1
|
Hays M. Genetic conflicts in budding yeast: The 2μ plasmid as a model selfish element. Semin Cell Dev Biol 2024; 161-162:31-41. [PMID: 38598944 DOI: 10.1016/j.semcdb.2024.04.002] [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: 09/26/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]
Abstract
Antagonistic coevolution, arising from genetic conflict, can drive rapid evolution and biological innovation. Conflict can arise both between organisms and within genomes. This review focuses on budding yeasts as a model system for exploring intra- and inter-genomic genetic conflict, highlighting in particular the 2-micron (2μ) plasmid as a model selfish element. The 2μ is found widely in laboratory strains and industrial isolates of Saccharomyces cerevisiae and has long been known to cause host fitness defects. Nevertheless, the plasmid is frequently ignored in the context of genetic, fitness, and evolution studies. Here, I make a case for further exploring the evolutionary impact of the 2μ plasmid as well as other selfish elements of budding yeasts, discuss recent advances, and, finally, future directions for the field.
Collapse
Affiliation(s)
- Michelle Hays
- Department of Genetics, Stanford University, Stanford, CA, United States.
| |
Collapse
|
2
|
Chen P, Pan KC, Park EH, Luo Y, Lee YCG, Aravin AA. Escalation of genome defense capacity enables control of an expanding meiotic driver. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598716. [PMID: 38915551 PMCID: PMC11195268 DOI: 10.1101/2024.06.12.598716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
From RNA interference to chromatin silencing, diverse genome defense pathways silence selfish genetic elements to safeguard genome integrity1,2. Despite their diversity, different defense pathways share a modular organization, where numerous specificity factors identify diverse targets and common effectors silence them. In the PIWI-interacting RNA (piRNA) pathway, which controls selfish elements in the metazoan germline, diverse target RNAs are first identified by complementary base pairing with piRNAs and then silenced by PIWI-clade nucleases via enzymatic cleavage1,3. Such a binary architecture allows the defense systems to be readily adaptable, where new targets can be captured via the innovation of new specificity factors4,5. Thus, our current understanding of genome defense against lineage-specific selfish genes has been largely limited to the evolution of specificity factors, while it remains poorly understood whether other types of innovations are required. Here, we describe a new type of innovation, which escalates the defense capacity of the piRNA pathway to control a recently expanded selfish gene in Drosophila melanogaster. Through an in vivo RNAi screen for repressors of Stellate-a recently evolved and expanded selfish meiotic driver6-8-we discovered a novel defense factor, Trailblazer. Trailblazer is a transcription factor that promotes the expression of two PIWI-clade nucleases, Aub and AGO3, to match Stellate in abundance. Recent innovation in the DNA-binding domain of Trailblazer enabled it to drastically elevate Aub and AGO3 expression in the D. melanogaster lineage, thereby escalating the silencing capacity of the piRNA pathway to control expanded Stellate and safeguard fertility. As copy-number expansion is a recurrent feature of diverse selfish genes across the tree of life9-12, we envision that augmenting the defense capacity to quantitatively match selfish genes is likely a repeatedly employed defense strategy in evolution.
Collapse
Affiliation(s)
- Peiwei Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Katherine C. Pan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Eunice H. Park
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Yicheng Luo
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Yuh Chwen G. Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California 92697, USA
| | - Alexei A. Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| |
Collapse
|
3
|
Gluck-Thaler E, Vogan A. Systematic identification of cargo-mobilizing genetic elements reveals new dimensions of eukaryotic diversity. Nucleic Acids Res 2024; 52:5496-5513. [PMID: 38686785 PMCID: PMC11162782 DOI: 10.1093/nar/gkae327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/12/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Cargo-mobilizing mobile elements (CMEs) are genetic entities that faithfully transpose diverse protein coding sequences. Although common in bacteria, we know little about eukaryotic CMEs because no appropriate tools exist for their annotation. For example, Starships are giant fungal CMEs whose functions are largely unknown because they require time-intensive manual curation. To address this knowledge gap, we developed starfish, a computational workflow for high-throughput eukaryotic CME annotation. We applied starfish to 2 899 genomes of 1 649 fungal species and found that starfish recovers known Starships with 95% combined precision and recall while expanding the number of annotated elements ten-fold. Extant Starship diversity is partitioned into 11 families that differ in their enrichment patterns across fungal classes. Starship cargo changes rapidly such that elements from the same family differ substantially in their functional repertoires, which are predicted to contribute to diverse biological processes such as metabolism. Many elements have convergently evolved to insert into 5S rDNA and AT-rich sequence while others integrate into random locations, revealing both specialist and generalist strategies for persistence. Our work establishes a framework for advancing mobile element biology and provides the means to investigate an emerging dimension of eukaryotic genetic diversity, that of genomes within genomes.
Collapse
Affiliation(s)
- Emile Gluck-Thaler
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Neuchâtel 2000, Switzerland
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Wisconsin Institute for Discovery, Madison, WI 53706, USA
| | - Aaron A Vogan
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, 752 36, Sweden
| |
Collapse
|
4
|
Wang C, Yu X, Wang J, Zhao Z, Wan J. Genetic and molecular mechanisms of reproductive isolation in the utilization of heterosis for breeding hybrid rice. J Genet Genomics 2024; 51:583-593. [PMID: 38325701 DOI: 10.1016/j.jgg.2024.01.007] [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: 12/13/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Heterosis, also known as hybrid vigor, is commonly observed in rice crosses. The hybridization of rice species or subspecies exhibits robust hybrid vigor, however, the direct harnessing of this vigor is hindered by reproductive isolation. Here, we review recent advances in the understanding of the molecular mechanisms governing reproductive isolation in inter-subspecific and inter-specific hybrids. This review encompasses the genetic model of reproductive isolation within and among Oryza sativa species, emphasizing the essential role of mitochondria in this process. Additionally, we delve into the molecular intricacies governing the interaction between mitochondria and autophagosomes, elucidating their significant contribution to reproductive isolation. Furthermore, our exploration extends to comprehending the evolutionary dynamics of reproductive isolation and speciation in rice. Building on these advances, we offer a forward-looking perspective on how to overcome the challenges of reproductive isolation and facilitate the utilization of heterosis in future hybrid rice breeding endeavors.
Collapse
Affiliation(s)
- Chaolong Wang
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaowen Yu
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Jian Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhigang Zhao
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China.
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| |
Collapse
|
5
|
Narunsky A, Higgs GA, Torres BM, Yu D, de Andrade GB, Kavita K, Breaker RR. The discovery of novel noncoding RNAs in 50 bacterial genomes. Nucleic Acids Res 2024; 52:5152-5165. [PMID: 38647067 PMCID: PMC11109978 DOI: 10.1093/nar/gkae248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 03/20/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024] Open
Abstract
Structured noncoding RNAs (ncRNAs) contribute to many important cellular processes involving chemical catalysis, molecular recognition and gene regulation. Few ncRNA classes are broadly distributed among organisms from all three domains of life, but the list of rarer classes that exhibit surprisingly diverse functions is growing. We previously developed a computational pipeline that enables the near-comprehensive identification of structured ncRNAs expressed from individual bacterial genomes. The regions between protein coding genes are first sorted based on length and the fraction of guanosine and cytidine nucleotides. Long, GC-rich intergenic regions are then examined for sequence and structural similarity to other bacterial genomes. Herein, we describe the implementation of this pipeline on 50 bacterial genomes from varied phyla. More than 4700 candidate intergenic regions with the desired characteristics were identified, which yielded 44 novel riboswitch candidates and numerous other putative ncRNA motifs. Although experimental validation studies have yet to be conducted, this rate of riboswitch candidate discovery is consistent with predictions that many hundreds of novel riboswitch classes remain to be discovered among the bacterial species whose genomes have already been sequenced. Thus, many thousands of additional novel ncRNA classes likely remain to be discovered in the bacterial domain of life.
