative damage and hypoxia gene expression are associated with age-related division of labor in honey bee ( Apis mellifera L.) workers. ACTA ACUST UNITED AC 2017; 220:4035-4046. [PMID: 28912256 DOI: 10.1242/jeb.161844] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/07/2017] [Indexed: 12/30/2022]
Abstract
During adult life, honey bee workers undergo a succession of behavioral states. Nurse bees perform tasks inside the nest, and when they are about 2-3 weeks old they initiate foraging. This switch is associated with alterations in diet, and with the levels of juvenile hormone and vitellogenin circulating in hemolymph. It is not clear whether this behavioral maturation involves major changes at the cellular level, such as mitochondrial activity and the redox environment in the head, thorax and abdomen. Using high-resolution respirometry, biochemical assays and RT-qPCR, we evaluated the association of these parameters with this behavioral change. We found that tissues from the head and abdomen of nurses have a higher oxidative phosphorylation capacity than those of foragers, while for the thorax we found the opposite situation. As higher mitochondrial activity tends to generate more H2O2, and H2O2 is known to stabilize HIF-1α, this would be expected to stimulate hypoxia signaling. The positive correlation that we observed between mitochondrial activity and hif-1α gene expression in abdomen and head tissue of nurses would be in line with this hypothesis. Higher expression of antioxidant enzyme genes was observed in foragers, which could explain their low levels of protein carbonylation. No alterations were seen in nitric oxide (NO) levels, suggesting that NO signaling is unlikely to be involved in behavioral maturation. We conclude that the behavioral change seen in honey bee workers is reflected in differential mitochondrial activities and redox parameters, and we consider that this can provide insights into the underlying aging process.
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Affiliation(s)
- Mário S Cervoni
- Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, 14049-900, Ribeirão Preto, São Paulo, Brazil
| | - Carlos A M Cardoso-Júnior
- Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, 14049-900, Ribeirão Preto, São Paulo, Brazil
| | - Giovana Craveiro
- Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, 14049-900, Ribeirão Preto, São Paulo, Brazil
| | - Anderson de O Souza
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café, s/n, 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Luciane C Alberici
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café, s/n, 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Klaus Hartfelder
- Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, 14049-900, Ribeirão Preto, São Paulo, Brazil
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21
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Toth AL, Rehan SM. Molecular Evolution of Insect Sociality: An Eco-Evo-Devo Perspective. ANNUAL REVIEW OF ENTOMOLOGY 2017; 62:419-442. [PMID: 27912247 DOI: 10.1146/annurev-ento-031616-035601] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The evolution of eusociality is a perennial issue in evolutionary biology, and genomic advances have fueled steadily growing interest in the genetic changes underlying social evolution. Along with a recent flurry of research on comparative and evolutionary genomics in different eusocial insect groups (bees, ants, wasps, and termites), several mechanistic explanations have emerged to describe the molecular evolution of eusociality from solitary behavior. These include solitary physiological ground plans, genetic toolkits of deeply conserved genes, evolutionary changes in protein-coding genes, cis regulation, and the structure of gene networks, epigenetics, and novel genes. Despite this proliferation of ideas, there has been little synthesis, even though these ideas are not mutually exclusive and may in fact be complementary. We review available data on molecular evolution of insect sociality and highlight key biotic and abiotic factors influencing social insect genomes. We then suggest both phylogenetic and ecological evolutionary developmental biology (eco-evo-devo) perspectives for a more synthetic view of molecular evolution in insect societies.
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Affiliation(s)
- Amy L Toth
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011;
- Department of Entomology, Iowa State University, Ames, Iowa 50011
| | - Sandra M Rehan
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire 03824;
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22
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Jones BM, Kingwell CJ, Wcislo WT, Robinson GE. Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality. Proc Biol Sci 2017; 284:20162228. [PMID: 28053060 PMCID: PMC5247497 DOI: 10.1098/rspb.2016.2228] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/05/2016] [Indexed: 12/18/2022] Open
Abstract
Developmental plasticity may accelerate the evolution of phenotypic novelty through genetic accommodation, but studies of genetic accommodation often lack knowledge of the ancestral state to place selected traits in an evolutionary context. A promising approach for assessing genetic accommodation involves using a comparative framework to ask whether ancestral plasticity is related to the evolution of a particular trait. Bees are an excellent group for such comparisons because caste-based societies (eusociality) have evolved multiple times independently and extant species exhibit different modes of eusociality. We measured brain and abdominal gene expression in a facultatively eusocial bee, Megalopta genalis, and assessed whether plasticity in this species is functionally linked to eusocial traits in other bee lineages. Caste-biased abdominal genes in M. genalis overlapped significantly with caste-biased genes in obligately eusocial bees. Moreover, caste-biased genes in M. genalis overlapped significantly with genes shown to be rapidly evolving in multiple studies of 10 bee species, particularly for genes in the glycolysis pathway and other genes involved in metabolism. These results provide support for the idea that eusociality can evolve via genetic accommodation, with plasticity in facultatively eusocial species like M. genalis providing a substrate for selection during the evolution of caste in obligately eusocial lineages.
