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Semenov GA, Sonnenberg BR, Branch CL, Heinen VK, Welklin JF, Padula SR, Patel AM, Bridge ES, Pravosudov VV, Taylor SA. Genes and gene networks underlying spatial cognition in food-caching chickadees. Curr Biol 2024; 34:1930-1939.e4. [PMID: 38636515 DOI: 10.1016/j.cub.2024.03.058] [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: 10/06/2023] [Revised: 12/06/2023] [Accepted: 03/26/2024] [Indexed: 04/20/2024]
Abstract
Substantial progress has been made in understanding the genetic architecture of phenotypes involved in a variety of evolutionary processes. Behavioral genetics remains, however, among the least understood. We explore the genetic architecture of spatial cognitive abilities in a wild passerine bird, the mountain chickadee (Poecile gambeli). Mountain chickadees cache thousands of seeds in the fall and require specialized spatial memory to recover these caches throughout the winter. We previously showed that variation in spatial cognition has a direct effect on fitness and has a genetic basis. It remains unknown which specific genes and developmental pathways are particularly important for shaping spatial cognition. To further dissect the genetic basis of spatial cognitive abilities, we combine experimental quantification of spatial cognition in wild chickadees with whole-genome sequencing of 162 individuals, a new chromosome-scale reference genome, and species-specific gene annotation. We have identified a set of genes and developmental pathways that play a key role in creating variation in spatial cognition and found that the mechanism shaping cognitive variation is consistent with selection against mildly deleterious non-coding mutations. Although some candidate genes were organized into connected gene networks, about half do not have shared regulation, highlighting that multiple independent developmental or physiological mechanisms contribute to variation in spatial cognitive abilities. A large proportion of the candidate genes we found are associated with synaptic plasticity, an intriguing result that leads to the hypothesis that certain genetic variants create antagonism between behavioral plasticity and long-term memory, each providing distinct benefits depending on ecological context.
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Affiliation(s)
- Georgy A Semenov
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA.
| | - Benjamin R Sonnenberg
- Department of Biology and Evolution, Ecology Evolution and Conservation Biology Graduate Program, University of Nevada, Reno, NV 89557, USA
| | - Carrie L Branch
- Department of Psychology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Virginia K Heinen
- Department of Biology and Evolution, Ecology Evolution and Conservation Biology Graduate Program, University of Nevada, Reno, NV 89557, USA
| | - Joseph F Welklin
- Department of Biology and Evolution, Ecology Evolution and Conservation Biology Graduate Program, University of Nevada, Reno, NV 89557, USA
| | - Sara R Padula
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Ajay M Patel
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Eli S Bridge
- Oklahoma Biological Survey, University of Oklahoma, Norman, OK 73019, USA
| | - Vladimir V Pravosudov
- Department of Biology and Evolution, Ecology Evolution and Conservation Biology Graduate Program, University of Nevada, Reno, NV 89557, USA
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA
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2
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Liu M, Song Y, Zhang S, Yu L, Yuan Z, Yang H, Zhang M, Zhou Z, Seim I, Liu S, Fan G, Yang H. A chromosome-level genome of electric catfish ( Malapterurus electricus) provided new insights into order Siluriformes evolution. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:1-14. [PMID: 38433969 PMCID: PMC10901758 DOI: 10.1007/s42995-023-00197-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 09/22/2023] [Indexed: 03/05/2024]
Abstract
The electric catfish (Malapterurus electricus), belonging to the family Malapteruridae, order Siluriformes (Actinopterygii: Ostariophysi), is one of the six branches that has independently evolved electrical organs. We assembled a 796.75 Mb M. electricus genome and anchored 88.72% sequences into 28 chromosomes. Gene family analysis revealed 295 expanded gene families that were enriched on functions related to glutamate receptors. Convergent evolutionary analyses of electric organs among different lineage of electric fishes further revealed that the coding gene of rho guanine nucleotide exchange factor 4-like (arhgef4), which is associated with G-protein coupled receptor (GPCR) signaling pathway, underwent adaptive parallel evolution. Gene identification suggests visual degradation in catfishes, and an important role for taste in environmental adaptation. Our findings fill in the genomic data for a branch of electric fish and provide a relevant genetic basis for the adaptive evolution of Siluriformes. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00197-8.