Collapse
Affiliation(s)
- Aya Narunsky
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Gadareth A Higgs
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Blake M Torres
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Diane Yu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Gabriel Belem de Andrade
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Kumari Kavita
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA
| |
Collapse
|
6
|
Myint ZM, Koide Y, Takanishi W, Ikegaya T, Kwan C, Hikichi K, Tokuyama Y, Okada S, Onishi K, Ishikawa R, Fujita D, Yamagata Y, Matsumura H, Kishima Y, Kanazawa A. OlCHR, encoding a chromatin remodeling factor, is a killer causing hybrid sterility between rice species Oryza sativa and O. longistaminata. iScience 2024; 27:109761. [PMID: 38706863 PMCID: PMC11067373 DOI: 10.1016/j.isci.2024.109761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/26/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
The genetic mechanisms of reproductive isolation have been widely investigated within Asian cultivated rice (Oryza sativa); however, relevant genes between diverged species have been in sighted rather less. Herein, a gene showing selfish behavior was discovered in hybrids between the distantly related rice species Oryza longistaminata and O. sativa. The selfish allele S13l in the S13 locus impaired male fertility, discriminately eliminating pollens containing the allele S13s from O. sativa in heterozygotes (S13s/S13l). Genetic analysis revealed that a gene encoding a chromatin-remodeling factor (CHR) is involved in this phenomenon and a variety of O. sativa owns the truncated gene OsCHR745, whereas its homologue OlCHR has a complete structure in O. longistaminata. CRISPR-Cas9-mediated loss of function mutants restored fertility in hybrids. African cultivated rice, which naturally lacks the OlCHR homologue, is compatible with both S13s and S13l carriers. These results suggest that OlCHR is a Killer gene, which leads to reproductive isolation.
Collapse
Affiliation(s)
- Zin Mar Myint
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yohei Koide
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Wakana Takanishi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Tomohito Ikegaya
- National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Choi Kwan
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kiwamu Hikichi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yoshiki Tokuyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Shuhei Okada
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kazumitsu Onishi
- Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Ryo Ishikawa
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | | | | | | | - Yuji Kishima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Akira Kanazawa
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| |
Collapse
|
7
|
Arter M, Keeney S. Divergence and conservation of the meiotic recombination machinery. Nat Rev Genet 2024; 25:309-325. [PMID: 38036793 DOI: 10.1038/s41576-023-00669-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 12/02/2023]
Abstract
Sexually reproducing eukaryotes use recombination between homologous chromosomes to promote chromosome segregation during meiosis. Meiotic recombination is almost universally conserved in its broad strokes, but specific molecular details often differ considerably between taxa, and the proteins that constitute the recombination machinery show substantial sequence variability. The extent of this variation is becoming increasingly clear because of recent increases in genomic resources and advances in protein structure prediction. We discuss the tension between functional conservation and rapid evolutionary change with a focus on the proteins that are required for the formation and repair of meiotic DNA double-strand breaks. We highlight phylogenetic relationships on different time scales and propose that this remarkable evolutionary plasticity is a fundamental property of meiotic recombination that shapes our understanding of molecular mechanisms in reproductive biology.
Collapse
Affiliation(s)
- Meret Arter
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
8
|
Bureš P, Elliott TL, Veselý P, Šmarda P, Forest F, Leitch IJ, Nic Lughadha E, Soto Gomez M, Pironon S, Brown MJM, Šmerda J, Zedek F. The global distribution of angiosperm genome size is shaped by climate. THE NEW PHYTOLOGIST 2024; 242:744-759. [PMID: 38264772 DOI: 10.1111/nph.19544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
Angiosperms, which inhabit diverse environments across all continents, exhibit significant variation in genome sizes, making them an excellent model system for examining hypotheses about the global distribution of genome size. These include the previously proposed large genome constraint, mutational hazard, polyploidy-mediated, and climate-mediated hypotheses. We compiled the largest genome size dataset to date, encompassing 16 017 (> 5% of known) angiosperm species, and analyzed genome size distribution using a comprehensive geographic distribution dataset for all angiosperms. We observed that angiosperms with large range sizes generally had small genomes, supporting the large genome constraint hypothesis. Climate was shown to exert a strong influence on genome size distribution along the global latitudinal gradient, while the frequency of polyploidy and the type of growth form had negligible effects. In contrast to the unimodal patterns along the global latitudinal gradient shown by plant size traits and polyploid proportions, the increase in angiosperm genome size from the equator to 40-50°N/S is probably mediated by different (mostly climatic) mechanisms than the decrease in genome sizes observed from 40 to 50°N northward. Our analysis suggests that the global distribution of genome sizes in angiosperms is mainly shaped by climatically mediated purifying selection, genetic drift, relaxed selection, and environmental filtering.
Collapse
Affiliation(s)
- Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Tammy L Elliott
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
- Department of Biological Sciences, University of Cape Town, Cape Town, 7700, South Africa
| | - Pavel Veselý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
| | | | | | | | - Samuel Pironon
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
- UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, CB3 0DL, UK
| | | | - Jakub Šmerda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - František Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| |
Collapse
|
9
|
Roman-Reyna V, Sharma A, Toth H, Konkel Z, Omiotek N, Murthy S, Faith S, Slot J, Peduto Hand F, Goss EM, Jacobs JM. Live tracking of a plant pathogen outbreak reveals rapid and successive, multidecade plasmid reduction. mSystems 2024; 9:e0079523. [PMID: 38275768 PMCID: PMC10878067 DOI: 10.1128/msystems.00795-23] [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: 07/27/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Quickly understanding the genomic changes that lead to pathogen emergence is necessary to launch mitigation efforts and reduce harm. In this study, we tracked in real time a 2022 bacterial plant disease outbreak in U.S. geraniums (Pelargonium × hortorum) caused by Xhp2022, a novel lineage of Xanthomonas hortorum. Genomes from 31 Xhp2022 isolates from seven states showed limited chromosomal variation and all contained a single plasmid (p93). Time tree and single nucleotide polymorphism whole-genome analysis estimated that Xhp2022 emerged within the last decade. The phylogenomic analysis determined that p93 resulted from the cointegration of three plasmids (p31, p45, and p66) found sporadically across isolates from previous outbreaks. Although p93 had a 49 kb nucleotide reduction, it retained putative fitness genes, which became predominant in the 2022 outbreak. Overall, we demonstrated, through rapid whole-genome sequencing and analysis, a recent, traceable event of genome reduction for niche adaptation typically observed over millennia in obligate and fastidious pathogens.IMPORTANCEThe geranium industry, valued at $4 million annually, faces an ongoing Xanthomonas hortorum pv. pelargonii (Xhp) pathogen outbreak. To track and describe the outbreak, we compared the genome structure across historical and globally distributed isolates. Our research revealed Xhp population has not had chromosome rearrangements since 1974 and has three distinct plasmids. In 2012, we found all three plasmids in individual Xhp isolates. However, in 2022, the three plasmids co-integrated into one plasmid named p93. p93 retained putative fitness genes but lost extraneous genomic material. Our findings show that the 2022 strain group of the bacterial plant pathogen Xanthomonas hortorum underwent a plasmid reduction. We also observed several Xanthomonas species from different years, hosts, and continents have similar plasmids to p93, possibly due to shared agricultural settings. We noticed parallels between genome efficiency and reduction that we see across millennia with obligate parasites with increased niche specificity.