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Affiliation(s)
- Beryl M Jones
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Smithsonian Tropical Research Institute, Panama City 20521-9100, Panama
| | - Callum J Kingwell
- Smithsonian Tropical Research Institute, Panama City 20521-9100, Panama
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - William T Wcislo
- Smithsonian Tropical Research Institute, Panama City 20521-9100, Panama
| | - Gene E Robinson
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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23
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Doublet V, Paxton RJ, McDonnell CM, Dubois E, Nidelet S, Moritz RF, Alaux C, Le Conte Y. Brain transcriptomes of honey bees ( Apis mellifera) experimentally infected by two pathogens: Black queen cell virus and Nosema ceranae. GENOMICS DATA 2016; 10:79-82. [PMID: 27747157 PMCID: PMC5054260 DOI: 10.1016/j.gdata.2016.09.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 09/26/2016] [Indexed: 01/25/2023]
Abstract
Regulation of gene expression in the brain plays an important role in behavioral plasticity and decision making in response to external stimuli. However, both can be severely affected by environmental factors, such as parasites and pathogens. In honey bees, the emergence and re-emergence of pathogens and potential for pathogen co-infection and interaction have been suggested as major components that significantly impaired social behavior and survival. To understand how the honey bee is affected and responds to interacting pathogens, we co-infected workers with two prevalent pathogens of different nature, the positive single strand RNA virus Black queen cell virus (BQCV), and the Microsporidia Nosema ceranae, and explored gene expression changes in brains upon single infections and co-infections. Our data provide an important resource for research on honey bee diseases, and more generally on insect host-pathogen and pathogen-pathogen interactions. Raw and processed data are publicly available in the NCBI/GEO database: (http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE81664.
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Affiliation(s)
- Vincent Doublet
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, 06099 Halle (Salle), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn TR11 9FE, UK
| | - Robert J. Paxton
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, 06099 Halle (Salle), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | | | - Emeric Dubois
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094 Cedex 5 Montpellier, France
| | - Sabine Nidelet
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094 Cedex 5 Montpellier, France
| | - Robin F.A. Moritz
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, 06099 Halle (Salle), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Cédric Alaux
- INRA, UR 406 Abeilles et Environnement, 84914 Avignon Cedex 09, France
| | - Yves Le Conte
- INRA, UR 406 Abeilles et Environnement, 84914 Avignon Cedex 09, France
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24
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Gehring KB, Heufelder K, Feige J, Bauer P, Dyck Y, Ehrhardt L, Kühnemund J, Bergmann A, Göbel J, Isecke M, Eisenhardt D. Involvement of phosphorylated Apis mellifera CREB in gating a honeybee's behavioral response to an external stimulus. Learn Mem 2016; 23:195-207. [PMID: 27084927 PMCID: PMC4836635 DOI: 10.1101/lm.040964.115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/23/2016] [Indexed: 11/24/2022]
Abstract
The transcription factor cAMP-response element-binding protein (CREB) is involved in neuronal plasticity. Phosphorylation activates CREB and an increased level of phosphorylated CREB is regarded as an indicator of CREB-dependent transcriptional activation. In honeybees(Apis mellifera)we recently demonstrated a particular high abundance of the phosphorylated honeybee CREB homolog (pAmCREB) in the central brain and in a subpopulation of mushroom body neurons. We hypothesize that these high pAmCREB levels are related to learning and memory formation. Here, we tested this hypothesis by analyzing brain pAmCREB levels in classically conditioned bees and bees experiencing unpaired presentations of conditioned stimulus (CS) and unconditioned stimulus (US). We demonstrate that both behavioral protocols display differences in memory formation but do not alter the level of pAmCREB in bee brains directly after training. Nevertheless, we report that bees responding to the CS during unpaired stimulus presentations exhibit higher levels of pAmCREB than nonresponding bees. In addition, Trichostatin A, a histone deacetylase inhibitor that is thought to enhance histone acetylation by CREB-binding protein, increases the bees' CS responsiveness. We conclude that pAmCREB is involved in gating a bee's behavioral response driven by an external stimulus.