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Affiliation(s)
- Meiru Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Yue Song
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Suyu Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Lili Yu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Zengbao Yuan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Hengjia Yang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Mengqi Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Zhuocheng Zhou
- Professional Committee of Native Aquatic Organisms and Water Ecosystem of China Fisheries Association, Beijing, 100125 China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210023 China
| | - Shanshan Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083 China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
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Schartz ND, Liang HY, Carvalho K, Chu SH, Mendoza-Arvilla A, Petrisko TJ, Gomez-Arboledas A, Mortazavi A, Tenner AJ. C5aR1 antagonism suppresses inflammatory glial gene expression and alters cellular signaling in an aggressive Alzheimer's model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554306. [PMID: 37662399 PMCID: PMC10473603 DOI: 10.1101/2023.08.22.554306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Alzheimer's disease (AD) is the leading cause of dementia in older adults, and the need for effective, sustainable therapeutic targets is imperative. Pharmacologic inhibition of C5aR1 reduces plaque load, gliosis and memory deficits in animal models. However, the cellular basis underlying this neuroprotection and which processes were the consequence of amyloid reduction vs alteration of the response to amyloid were unclear. In the Arctic model, the C5aR1 antagonist PMX205 did not reduce plaque load, but deficits in short-term memory in female mice were prevented. Hippocampal single cell and single nucleus RNA-seq clusters revealed C5aR1 dependent and independent gene expression and cell-cell communication. Microglial clusters containing neurotoxic disease-associated microglial genes were robustly upregulated in Arctic mice and drastically reduced with PMX205 treatment, while genes in microglia clusters that were overrepresented in the Arctic-PMX205 vs Arctic group were associated with synapse organization and transmission and learning. PMX205 treatment also reduced some A-1 astrocyte genes. In spite of changes in transcript levels, overall protein levels of some reactive glial markers were relatively unchanged by C5aR1 antagonism, as were clusters associated with protective responses to injury. C5aR1 inhibition promoted signaling pathways associated with cell growth and repair, such as TGFβ and FGF, in Arctic mice, while suppressing inflammatory pathways including PROS, Pecam1, and EPHA. In conclusion, pharmacologic C5aR1 inhibition prevents cognitive loss, limits microglial polarization to a detrimental inflammatory state and permits neuroprotective responses, as well as leaving protective functions of complement intact, making C5aR1 antagonism an attractive therapeutic strategy for individuals with AD.
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Affiliation(s)
- Nicole D. Schartz
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA 92697
| | - Heidi Y. Liang
- Department of Developmental & Cell Biology, University of California, Irvine, Irvine, CA 92697
| | - Klebea Carvalho
- Department of Developmental & Cell Biology, University of California, Irvine, Irvine, CA 92697
| | - Shu-Hui Chu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA 92697
| | - Adrian Mendoza-Arvilla
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA 92697
| | - Tiffany J. Petrisko
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA 92697
| | - Angela Gomez-Arboledas
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA 92697
| | - Ali Mortazavi
- Department of Developmental & Cell Biology, University of California, Irvine, Irvine, CA 92697
| | - Andrea J. Tenner
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA 92697
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697
- Department of Pathology and Laboratory Medicine, University of California, Irvine, School of Medicine, Irvine, CA 92697
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Lee K, Yoo KS, Park YS, Kim HK. Activity of Arhgef4 is modulated through Staufen1 in neurons. Neurosci Lett 2021; 756:135962. [PMID: 34022264 DOI: 10.1016/j.neulet.2021.135962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/10/2021] [Accepted: 05/14/2021] [Indexed: 12/26/2022]
Abstract
The role of Arhgef4, also known as adenomatous polyposis coli (APC)-stimulated guanine nucleotide exchange factor 1 (Asef1), has been identified in colorectal cancers. Interestingly, Arhgef4 is more highly expressed in brain regions than intestinal regions, suggesting a role in neurons. In our previous study, we reported that Arhgef4 negatively regulates the level of PSD-95 in excitatory post-synaptic regions by binding with Staufen1. However, modulation of Arhgef4 guanine nucleotide exchange factor (GEF) activity in neurons has not been reported. We examined the configuration of protein interactions when Arhgef4 binds to APC and/or Staufen1. Arhgef4 simultaneously binds to Staufen1 with APC. Staufen1 overexpression blocked the GEF activity of Arhgef4. Consistent with this, Staufen1 overexpression blocked the Arhgef4-induced increase in dendritic protrusions in cultured neurons. Taken together, our data suggest that the GEF activity of Arhgef4 could be negatively modulated by Staufen1 binding.
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Affiliation(s)
- Kina Lee
- Department of Medicine and Microbiology, Graduate Program in Neuroscience, College of Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ki-Seo Yoo
- Department of Medicine and Microbiology, Graduate Program in Neuroscience, College of Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Young-Seok Park
- Department of Neurosurgery, Graduate Program in Neuroscience, College of Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Hyong Kyu Kim
- Department of Medicine and Microbiology, Graduate Program in Neuroscience, College of Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea.
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