Collapse
Affiliation(s)
- Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Anuj Sharma
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Hannah Toth
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Zachary Konkel
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Nicolle Omiotek
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Shashanka Murthy
- Applied Microbiology Services Laboratory, The Ohio State University, Columbus, Ohio, USA
| | - Seth Faith
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Applied Microbiology Services Laboratory, The Ohio State University, Columbus, Ohio, USA
| | - Jason Slot
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
| | | | - Erica M. Goss
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Jonathan M. Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
10
|
Benson CW, Sheltra MR, Huff DR. The genome of Salmacisia buchloëana, the parasitic puppet master pulling strings of sexual phenotypic monstrosities in buffalograss. G3 (BETHESDA, MD.) 2024; 14:jkad238. [PMID: 37847611 PMCID: PMC10849329 DOI: 10.1093/g3journal/jkad238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/19/2023]
Abstract
To complete its parasitic lifecycle, Salmacisia buchloëana, a biotrophic fungus, manipulates reproductive organ development, meristem determinacy, and resource allocation in its dioecious plant host, buffalograss (Bouteloua dactyloides; Poaceae). To gain insight into S. buchloëana's ability to manipulate its host, we sequenced and assembled the 20.1 Mb genome of S. buchloëana into 22 chromosome-level pseudomolecules. Phylogenetic analysis suggests that S. buchloëana is nested within the genus Tilletia and diverged from Tilletia caries and Tilletia walkeri ∼40 MYA. We find that S. buchloëana contains a novel chromosome arm with no syntenic relationship to other publicly available Tilletia genomes, and that genes on the novel arm are upregulated upon infection, suggesting that this unique chromosomal segment may have played a critical role in S. buchloëana's evolution and host specificity. Salmacisia buchloëana has one of the largest fractions of serine peptidases (1.53% of the proteome) and one of the highest GC contents (62.3%) in all classified fungi. Analysis of codon base composition indicated that GC content is controlled more by selective constraints than directional mutation, and that S. buchloëana has a unique bias for the serine codon UCG. Finally, we identify 3 inteins within the S. buchloëana genome, 2 of which are located in a gene often used in fungal taxonomy. The genomic and transcriptomic resources generated here will aid plant pathologists and breeders by providing insight into the extracellular components contributing to sex determination in dioecious grasses.
Collapse
Affiliation(s)
- Christopher W Benson
- Department of Plant Science, Pennsylvania State University, University Park, PA 16801, USA
- Intercollegiate Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA 16801, USA
| | - Matthew R Sheltra
- Department of Plant Science, Pennsylvania State University, University Park, PA 16801, USA
- Intercollegiate Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA 16801, USA
| | - David R Huff
- Department of Plant Science, Pennsylvania State University, University Park, PA 16801, USA
| |
Collapse
|
11
|
Hammer TJ. Why do hosts malfunction without microbes? Missing benefits versus evolutionary addiction. Trends Microbiol 2024; 32:132-141. [PMID: 37652785 DOI: 10.1016/j.tim.2023.07.012] [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: 06/09/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 09/02/2023]
Abstract
Microbes are widely recognized to be vital to host health. This new consensus rests, in part, on experiments showing how hosts malfunction when microbes are removed. More and more microbial dependencies are being discovered, even in fundamental processes such as development, immunity, physiology, and behavior. But why do they exist? The default explanation is that microbes are beneficial; when hosts lose microbes, they also lose benefits. Here I call attention to evolutionary addiction, whereby a host trait evolves a need for microbes without having been improved by them. Evolutionary addiction should be considered when interpreting microbe-removal experiments, as it is a distinct and potentially common process. Further, it may have unique implications for the evolution and stability of host-microbe interactions.
Collapse
Affiliation(s)
- Tobin J Hammer
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA.
| |
Collapse
|
12
|
Mandal AK. Recent insights into crosstalk between genetic parasites and their host genome. Brief Funct Genomics 2024; 23:15-23. [PMID: 36307128 PMCID: PMC10799329 DOI: 10.1093/bfgp/elac032] [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: 08/04/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 01/21/2024] Open
Abstract
The bulk of higher order organismal genomes is comprised of transposable element (TE) copies, i.e. genetic parasites. The host-parasite relation is multi-faceted, varying across genomic region (genic versus intergenic), life-cycle stages, tissue-type and of course in health versus pathological state. The reach of functional genomics though, in investigating genotype-to-phenotype relations, has been limited when TEs are involved. The aim of this review is to highlight recent progress made in understanding how TE origin biochemical activity interacts with the central dogma stages of the host genome. Such interaction can also bring about modulation of the immune context and this could have important repercussions in disease state where immunity has a role to play. Thus, the review is to instigate ideas and action points around identifying evolutionary adaptations that the host genome and the genetic parasite have evolved and why they could be relevant.
Collapse
Affiliation(s)
- Amit K Mandal
- Corresponding author: A.K. Mandal, Nuffield Department of Surgical Sciences (NDS), University of Oxford, Old Road Campus Research building (ORCRB), Oxford OX3 7DQ, UK. Tel: +44 (0)1865 617123; Fax: +44 (0)1865 768876; E-mail:
| |
Collapse
|
13
|
Sengupta P, Dutta S, Liew FF, Dhawan V, Das B, Mottola F, Slama P, Rocco L, Roychoudhury S. Environmental and Genetic Traffic in the Journey from Sperm to Offspring. Biomolecules 2023; 13:1759. [PMID: 38136630 PMCID: PMC10741607 DOI: 10.3390/biom13121759] [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: 09/12/2023] [Revised: 11/04/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
Recent advancements in the understanding of how sperm develop into offspring have shown complex interactions between environmental influences and genetic factors. The past decade, marked by a research surge, has not only highlighted the profound impact of paternal contributions on fertility and reproductive outcomes but also revolutionized our comprehension by unveiling how parental factors sculpt traits in successive generations through mechanisms that extend beyond traditional inheritance patterns. Studies have shown that offspring are more susceptible to environmental factors, especially during critical phases of growth. While these factors are broadly detrimental to health, their effects are especially acute during these periods. Moving beyond the immutable nature of the genome, the epigenetic profile of cells emerges as a dynamic architecture. This flexibility renders it susceptible to environmental disruptions. The primary objective of this review is to shed light on the diverse processes through which environmental agents affect male reproductive capacity. Additionally, it explores the consequences of paternal environmental interactions, demonstrating how interactions can reverberate in the offspring. It encompasses direct genetic changes as well as a broad spectrum of epigenetic adaptations. By consolidating current empirically supported research, it offers an exhaustive perspective on the interwoven trajectories of the environment, genetics, and epigenetics in the elaborate transition from sperm to offspring.