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Affiliation(s)
- Katrin B Gehring
- Freie Universität Berlin, Institut für Biologie - Neurobiologie, D-14195 Berlin, Germany
| | - Karin Heufelder
- Freie Universität Berlin, Institut für Biologie - Neurobiologie, D-14195 Berlin, Germany
| | - Janina Feige
- Freie Universität Berlin, Institut für Biologie - Neurobiologie, D-14195 Berlin, Germany
| | - Paul Bauer
- Freie Universität Berlin, Institut für Biologie - Neurobiologie, D-14195 Berlin, Germany
| | - Yan Dyck
- Freie Universität Berlin, Institut für Biologie - Neurobiologie, D-14195 Berlin, Germany
| | - Lea Ehrhardt
- Freie Universität Berlin, Institut für Biologie - Neurobiologie, D-14195 Berlin, Germany
| | - Johannes Kühnemund
- Freie Universität Berlin, Institut für Biologie - Neurobiologie, D-14195 Berlin, Germany
| | - Anja Bergmann
- Freie Universität Berlin, Institut für Biologie - Neurobiologie, D-14195 Berlin, Germany
| | - Josefine Göbel
- Freie Universität Berlin, Institut für Biologie - Neurobiologie, D-14195 Berlin, Germany
| | - Marlene Isecke
- Freie Universität Berlin, Institut für Biologie - Neurobiologie, D-14195 Berlin, Germany
| | - Dorothea Eisenhardt
- Freie Universität Berlin, Institut für Biologie - Neurobiologie, D-14195 Berlin, Germany
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Complex patterns of differential expression in candidate master regulatory genes for social behavior in honey bees. Behav Ecol Sociobiol 2016. [DOI: 10.1007/s00265-016-2071-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Assessment of fight outcome is needed to activate socially driven transcriptional changes in the zebrafish brain. Proc Natl Acad Sci U S A 2016; 113:E654-61. [PMID: 26787876 DOI: 10.1073/pnas.1514292113] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Group living animals must be able to express different behavior profiles depending on their social status. Therefore, the same genotype may translate into different behavioral phenotypes through socially driven differential gene expression. However, how social information is translated into a neurogenomic response and what are the specific cues in a social interaction that signal a change in social status are questions that have remained unanswered. Here, we show for the first time, to our knowledge, that the switch between status-specific neurogenomic states relies on the assessment of fight outcome rather than just on self- or opponent-only assessment of fighting ability. For this purpose, we manipulated the perception of fight outcome in male zebrafish and measured its impact on the brain transcriptome using a zebrafish whole genome gene chip. Males fought either a real opponent, and a winner and a loser were identified, or their own image on a mirror, in which case, despite expressing aggressive behavior, males did not experience either a victory or a defeat. Massive changes in the brain transcriptome were observed in real opponent fighters, with losers displaying both a higher number of differentially expressed genes and of coexpressed gene modules than winners. In contrast, mirror fighters expressed a neurogenomic state similar to that of noninteracting fish. The genes that responded to fight outcome included immediate early genes and genes involved in neuroplasticity and epigenetic modifications. These results indicate that, even in cognitively simple organisms such as zebrafish, neurogenomic responses underlying changes in social status rely on mutual assessment of fighting ability.
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Brain Transcriptomic Response to Social Eavesdropping in Zebrafish (Danio rerio). PLoS One 2015; 10:e0145801. [PMID: 26713440 PMCID: PMC4700982 DOI: 10.1371/journal.pone.0145801] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 12/08/2015] [Indexed: 01/05/2023] Open
Abstract
Public information is widely available at low cost to animals living in social groups. For instance, bystanders may eavesdrop on signaling interactions between conspecifics and use it to adapt their subsequent behavior towards the observed individuals. This social eavesdropping ability is expected to require specialized mechanisms such as social attention, which selects social information available for learning. To begin exploring the genetic basis of social eavesdropping, we used a previously established attention paradigm in the lab to study the brain gene expression profile of male zebrafish (Danio rerio) in relation to the attention they paid towards conspecifics involved or not involved in agonistic interactions. Microarray gene chips were used to characterize their brain transcriptomes based on differential expression of single genes and gene sets. These analyses were complemented by promoter region-based techniques. Using data from both approaches, we further drafted protein interaction networks. Our results suggest that attentiveness towards conspecifics, whether interacting or not, activates pathways linked to neuronal plasticity and memory formation. The network analyses suggested that fos and jun are key players on this response, and that npas4a, nr4a1 and egr4 may also play an important role. Furthermore, specifically observing fighting interactions further triggered pathways associated to a change in the alertness status (dnajb5) and to other genes related to memory formation (btg2, npas4b), which suggests that the acquisition of eavesdropped information about social relationships activates specific processes on top of those already activated just by observing conspecifics.