Collapse
Affiliation(s)
- Pallav Sengupta
- Department of Biomedical Sciences, College of Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates
| | - Sulagna Dutta
- School of Life Sciences, Manipal Academy of Higher Education (MAHE), Dubai 345050, United Arab Emirates
| | - Fong Fong Liew
- Department of Preclinical Sciences, Faculty of Dentistry, MAHSA University, Jenjarom 42610, Selangor, Malaysia
| | - Vidhu Dhawan
- Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Biprojit Das
- Department of Life Science and Bioinformatics, Assam University, Silchar 788011, India
| | - Filomena Mottola
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy
| | - Petr Slama
- Laboratory of Animal Immunology and Biotechnology, Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic
| | - Lucia Rocco
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy
| | | |
Collapse
|
14
|
Kumam Y, Trick HN, Vara Prasad P, Jugulam M. Transformative Approaches for Sustainable Weed Management: The Power of Gene Drive and CRISPR-Cas9. Genes (Basel) 2023; 14:2176. [PMID: 38136999 PMCID: PMC10742955 DOI: 10.3390/genes14122176] [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: 10/27/2023] [Revised: 11/25/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Weeds can negatively impact crop yields and the ecosystem's health. While many weed management strategies have been developed and deployed, there is a greater need for the development of sustainable methods for employing integrated weed management. Gene drive systems can be used as one of the approaches to suppress the aggressive growth and reproductive behavior of weeds, although their efficacy is yet to be tested. Their popularity in insect pest management has increased, however, with the advent of CRISPR-Cas9 technology, which provides specificity and precision in editing the target gene. This review focuses on the different types of gene drive systems, including the use of CRISPR-Cas9-based systems and their success stories in pest management, while also exploring their possible applications in weed species. Factors that govern the success of a gene drive system in weeds, including the mode of reproduction, the availability of weed genome databases, and well-established transformation protocols are also discussed. Importantly, the risks associated with the release of weed populations with gene drive-bearing alleles into wild populations are also examined, along with the importance of addressing ecological consequences and ethical concerns.
Collapse
Affiliation(s)
- Yaiphabi Kumam
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (Y.K.); (P.V.V.P.)
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA;
| | - P.V. Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (Y.K.); (P.V.V.P.)
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (Y.K.); (P.V.V.P.)
| |
Collapse
|
15
|
Roy SW. Did the creeping vole sex chromosomes evolve through a cascade of adaptive responses to a selfish x chromosome? Bioessays 2023; 45:e2100164. [PMID: 37941456 DOI: 10.1002/bies.202100164] [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: 10/27/2021] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 11/10/2023]
Abstract
The creeping vole Microtus oregoni exhibits remarkably transformed sex chromosome biology, with complete chromosome drive/drag, X-Y fusions, sex reversed X complements, biased X inactivation, and X chromosome degradation. Beginning with a selfish X chromosome, I propose a series of adaptations leading to this system, each compensating for deleterious consequences of the preceding adaptation: (1) YY embryonic inviability favored evolution of a selfish feminizing X chromosome; (2) the consequent Y chromosome transmission disadvantage favored X-Y fusion ("XP "); (3) Xist-based silencing of Y-derived XP genes favored a second X-Y fusion ("XM "); (4) X chromosome dosage-related costs in XP XM males favored the evolution of XM loss during spermatogenesis; (5) X chromosomal dosage-related costs in XM 0 females favored the evolution of XM drive during oogenesis; and (6) degradation of the non-recombining XP favored the evolution of biased X chromosome inactivation. I discuss recurrent rodent sex chromosome transformation, and selfish genes as a constructive force in evolution.
Collapse
|
16
|
Vontzou N, Pei Y, Mueller JC, Reifová R, Ruiz-Ruano FJ, Schlebusch SA, Suh A. Songbird germline-restricted chromosome as a potential arena of genetic conflicts. Curr Opin Genet Dev 2023; 83:102113. [PMID: 37734346 DOI: 10.1016/j.gde.2023.102113] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/03/2023] [Accepted: 08/20/2023] [Indexed: 09/23/2023]
Abstract
Genetic conflicts can arise between components of the genome with different inheritance strategies. The germline-restricted chromosome (GRC) of songbirds shows unusual mitotic and meiotic transmission compared with the rest of the genome. It is excluded from somatic cells and maintained only in the germline. It is usually present in one copy in the male germline and eliminated during spermatogenesis, while in the female germline, it usually occurs in two copies and behaves as a regular chromosome. Here, we review what is known about the GRC's evolutionary history, genetic content, and expression and discuss how it may be involved in different types of genetic conflicts. Finally, we interrogate the potential role of the GRC in songbird germline development, highlighting several unsolved mysteries.
Collapse
Affiliation(s)
- Niki Vontzou
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113 Bonn, Germany; School of Biological Sciences, University of East Anglia, Norwich, UK.
| | - Yifan Pei
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113 Bonn, Germany; Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121 Bonn, Germany; Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Jakob C Mueller
- Department of Ornithology, Max Planck Institute for Biological Intelligence, 82319 Seewiesen, Germany
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Francisco J Ruiz-Ruano
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113 Bonn, Germany; Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121 Bonn, Germany. https://twitter.com/@fjruizruano
| | - Stephen A Schlebusch
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Alexander Suh
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113 Bonn, Germany; Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121 Bonn, Germany; Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
17
|
Ariza-Mateos A, Briones C, Perales C, Bayo-Jiménez MT, Domingo E, Gómez J. Viruses as archaeological tools for uncovering ancient molecular relationships. Ann N Y Acad Sci 2023; 1529:3-13. [PMID: 37801367 DOI: 10.1111/nyas.15071] [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: 10/08/2023]
Abstract
The entry of a virus into the host cell always implies the alteration of certain intracellular molecular relationships, some of which may involve the recovery of ancient cellular activities. In this sense, viruses are archaeological tools for identifying unexpressed activities in noninfected cells. Among these, activities that hinder virus propagation may represent cellular defense mechanisms, for example, activities that mutagenize the viral genome such as ADAR-1 or APOBEC activities. Instead, those that facilitate virus propagation can be interpreted as the result of viral adaptation to-or mimicking-cellular structures, enabling the virus to perform anthropomorphic activities, including hijacking, manipulating, and reorganizing cellular factors for their own benefit. The alternative we consider here is that some of these second set of cellular activities were already in the uninfected cell but silenced, under the negative control of the cell or lineage, and that they represent a necessary precondition for viral infection. For example, specifically loading an amino acid at the 3'-end of the mRNA of some plant viruses by aminoacyl-tRNA synthetases has proved essential for virus infection despite this reaction not occurring with cellular mRNAs. Other activities of this type are discussed here, together with the biological context in which they acquire a coherent meaning, that is, genetic latency and molecular conflict.
Collapse
Affiliation(s)
- Ascensión Ariza-Mateos
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Granada, Spain
| | - Carlos Briones
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Celia Perales
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CSIC), Madrid, Spain
| | - María Teresa Bayo-Jiménez
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Granada, Spain
| | - Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Jordi Gómez
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Granada, Spain
| |
Collapse
|
18
|
Long L, Xu W, Valencia F, Paaby AB, McGrath PT. A toxin-antidote selfish element increases fitness of its host. eLife 2023; 12:e81640. [PMID: 37874324 PMCID: PMC10629817 DOI: 10.7554/elife.81640] [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: 07/05/2022] [Accepted: 10/23/2023] [Indexed: 10/25/2023] Open
Abstract
Selfish genetic elements can promote their transmission at the expense of individual survival, creating conflict between the element and the rest of the genome. Recently, a large number of toxin-antidote (TA) post-segregation distorters have been identified in non-obligate outcrossing nematodes. Their origin and the evolutionary forces that keep them at intermediate population frequencies are poorly understood. Here, we study a TA element in Caenorhabditis elegans called zeel-1;peel-1. Two major haplotypes of this locus, with and without the selfish element, segregate in C. elegans. We evaluate the fitness consequences of the zeel-1;peel-1 element outside of its role in gene drive in non-outcrossing animals and demonstrate that loss of the toxin peel-1 decreased fitness of hermaphrodites and resulted in reductions in fecundity and body size. These findings suggest a biological role for peel-1 beyond toxin lethality. This work demonstrates that a TA element can provide a fitness benefit to its hosts either during their initial evolution or by being co-opted by the animals following their selfish spread. These findings guide our understanding on how TA elements can remain in a population where gene drive is minimized, helping resolve the mystery of prevalent TA elements in selfing animals.
Collapse
Affiliation(s)
- Lijiang Long
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Wen Xu
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Francisco Valencia
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Annalise B Paaby
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Patrick T McGrath
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| |
Collapse
|
19
|
Bourke AFG. Conflict and conflict resolution in the major transitions. Proc Biol Sci 2023; 290:20231420. [PMID: 37817595 PMCID: PMC10565403 DOI: 10.1098/rspb.2023.1420] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/14/2023] [Indexed: 10/12/2023] Open
Abstract
Conflict and conflict resolution have been argued to be fundamental to the major transitions in evolution. These were key events in life's history in which previously independently living individuals cooperatively formed a higher-level individual, such as a multicellular organism or eusocial colony. Conflict has its central role because, to proceed stably, the evolution of individuality in each major transition required within-individual conflict to be held in check. This review revisits the role of conflict and conflict resolution in the major transitions, addressing recent work arguing for a minor role. Inclusive fitness logic suggests that differences between the kin structures of clones and sexual families support the absence of conflict at the origin of multicellularity but, by contrast, suggest that key conflicts existed at the origin of eusociality. A principal example is conflict over replacing the founding queen (queen replacement). Following the origin of each transition, conflict remained important, because within-individual conflict potentially disrupts the attainment of maximal individuality (organismality) in the system. The conclusion is that conflict remains central to understanding the major transitions, essentially because conflict arises from differences in inclusive fitness optima while conflict resolution can help the system attain a high degree of coincidence of inclusive fitness interests.
Collapse
Affiliation(s)
- Andrew F. G. Bourke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| |
Collapse
|
20
|
Patten MM, Schenkel MA, Ågren JA. Adaptation in the face of internal conflict: the paradox of the organism revisited. Biol Rev Camb Philos Soc 2023; 98:1796-1811. [PMID: 37203364 DOI: 10.1111/brv.12983] [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: 12/08/2022] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/20/2023]
Abstract
The paradox of the organism refers to the observation that organisms appear to function as coherent purposeful entities, despite the potential for within-organismal components like selfish genetic elements and cancer cells to erode them from within. While it is commonly accepted that organisms may pursue fitness maximisation and can be thought to hold particular agendas, there is a growing recognition that genes and cells do so as well. This can lead to evolutionary conflicts between an organism and the parts that reside within it. Here, we revisit the paradox of the organism. We first outline its conception and relationship to debates about adaptation in evolutionary biology. Second, we review the ways selfish elements may exploit organisms, and the extent to which this threatens organismal integrity. To this end, we introduce a novel classification scheme that distinguishes between selfish elements that seek to distort transmission versus those that seek to distort phenotypic traits. Our classification scheme also highlights how some selfish elements elude a multi-level selection decomposition using the Price equation. Third, we discuss how the organism can retain its status as the primary fitness-maximising agent in the face of selfish elements. The success of selfish elements is often constrained by their strategy and further limited by a combination of fitness alignment and enforcement mechanisms controlled by the organism. Finally, we argue for the need for quantitative measures of both internal conflicts and organismality.
Collapse
Affiliation(s)
- Manus M Patten
- Department of Biology, Georgetown University, 37th and O St. NW, Washington, DC, 20057, USA
| | - Martijn A Schenkel
- Department of Biology, Georgetown University, 37th and O St. NW, Washington, DC, 20057, USA
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - J Arvid Ågren
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden
- Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
| |
Collapse
|
21
|
Liu HW, Roisné-Hamelin F, Gruber S. SMC-based immunity against extrachromosomal DNA elements. Biochem Soc Trans 2023; 51:1571-1583. [PMID: 37584323 PMCID: PMC10586767 DOI: 10.1042/bst20221395] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/17/2023]
Abstract
SMC and SMC-like complexes promote chromosome folding and genome maintenance in all domains of life. Recently, they were also recognized as factors in cellular immunity against foreign DNA. In bacteria and archaea, Wadjet and Lamassu are anti-plasmid/phage defence systems, while Smc5/6 and Rad50 complexes play a role in anti-viral immunity in humans. This raises an intriguing paradox - how can the same, or closely related, complexes on one hand secure the integrity and maintenance of chromosomal DNA, while on the other recognize and restrict extrachromosomal DNA? In this minireview, we will briefly describe the latest understanding of each of these complexes in immunity including speculations on how principles of SMC(-like) function may explain how the systems recognize linear or circular forms of invading DNA.