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Wheeler MM, Ament SA, Rodriguez-Zas SL, Southey B, Robinson GE. Diet and endocrine effects on behavioral maturation-related gene expression in the pars intercerebralis of the honey bee brain. ACTA ACUST UNITED AC 2015; 218:4005-14. [PMID: 26567353 DOI: 10.1242/jeb.119420] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 10/22/2015] [Indexed: 01/05/2023]
Abstract
Nervous and neuroendocrine systems mediate environmental conditions to control a variety of life history traits. Our goal was to provide mechanistic insights as to how neurosecretory signals mediate division of labor in the honey bee (Apis mellifera). Worker division of labor is based on a process of behavioral maturation by individual bees, which involves performing in-hive tasks early in adulthood, then transitioning to foraging for food outside the hive. Social and nutritional cues converge on endocrine factors to regulate behavioral maturation, but whether neurosecretory systems are central to this process is not known. To explore this, we performed transcriptomic profiling of a neurosecretory region of the brain, the pars intercerebralis (PI). We first compared PI transcriptional profiles for bees performing in-hive tasks and bees engaged in foraging. Using these results as a baseline, we then performed manipulative experiments to test whether the PI is responsive to dietary changes and/or changes in juvenile hormone (JH) levels. Results reveal a robust molecular signature of behavioral maturation in the PI, with a subset of gene expression changes consistent with changes elicited by JH treatment. In contrast, dietary changes did not induce transcriptomic changes in the PI consistent with behavioral maturation or JH treatment. Based on these results, we propose a new verbal model of the regulation of division of labor in honey bees in which the relationship between diet and nutritional physiology is attenuated, and in its place is a relationship between social signals and nutritional physiology that is mediated by JH.
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Affiliation(s)
| | - Seth A Ament
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Bruce Southey
- Department of Animal Sciences, UIUC, Urbana, IL 61801, USA
| | - Gene E Robinson
- Department of Entomology, UIUC, Urbana, IL 61801, USA Institute for Genomic Biology, UIUC, Urbana, IL 61801, USA
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32
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Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies. Proc Natl Acad Sci U S A 2015; 112:13970-5. [PMID: 26483466 DOI: 10.1073/pnas.1515937112] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Phenotypic plasticity is important in adaptation and shapes the evolution of organisms. However, we understand little about what aspects of the genome are important in facilitating plasticity. Eusocial insect societies produce plastic phenotypes from the same genome, as reproductives (queens) and nonreproductives (workers). The greatest plasticity is found in the simple eusocial insect societies in which individuals retain the ability to switch between reproductive and nonreproductive phenotypes as adults. We lack comprehensive data on the molecular basis of plastic phenotypes. Here, we sequenced genomes, microRNAs (miRNAs), and multiple transcriptomes and methylomes from individual brains in a wasp (Polistes canadensis) and an ant (Dinoponera quadriceps) that live in simple eusocial societies. In both species, we found few differences between phenotypes at the transcriptional level, with little functional specialization, and no evidence that phenotype-specific gene expression is driven by DNA methylation or miRNAs. Instead, phenotypic differentiation was defined more subtly by nonrandom transcriptional network organization, with roles in these networks for both conserved and taxon-restricted genes. The general lack of highly methylated regions or methylome patterning in both species may be an important mechanism for achieving plasticity among phenotypes during adulthood. These findings define previously unidentified hypotheses on the genomic processes that facilitate plasticity and suggest that the molecular hallmarks of social behavior are likely to differ with the level of social complexity.
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Gehring KB, Heufelder K, Kersting I, Eisenhardt D. Abundance of phosphorylatedApis melliferaCREB in the honeybee's mushroom body inner compact cells varies with age. J Comp Neurol 2015; 524:1165-80. [DOI: 10.1002/cne.23894] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/24/2015] [Accepted: 08/25/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Katrin B. Gehring
- Institute for Biology-Neurobiology; Freie Universität Berlin; D-14195 Berlin Germany
| | - Karin Heufelder
- Institute for Biology-Neurobiology; Freie Universität Berlin; D-14195 Berlin Germany
| | - Isabella Kersting
- Institute for Biology-Neurobiology; Freie Universität Berlin; D-14195 Berlin Germany
| | - Dorothea Eisenhardt
- Institute for Biology-Neurobiology; Freie Universität Berlin; D-14195 Berlin Germany
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Reiss DJ, Plaisier CL, Wu WJ, Baliga NS. cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism. Nucleic Acids Res 2015; 43:e87. [PMID: 25873626 PMCID: PMC4513845 DOI: 10.1093/nar/gkv300] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 03/05/2015] [Accepted: 03/26/2015] [Indexed: 12/25/2022] Open
Abstract
The cMonkey integrated biclustering algorithm identifies conditionally co-regulated modules of genes (biclusters). cMonkey integrates various orthogonal pieces of information which support evidence of gene co-regulation, and optimizes biclusters to be supported simultaneously by one or more of these prior constraints. The algorithm served as the cornerstone for constructing the first global, predictive Environmental Gene Regulatory Influence Network (EGRIN) model for a free-living cell, and has now been applied to many more organisms. However, due to its computational inefficiencies, long run-time and complexity of various input data types, cMonkey was not readily usable by the wider community. To address these primary concerns, we have significantly updated the cMonkey algorithm and refactored its implementation, improving its usability and extendibility. These improvements provide a fully functioning and user-friendly platform for building co-regulated gene modules and the tools necessary for their exploration and interpretation. We show, via three separate analyses of data for E. coli, M. tuberculosis and H. sapiens, that the updated algorithm and inclusion of novel scoring functions for new data types (e.g. ChIP-seq and transcription factor over-expression [TFOE]) improve discovery of biologically informative co-regulated modules. The complete cMonkey2 software package, including source code, is available at https://github.com/baliga-lab/cmonkey2.