Collapse
Affiliation(s)
- Hon Wing Liu
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland
| | - Florian Roisné-Hamelin
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland
| |
Collapse
|
22
|
Reinhardt JA, Baker RH, Zimin AV, Ladias C, Paczolt KA, Werren JH, Hayashi CY, Wilkinson GS. Impacts of Sex Ratio Meiotic Drive on Genome Structure and Function in a Stalk-Eyed Fly. Genome Biol Evol 2023; 15:evad118. [PMID: 37364298 PMCID: PMC10319772 DOI: 10.1093/gbe/evad118] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 06/02/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
Stalk-eyed flies in the genus Teleopsis carry selfish genetic elements that induce sex ratio (SR) meiotic drive and impact the fitness of male and female carriers. Here, we assemble and describe a chromosome-level genome assembly of the stalk-eyed fly, Teleopsis dalmanni, to elucidate patterns of divergence associated with SR. The genome contains tens of thousands of transposable element (TE) insertions and hundreds of transcriptionally and insertionally active TE families. By resequencing pools of SR and ST males using short and long reads, we find widespread differentiation and divergence between XSR and XST associated with multiple nested inversions involving most of the SR haplotype. Examination of genomic coverage and gene expression data revealed seven X-linked genes with elevated expression and coverage in SR males. The most extreme and likely drive candidate involves an XSR-specific expansion of an array of partial copies of JASPer, a gene necessary for maintenance of euchromatin and associated with regulation of TE expression. In addition, we find evidence for rapid protein evolution between XSR and XST for testis expressed and novel genes, that is, either recent duplicates or lacking a Dipteran ortholog, including an X-linked duplicate of maelstrom, which is also involved in TE silencing. Overall, the evidence suggests that this ancient XSR polymorphism has had a variety of impacts on repetitive DNA and its regulation in this species.
Collapse
Affiliation(s)
| | - Richard H Baker
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Chloe Ladias
- Biology Department, State University of New York at Geneseo, Geneseo, New York, USA
| | - Kimberly A Paczolt
- Department of Biology, University of Maryland, College Park, Maryland, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, New York, USA
| | - Cheryl Y Hayashi
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Gerald S Wilkinson
- Department of Biology, University of Maryland, College Park, Maryland, USA
| |
Collapse
|
23
|
Rathnapala JMSN, Ragab W, Kawato S, Furukawa M, Nozaki R, Kondo H, Hirono I. Genomic characterization and identification of virulence-related genes in Vibrio nigripulchritudo isolated from white leg shrimp Penaeus vannamei. JOURNAL OF FISH DISEASES 2023; 46:779-790. [PMID: 36989191 DOI: 10.1111/jfd.13786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 06/07/2023]
Abstract
Vibrio nigripulchritudo causes vibriosis in penaeid shrimps. Here, we used Illumina and Nanopore sequencing technologies to sequence the genomes of three of its strains (TUMSAT-V. nig1, TUMSAT-V. nig2, and TUMSAT-V. nig3) to explore opportunities for disease management. Putative virulence factors and mobile genetic elements were detected while evaluating the phylogenetic relationship of each isolated strain. The genomes consisted of two circular chromosomes (I and II) plus one or two plasmids. The size of chromosome I ranged from 4.02 to 4.07 Mb with an average GC content of 46%, while the number of predicted CDSs ranged from 3563 to 3644. The size of chromosome II ranged from 2.16 to 2.18 Mb, with an average GC content of 45.5%, and the number of predicted CDSs ranged from 1970 to 1987. Numerous virulence genes were identified related to adherence, antiphagocytosis, chemotaxis, motility, iron uptake, quorum sensing, secretion systems, and toxins in all three genomes. Higher numbers of prophages and genomic islands found in TUMSAT-V. nig1 suggest that the strain has experienced numerous horizontal gene transfer events. The presence of antimicrobial resistance genes suggests that the strains have multidrug resistance. Comparative genomic analysis showed that all three strains belonged to the same clade.
Collapse
Affiliation(s)
- Jayasundara Mudiyanselage Sajani Nisansala Rathnapala
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Tokyo, Japan
- Department of Fisheries and Aquaculture, Faculty of Fisheries and Marine Sciences and Technology, University of Ruhuna, Matara, Sri Lanka
| | - Wafaa Ragab
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Tokyo, Japan
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Satoshi Kawato
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Miho Furukawa
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Reiko Nozaki
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Tokyo, Japan
| |
Collapse
|
24
|
Vedanayagam J, Herbette M, Mudgett H, Lin CJ, Lai CM, McDonough-Goldstein C, Dorus S, Loppin B, Meiklejohn C, Dubruille R, Lai EC. Essential and recurrent roles for hairpin RNAs in silencing de novo sex chromosome conflict in Drosophila simulans. PLoS Biol 2023; 21:e3002136. [PMID: 37289846 DOI: 10.1371/journal.pbio.3002136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 04/21/2023] [Indexed: 06/10/2023] Open
Abstract
Meiotic drive loci distort the normally equal segregation of alleles, which benefits their own transmission even in the face of severe fitness costs to their host organism. However, relatively little is known about the molecular identity of meiotic drivers, their strategies of action, and mechanisms that can suppress their activity. Here, we present data from the fruitfly Drosophila simulans that address these questions. We show that a family of de novo, protamine-derived X-linked selfish genes (the Dox gene family) is silenced by a pair of newly emerged hairpin RNA (hpRNA) small interfering RNA (siRNA)-class loci, Nmy and Tmy. In the w[XD1] genetic background, knockout of nmy derepresses Dox and MDox in testes and depletes male progeny, whereas knockout of tmy causes misexpression of PDox genes and renders males sterile. Importantly, genetic interactions between nmy and tmy mutant alleles reveal that Tmy also specifically maintains male progeny for normal sex ratio. We show the Dox loci are functionally polymorphic within D. simulans, such that both nmy-associated sex ratio bias and tmy-associated sterility can be rescued by wild-type X chromosomes bearing natural deletions in different Dox family genes. Finally, using tagged transgenes of Dox and PDox2, we provide the first experimental evidence Dox family genes encode proteins that are strongly derepressed in cognate hpRNA mutants. Altogether, these studies support a model in which protamine-derived drivers and hpRNA suppressors drive repeated cycles of sex chromosome conflict and resolution that shape genome evolution and the genetic control of male gametogenesis.
Collapse
Affiliation(s)
- Jeffrey Vedanayagam
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
| | - Marion Herbette
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon CNRS UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Holly Mudgett
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Ching-Jung Lin
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
- Weill Graduate School of Medical Sciences, Weill Cornell Medical College, New York, New York, United States of America
| | - Chun-Ming Lai
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
| | | | - Stephen Dorus
- Center for Reproductive Evolution, Syracuse University, Syracuse, New York, United States of America
| | - Benjamin Loppin
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon CNRS UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Colin Meiklejohn
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Raphaëlle Dubruille
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon CNRS UMR5239, Université Claude Bernard Lyon 1, Lyon, France
| | - Eric C Lai
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
- Weill Graduate School of Medical Sciences, Weill Cornell Medical College, New York, New York, United States of America
| |
Collapse
|
25
|
Hanlon SL, Hawley RS. B chromosomes reveal a female meiotic drive suppression system in Drosophila melanogaster. Curr Biol 2023:S0960-9822(23)00476-1. [PMID: 37146608 DOI: 10.1016/j.cub.2023.04.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 03/08/2023] [Accepted: 04/13/2023] [Indexed: 05/07/2023]
Abstract
Selfish genetic elements use a myriad of mechanisms to drive their inheritance and ensure their survival into the next generation, often at a fitness cost to its host.1,2 Although the catalog of selfish genetic elements is rapidly growing, our understanding of host drive suppression systems that counteract self-seeking behavior is lacking. Here, we demonstrate that the biased transmission of the non-essential, non-driving B chromosomes in Drosophila melanogaster can be achieved in a specific genetic background. Combining a null mutant of matrimony, a gene that encodes a female-specific meiotic regulator of Polo kinase,3,4 with the TM3 balancer chromosome creates a driving genotype that is permissive for the biased transmission of the B chromosomes. This drive is female-specific, and both genetic components are necessary, but not individually sufficient, for permitting a strong drive of the B chromosomes. Examination of metaphase I oocytes reveals that B chromosome localization within the DNA mass is mostly abnormal when drive is the strongest, indicating a failure of the mechanism(s) responsible for the proper distribution of B chromosomes. We propose that some proteins important for proper chromosome segregation during meiosis, like Matrimony, may have an essential role as part of a meiotic drive suppression system that modulates chromosome segregation to prevent genetic elements from exploiting the inherent asymmetry of female meiosis.