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Affiliation(s)
- David J Reiss
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | | | - Wei-Ju Wu
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Nitin S Baliga
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA Department of Microbiology, University of Washington, Seattle, WA 98103, USA
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Khamis AM, Hamilton AR, Medvedeva YA, Alam T, Alam I, Essack M, Umylny B, Jankovic BR, Naeger NL, Suzuki M, Harbers M, Robinson GE, Bajic VB. Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera. Sci Rep 2015; 5:11136. [PMID: 26073445 PMCID: PMC4466890 DOI: 10.1038/srep11136] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 05/01/2015] [Indexed: 12/30/2022] Open
Abstract
Honey bee colonies exhibit an age-related division of labor, with worker bees performing discrete sets of behaviors throughout their lifespan. These behavioral states are associated with distinct brain transcriptomic states, yet little is known about the regulatory mechanisms governing them. We used CAGEscan (a variant of the Cap Analysis of Gene Expression technique) for the first time to characterize the promoter regions of differentially expressed brain genes during two behavioral states (brood care (aka “nursing”) and foraging) and identified transcription factors (TFs) that may govern their expression. More than half of the differentially expressed TFs were associated with motifs enriched in the promoter regions of differentially expressed genes (DEGs), suggesting they are regulators of behavioral state. Strikingly, five TFs (nf-kb, egr, pax6, hairy, and clockwork orange) were predicted to co-regulate nearly half of the genes that were upregulated in foragers. Finally, differences in alternative TSS usage between nurses and foragers were detected upstream of 646 genes, whose functional analysis revealed enrichment for Gene Ontology terms associated with neural function and plasticity. This demonstrates for the first time that alternative TSSs are associated with stable differences in behavior, suggesting they may play a role in organizing behavioral state.
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Affiliation(s)
- Abdullah M Khamis
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Adam R Hamilton
- Departments of Entomology and Institute for Genomic Biology, Urbana, IL 61801; and Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Yulia A Medvedeva
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Tanvir Alam
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Intikhab Alam
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Magbubah Essack
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Boris Umylny
- Lumenogix Inc., 2935 Rodeo Park Drive East, Santa Fe NM, 87505, USA
| | - Boris R Jankovic
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Nicholas L Naeger
- Departments of Entomology and Institute for Genomic Biology, Urbana, IL 61801; and Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Makoto Suzuki
- DNAFORM Inc., Leading Venture Plaza-2, 75-1, Ono-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0046, Japan
| | - Matthias Harbers
- 1] DNAFORM Inc., Leading Venture Plaza-2, 75-1, Ono-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0046, Japan [2] RIKEN Center for Life Science Technologies, Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Gene E Robinson
- Departments of Entomology and Institute for Genomic Biology, Urbana, IL 61801; and Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Vladimir B Bajic
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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36
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Rehan SM, Toth AL. Climbing the social ladder: the molecular evolution of sociality. Trends Ecol Evol 2015; 30:426-33. [PMID: 26051561 DOI: 10.1016/j.tree.2015.05.004] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 11/24/2022]
Abstract
Genomic tools are allowing us to dissect the roles of genes and genetic architecture in social evolution, and eusocial insects are excellent models. Numerous hypotheses for molecular evolution of eusociality have been proposed, ranging from regulatory shifts in 'old' genes to rapid evolution of 'new' genes. A broad model to explain this major transition in evolution has been lacking. We provide a synthetic framework centered on the idea that different evolutionary processes dominate during different transitional stages, beginning with changes in gene regulation and culminating in novel genes later on. By considering multiple mechanisms as we 'climb the social ladder', we can test whether the transitions from solitary to simple sociality to complex sociality represent incremental changes or genetic revolutions.