Collapse
Affiliation(s)
- Stacey L Hanlon
- Genetics and Genomics, Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
| | - R Scott Hawley
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| |
Collapse
|
26
|
Cutter AD. Synthetic gene drives as an anthropogenic evolutionary force. Trends Genet 2023; 39:347-357. [PMID: 36997427 DOI: 10.1016/j.tig.2023.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 03/30/2023]
Abstract
Genetic drive represents a fundamental evolutionary force that can exact profound change to the genetic composition of populations by biasing allele transmission. Herein I propose that the use of synthetic homing gene drives, the human-mediated analog of endogenous genetic drives, warrants the designation of 'genetic welding' as an anthropogenic evolutionary force. Conceptually, this distinction parallels that of artificial and natural selection. Genetic welding is capable of imposing complex and rapid heritable phenotypic change on entire populations, whether motivated by biodiversity conservation or public health. Unanticipated possible long-term evolutionary outcomes, however, demand further investigation and bioethical consideration. The emerging importance of genetic welding also compels our explicit recognition of genetic drive as an addition to the other four fundamental forces of evolution.
Collapse
|
27
|
Li F, Wang J, Jiang Y, Guo Y, Liu N, Xiao S, Yao L, Li J, Zhuo C, He N, Liu B, Zhuo C. Adaptive Evolution Compensated for the Plasmid Fitness Costs Brought by Specific Genetic Conflicts. Pathogens 2023; 12:pathogens12010137. [PMID: 36678485 PMCID: PMC9861728 DOI: 10.3390/pathogens12010137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/30/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
New Delhi metallo-β-lactamase (NDM)-carrying IncX3 plasmids is important in the transmission of carbapenem resistance in Escherichia coli. Fitness costs related to plasmid carriage are expected to limit gene exchange; however, the causes of these fitness costs are poorly understood. Compensatory mutations are believed to ameliorate plasmid fitness costs and enable the plasmid's wide spread, suggesting that such costs are caused by specific plasmid-host genetic conflicts. By combining conjugation tests and experimental evolution with comparative genetic analysis, we showed here that the fitness costs related to ndm/IncX3 plasmids in E. coli C600 are caused by co-mutations of multiple host chromosomal genes related to sugar metabolism and cell membrane function. Adaptive evolution revealed that mutations in genes associated with oxidative stress, nucleotide and short-chain fatty acid metabolism, and cell membranes ameliorated the costs associated with plasmid carriage. Specific genetic conflicts associated with the ndm/IncX3 plasmid in E. coli C600 involve metabolism and cell-membrane-related genes, which could be ameliorated by compensatory mutations. Collectively, our findings could explain the wide spread of IncX3 plasmids in bacterial genomes, despite their potential cost.
Collapse
Affiliation(s)
- Feifeng Li
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Jiong Wang
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Ying Jiang
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Yingyi Guo
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Ningjing Liu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Shunian Xiao
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Likang Yao
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Jiahui Li
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Chuyue Zhuo
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Nanhao He
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Baomo Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen Univesity, Guangzhou 510030, China
- Correspondence: (B.L.); (C.Z.)
| | - Chao Zhuo
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
- Correspondence: (B.L.); (C.Z.)
| |
Collapse
|
28
|
Agarie A, Miyaguni Y, Sugio K, Tsuji K, Kobayashi K. Male’s influence on the primary sex ratio bias in Ryukyu drywood termite. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.1081043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Selfish genetic elements (SGEs) increase their transmission efficiency relative to the rest of the individual genome, which is often deleterious to individual fitness. Theoretical studies have suggested that intragenomic conflict over the sex ratio distortion between SGEs and the rest of the genome should lead to the evolution of sex-determining systems. However, in insects, there are relatively few studies other than those on Dipterans, which makes it difficult to understand the role of SGEs in the evolution of insect sex determination. This is partially due to the difficulties in observing SGEs under field conditions. The effect of SGEs is often masked by the counter-evolution of the resistance genes. Interpopulation cross-breeding experiments are effective to detect the SGEs and their resistance genes. If these populations have different SGEs and resistance genes, cross-breeding experiments reveal their existence by collapsing the evolutionary antagonistic state. The Ryukyu drywood termites Neotermes sugioi, distributed in the Ryukyu Islands, show male-biased sex ratios in pseudergates, nymphs, alates and soldiers both in Okinawa and Ishigaki Islands, but different degrees of bias have been reported between the islands. Male-specific microsatellite alleles have been reported in this species, which allowed us to identify the sex of the eggs and young larvae. In this study, we used the microsatellite locus with male-specific alleles to investigate the primary sex ratio of field colonies on Okinawa and Ishigaki islands and the sex ratio of offspring obtained through cross-breeding experiments between the islands. The primary sex ratios of field colonies were male-biased in Okinawa but not in Ishigaki. Cross-breeding experiments showed that Okinawa males tend to have a male-biased sex ratio in their offspring, but Ishigaki males do not. This result is consistent with the hypothesis that the male bias in this species is caused by SGEs, even though termites are phylogenetically distant from Diptera. Accumulation of knowledge on genetic conflicts in a wide range of taxa might be an important step toward elucidating the mechanisms of diversification of sex determination systems in insects.
Collapse
|
29
|
Durand S, Lheraud B, Giraud I, Bech N, Grandjean F, Rigaud T, Peccoud J, Cordaux R. Heterogeneous distribution of sex ratio distorters in natural populations of the isopod Armadillidium vulgare. Biol Lett 2023; 19:20220457. [PMID: 36628964 PMCID: PMC9832340 DOI: 10.1098/rsbl.2022.0457] [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: 10/03/2022] [Accepted: 12/15/2022] [Indexed: 01/12/2023] Open
Abstract
In the isopod Armadillidium vulgare, many females produce progenies with female-biased sex ratios, owing to two feminizing sex ratio distorters (SRD): Wolbachia endosymbionts and the f element. We investigated the distribution and population dynamics of these SRD and mitochondrial DNA variation in 16 populations from Europe and Japan. Confirming and extending results from the 1990s, we found that the SRD are present at variable frequencies in populations and that the f element is overall more frequent than Wolbachia. The two SRD never co-occur at high frequency in any population, suggesting an apparent mutual exclusion. We also detected Wolbachia or the f element in some males, which probably reflects insufficient titer to induce feminization or presence of masculinizing alleles. Our results are consistent with a single integration event of a Wolbachia genome in the A. vulgare genome at the origin of the f element, which contradicts an earlier hypothesis of frequent losses and gains. We identified strong linkage between Wolbachia strains and mitochondrial haplotypes, but no association between the f element and mitochondrial background. Our results open new perspectives on SRD evolutionary dynamics in A. vulgare, the evolution of genetic conflicts and their impact on the variability of sex determination systems.