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Affiliation(s)
- Sandra M Rehan
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA.
| | - Amy L Toth
- Department of Evolution, Ecology, and Organismal Biology, and Department of Entomology, Iowa State University, Ames, IA 50011, USA
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37
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Blatti C, Kazemian M, Wolfe S, Brodsky M, Sinha S. Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism. Nucleic Acids Res 2015; 43:3998-4012. [PMID: 25791631 PMCID: PMC4417154 DOI: 10.1093/nar/gkv195] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 02/24/2015] [Indexed: 11/17/2022] Open
Abstract
Characterization of cell type specific regulatory networks and elements is a major challenge in genomics, and emerging strategies frequently employ high-throughput genome-wide assays of transcription factor (TF) to DNA binding, histone modifications or chromatin state. However, these experiments remain too difficult/expensive for many laboratories to apply comprehensively to their system of interest. Here, we explore the potential of elucidating regulatory systems in varied cell types using computational techniques that rely on only data of gene expression, low-resolution chromatin accessibility, and TF–DNA binding specificities (‘motifs’). We show that static computational motif scans overlaid with chromatin accessibility data reasonably approximate experimentally measured TF–DNA binding. We demonstrate that predicted binding profiles and expression patterns of hundreds of TFs are sufficient to identify major regulators of ∼200 spatiotemporal expression domains in the Drosophila embryo. We are then able to learn reliable statistical models of enhancer activity for over 70 expression domains and apply those models to annotate domain specific enhancers genome-wide. Throughout this work, we apply our motif and accessibility based approach to comprehensively characterize the regulatory network of fruitfly embryonic development and show that the accuracy of our computational method compares favorably to approaches that rely on data from many experimental assays.
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Affiliation(s)
- Charles Blatti
- Department of Computer Science, University of Illinois, Urbana, IL 61801, USA
| | - Majid Kazemian
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Scot Wolfe
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01655, USA Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Michael Brodsky
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01655, USA Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Saurabh Sinha
- Department of Computer Science, University of Illinois, Urbana, IL 61801, USA Institute of Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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Neuromolecular responses to social challenge: common mechanisms across mouse, stickleback fish, and honey bee. Proc Natl Acad Sci U S A 2014; 111:17929-34. [PMID: 25453090 DOI: 10.1073/pnas.1420369111] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Certain complex phenotypes appear repeatedly across diverse species due to processes of evolutionary conservation and convergence. In some contexts like developmental body patterning, there is increased appreciation that common molecular mechanisms underlie common phenotypes; these molecular mechanisms include highly conserved genes and networks that may be modified by lineage-specific mutations. However, the existence of deeply conserved mechanisms for social behaviors has not yet been demonstrated. We used a comparative genomics approach to determine whether shared neuromolecular mechanisms could underlie behavioral response to territory intrusion across species spanning a broad phylogenetic range: house mouse (Mus musculus), stickleback fish (Gasterosteus aculeatus), and honey bee (Apis mellifera). Territory intrusion modulated similar brain functional processes in each species, including those associated with hormone-mediated signal transduction and neurodevelopment. Changes in chromosome organization and energy metabolism appear to be core, conserved processes involved in the response to territory intrusion. We also found that several homologous transcription factors that are typically associated with neural development were modulated across all three species, suggesting that shared neuronal effects may involve transcriptional cascades of evolutionarily conserved genes. Furthermore, immunohistochemical analyses of a subset of these transcription factors in mouse again implicated modulation of energy metabolism in the behavioral response. These results provide support for conserved genetic "toolkits" that are used in independent evolutions of the response to social challenge in diverse taxa.
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Abstract
The Motif Enrichment Tool (MET) provides an online interface that enables users to find major transcriptional regulators of their gene sets of interest. MET searches the appropriate regulatory region around each gene and identifies which transcription factor DNA-binding specificities (motifs) are statistically overrepresented. Motif enrichment analysis is currently available for many metazoan species including human, mouse, fruit fly, planaria and flowering plants. MET also leverages high-throughput experimental data such as ChIP-seq and DNase-seq from ENCODE and ModENCODE to identify the regulatory targets of a transcription factor with greater precision. The results from MET are produced in real time and are linked to a genome browser for easy follow-up analysis. Use of the web tool is free and open to all, and there is no login requirement. Address: http://veda.cs.uiuc.edu/MET/.
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Affiliation(s)
- Charles Blatti
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Saurabh Sinha
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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40
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Corrado G, Tebaldi T, Bertamini G, Costa F, Quattrone A, Viero G, Passerini A. PTRcombiner: mining combinatorial regulation of gene expression from post-transcriptional interaction maps. BMC Genomics 2014; 15:304. [PMID: 24758252 PMCID: PMC4234518 DOI: 10.1186/1471-2164-15-304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 04/02/2014] [Indexed: 02/07/2023] Open
Abstract
Background The progress in mapping RNA-protein and RNA-RNA interactions at the transcriptome-wide level paves the way to decipher possible combinatorial patterns embedded in post-transcriptional regulation of gene expression. Results Here we propose an innovative computational tool to extract clusters of mRNA trans-acting co-regulators (RNA binding proteins and non-coding RNAs) from pairwise interaction annotations. In addition the tool allows to analyze the binding site similarity of co-regulators belonging to the same cluster, given their positional binding information. The tool has been tested on experimental collections of human and yeast interactions, identifying modules that coordinate functionally related messages. Conclusions This tool is an original attempt to uncover combinatorial patterns using all the post-transcriptional interaction data available so far. PTRcombiner is available at http://disi.unitn.it/~passerini/software/PTRcombiner/.
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Affiliation(s)
| | | | | | | | | | - Gabriella Viero
- Department of Information Engineering and Computer Science (DISI), University of Trento, 38123 Trento, Italy.
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Abstract
Across animals, there is remarkable diversity in behavior. Modern genomic approaches have made it possible to identify the molecular underpinnings of varied behavioral phenotypes. By examining species with plastic phenotypes we have begun to understand the dynamic and flexible nature of neural transcriptomes and identified gene modules associated with variation in social and reproductive behaviors in diverse species. Importantly, it is becoming increasingly clear that some candidate genes and gene networks are involved in complex social behaviors across even divergent species, yet few comparative transcriptomics studies have been conducted that examine a specific behavior across species. We discuss the implications of a range of important and insightful studies that have increased our understanding of the neurogenomics of behavioral plasticity. Despite its successes, behavioral genomics has been criticized for its lack of hypotheses and causative insights. We propose here a novel avenue to overcome some of these short-comings by complementing "forward genomics" studies (i.e., from phenotype to behaviorally relevant gene modules) with a "reverse genomics" approach (i.e., manipulating novel gene modules to examine effects on behavior, hormones, and the genome itself) to examine the functional causes and consequences of differential gene expression patterns. We discuss how several established approaches (such as pharmacological manipulations of a novel candidate pathway, fine scale mapping of novel candidate gene expression in the brain, or identifying direct targets of a novel transcription factor of interest) can be used in combination with the analysis of the accompanying neurogenomic responses to reveal unexpected biological processes. The integration of forward and reverse genomics will move the field beyond statistical associations and yield great insights into the neural and molecular control of social behavior and its evolution.
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Wheeler MM, Ament SA, Rodriguez-Zas SL, Robinson GE. Brain gene expression changes elicited by peripheral vitellogenin knockdown in the honey bee. INSECT MOLECULAR BIOLOGY 2013; 22:562-573. [PMID: 23889463 DOI: 10.1111/imb.12043] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Vitellogenin (Vg) is best known as a yolk protein precursor. Vg also functions to regulate behavioural maturation in adult honey bee workers, but the underlying molecular mechanisms by which it exerts this novel effect are largely unknown. We used abdominal vitellogenin (vg) knockdown with RNA interference (RNAi) and brain transcriptomic profiling to gain insights into how Vg influences honey bee behavioural maturation. We found that vg knockdown caused extensive gene expression changes in the bee brain, with much of this transcriptional response involving changes in central biological functions such as energy metabolism. vg knockdown targeted many of the same genes that show natural, maturation-related differences, but the direction of change for the genes in these two contrasts was not correlated. By contrast, vg knockdown targeted many of the same genes that are regulated by juvenile hormone (JH) and there was a significant correlation for the direction of change for the genes in these two contrasts. These results indicate that the tight coregulatory relationship that exists between JH and Vg in the regulation of honey bee behavioural maturation is manifest at the genomic level and suggest that these two physiological factors act through common pathways to regulate brain gene expression and behaviour.
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Affiliation(s)
- M M Wheeler
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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McDonnell CM, Alaux C, Parrinello H, Desvignes JP, Crauser D, Durbesson E, Beslay D, Le Conte Y. Ecto- and endoparasite induce similar chemical and brain neurogenomic responses in the honey bee (Apis mellifera). BMC Ecol 2013; 13:25. [PMID: 23866001 PMCID: PMC3725162 DOI: 10.1186/1472-6785-13-25] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 06/19/2013] [Indexed: 12/18/2022] Open
Abstract
Background Exclusion from a social group is an effective way to avoid parasite transmission. This type of social removal has also been proposed as a form of collective defense, or social immunity, in eusocial insect groups. If parasitic modification of host behavior is widespread in social insects, the underlying physiological and neuronal mechanisms remain to be investigated. We studied this phenomenon in honey bees parasitized by the mite Varroa destructor or microsporidia Nosema ceranae, which make bees leave the hive precociously. We characterized the chemical, behavioral and neurogenomic changes in parasitized bees, and compared the effects of both parasites. Results Analysis of cuticular hydrocarbon (CHC) profiles by gas chromatography coupled with mass spectrophotometry (GC-MS) showed changes in honey bees parasitized by either Nosema ceranae or Varroa destructor after 5 days of infestation. Levels of 10-HDA, an antiseptic important for social immunity, did not change in response to parasitism. Behavioral analysis of N. ceranae- or V. destructor- parasitized bees revealed no significant differences in their behavioral acts or social interactions with nestmates. Digital gene expression (DGE) analysis of parasitized honey bee brains demonstrated that, despite the difference in developmental stage at which the bee is parasitized, Nosema and Varroa-infested bees shared more gene changes with each other than with honey bee brain expression gene sets for forager or nurse castes. Conclusions Parasitism by Nosema or Varroa induces changes to both the CHC profiles on the surface of the bee and transcriptomic profiles in the brain, but within the social context of the hive, does not result in observable effects on her behavior or behavior towards her. While parasitized bees are reported to leave the hive as foragers, their brain transcription profiles suggest that their behavior is not driven by the same molecular pathways that induce foraging behavior.
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44
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Renn SC, Schumer ME. Genetic accommodation and behavioural evolution: insights from genomic studies. Anim Behav 2013. [DOI: 10.1016/j.anbehav.2013.02.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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45
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Hughes D. Pathways to understanding the extended phenotype of parasites in their hosts. J Exp Biol 2013; 216:142-7. [DOI: 10.1242/jeb.077461] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Summary
The study of the adaptive manipulation of animal behavior by parasites is entering very exciting times. Collectively the field has moved from its important and instructional natural history phase into proximate-level studies aiming to elucidate the mechanisms by which one organism controls another. Because many cases studies involve cross-kingdom control of behaviour, the findings are sure to be exciting. In this review I examine what possible pathways we can take to understanding the controlling behavior of parasites and how host behavior has become an extended phenotype of the parasites that is often hidden from view.
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Affiliation(s)
- David Hughes
- Centre for Infectious Disease Dynamics, Departments of Biology and Entomology, Huck Institute of the Life Sciences, W129 Millennium Science Complex, Pennsylvania State University, University Park, PA 16802, USA
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46
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Sanogo YO, Band M, Blatti C, Sinha S, Bell AM. Transcriptional regulation of brain gene expression in response to a territorial intrusion. Proc Biol Sci 2012; 279:4929-38. [PMID: 23097509 DOI: 10.1098/rspb.2012.2087] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Aggressive behaviour associated with territorial defence is widespread and has fitness consequences. However, excess aggression can interfere with other important biological functions such as immunity and energy homeostasis. How the expression of complex behaviours such as aggression is regulated in the brain has long intrigued ethologists, but has only recently become amenable for molecular dissection in non-model organisms. We investigated the transcriptomic response to territorial intrusion in four brain regions in breeding male threespined sticklebacks using expression microarrays and quantitative polymerase chain reaction (qPCR). Each region of the brain had a distinct genomic response to a territorial challenge. We identified a set of genes that were upregulated in the diencephalon and downregulated in the cerebellum and the brain stem. Cis-regulatory network analysis suggested transcription factors that regulated or co-regulated genes that were consistently regulated in all brain regions and others that regulated gene expression in opposing directions across brain regions. Our results support the hypothesis that territorial animals respond to social challenges via transcriptional regulation of genes in different brain regions. Finally, we found a remarkably close association between gene expression and aggressive behaviour at the individual level. This study sheds light on the molecular mechanisms in the brain that underlie the response to social challenges.
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Affiliation(s)
- Yibayiri O Sanogo
- Integrative Biology, University of Illinois, Urbana-Champaign, IL, USA
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47
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Zayed A, Robinson GE. Understanding the relationship between brain gene expression and social behavior: lessons from the honey bee. Annu Rev Genet 2012; 46:591-615. [PMID: 22994354 DOI: 10.1146/annurev-genet-110711-155517] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Behavior is a complex phenotype that is plastic and evolutionarily labile. The advent of genomics has revolutionized the field of behavioral genetics by providing tools to quantify the dynamic nature of brain gene expression in relation to behavioral output. The honey bee Apis mellifera provides an excellent platform for investigating the relationship between brain gene expression and behavior given both the remarkable behavioral repertoire expressed by members of its intricate society and the degree to which behavior is influenced by heredity and the social environment. Here, we review a linked series of studies that assayed changes in honey bee brain transcriptomes associated with natural and experimentally induced changes in behavioral state. These experiments demonstrate that brain gene expression is closely linked with behavior, that changes in brain gene expression mediate changes in behavior, and that the association between specific genes and behavior exists over multiple timescales, from physiological to evolutionary.
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Affiliation(s)
- Amro Zayed
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada.
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