Collapse
Affiliation(s)
- Sylvine Durand
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, UMR CNRS 7267, Bât. B31, 3 Rue Jacques Fort, TSA 51106, 86073 Poitiers Cedex 9, France
| | - Baptiste Lheraud
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, UMR CNRS 7267, Bât. B31, 3 Rue Jacques Fort, TSA 51106, 86073 Poitiers Cedex 9, France
| | - Isabelle Giraud
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, UMR CNRS 7267, Bât. B31, 3 Rue Jacques Fort, TSA 51106, 86073 Poitiers Cedex 9, France
| | - Nicolas Bech
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, UMR CNRS 7267, Bât. B31, 3 Rue Jacques Fort, TSA 51106, 86073 Poitiers Cedex 9, France
| | - Frédéric Grandjean
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, UMR CNRS 7267, Bât. B31, 3 Rue Jacques Fort, TSA 51106, 86073 Poitiers Cedex 9, France
| | - Thierry Rigaud
- Laboratoire Biogéosciences, Université Bourgogne Franche-Comté, UMR CNRS 6282, 6 Boulevard Gabriel, 21000 Dijon, France
| | - Jean Peccoud
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, UMR CNRS 7267, Bât. B31, 3 Rue Jacques Fort, TSA 51106, 86073 Poitiers Cedex 9, France
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, UMR CNRS 7267, Bât. B31, 3 Rue Jacques Fort, TSA 51106, 86073 Poitiers Cedex 9, France
| |
Collapse
|
30
|
Ågren JA, Patten MM. Genetic conflicts and the case for licensed anthropomorphizing. Behav Ecol Sociobiol 2022; 76:166. [DOI: 10.1007/s00265-022-03267-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 12/02/2022]
Abstract
Abstract
The use of intentional language in biology is controversial. It has been commonly applied by researchers in behavioral ecology, who have not shied away from employing agential thinking or even anthropomorphisms, but has been rarer among researchers from more mechanistic corners of the discipline, such as population genetics. One research area where these traditions come into contact—and occasionally clash—is the study of genetic conflicts, and its history offers a good window to the debate over the use of intentional language in biology. We review this debate, paying particular attention to how this interaction has played out in work on genomic imprinting and sex chromosomes. In light of this, we advocate for a synthesis of the two approaches, a form of licensed anthropomorphizing. Here, agential thinking’s creative potential and its ability to identify the fulcrum of evolutionary pressure are combined with the rigidity of formal mathematical modeling.
Collapse
|
31
|
Urban JA, Ranjan R, Chen X. Asymmetric Histone Inheritance: Establishment, Recognition, and Execution. Annu Rev Genet 2022; 56:113-143. [PMID: 35905975 PMCID: PMC10054593 DOI: 10.1146/annurev-genet-072920-125226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The discovery of biased histone inheritance in asymmetrically dividing Drosophila melanogaster male germline stem cells demonstrates one means to produce two distinct daughter cells with identical genetic material. This inspired further studies in different systems, which revealed that this phenomenon may be a widespread mechanism to introduce cellular diversity. While the extent of asymmetric histone inheritance could vary among systems, this phenomenon is proposed to occur in three steps: first, establishment of histone asymmetry between sister chromatids during DNA replication; second, recognition of sister chromatids carrying asymmetric histone information during mitosis; and third, execution of this asymmetry in the resulting daughter cells. By compiling the current knowledge from diverse eukaryotic systems, this review comprehensively details and compares known chromatin factors, mitotic machinery components, and cell cycle regulators that may contribute to each of these three steps. Also discussed are potential mechanisms that introduce and regulate variable histone inheritance modes and how these different modes may contribute to cell fate decisions in multicellular organisms.
Collapse
Affiliation(s)
- Jennifer A Urban
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA;
| | - Rajesh Ranjan
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA; .,Howard Hughes Medical Institute, The Johns Hopkins University, Baltimore, Maryland, USA; ,
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA; .,Howard Hughes Medical Institute, The Johns Hopkins University, Baltimore, Maryland, USA; ,
| |
Collapse
|
32
|
McInerney JO. Prokaryotic Pangenomes Act as Evolving Ecosystems. Mol Biol Evol 2022; 40:6775222. [PMID: 36288801 PMCID: PMC9851318 DOI: 10.1093/molbev/msac232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/11/2022] [Accepted: 10/20/2022] [Indexed: 01/24/2023] Open
Abstract
Understanding adaptation to the local environment is a central tenet and a major focus of evolutionary biology. But this is only part of the adaptionist story. In addition to the external environment, one of the main drivers of genome composition is genetic background. In this perspective, I argue that there is a growing body of evidence that intra-genomic selective pressures play a significant part in the composition of prokaryotic genomes and play a significant role in the origin, maintenance and structuring of prokaryotic pangenomes.
Collapse
|
33
|
Haudiquet M, de Sousa JM, Touchon M, Rocha EPC. Selfish, promiscuous and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210234. [PMID: 35989606 PMCID: PMC9393566 DOI: 10.1098/rstb.2021.0234] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Horizontal gene transfer (HGT) drives microbial adaptation but is often under the control of mobile genetic elements (MGEs) whose interests are not necessarily aligned with those of their hosts. In general, transfer is costly to the donor cell while potentially beneficial to the recipients. The diversity and plasticity of cell–MGEs interactions, and those among MGEs, result in complex evolutionary processes where the source, or even the existence of selection for maintaining a function in the genome, is often unclear. For example, MGE-driven HGT depends on cell envelope structures and defense systems, but many of these are transferred by MGEs themselves. MGEs can spur periods of intense gene transfer by increasing their own rates of horizontal transmission upon communicating, eavesdropping, or sensing the environment and the host physiology. This may result in high-frequency transfer of host genes unrelated to the MGE. Here, we review how MGEs drive HGT and how their transfer mechanisms, selective pressures and genomic traits affect gene flow, and therefore adaptation, in microbial populations. The encoding of many adaptive niche-defining microbial traits in MGEs means that intragenomic conflicts and alliances between cells and their MGEs are key to microbial functional diversification. This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
Collapse
Affiliation(s)
- Matthieu Haudiquet
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
| | - Jorge Moura de Sousa
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
| | - Marie Touchon
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
| |
Collapse
|
34
|
Magnon V, Corbara B. When the “satisficing” is the new “fittest”: how a proscriptive definition of adaptation can change our view of cognition and culture. Naturwissenschaften 2022; 109:42. [PMID: 35960360 PMCID: PMC9372954 DOI: 10.1007/s00114-022-01814-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Valentin Magnon
- University Clermont Auvergne, CNRS, LaPSCo, Clermont-Ferrand, France.
| | - Bruno Corbara
- University Clermont Auvergne, CNRS, LMGE, Clermont-Ferrand, France
| |
Collapse
|
35
|
Vihinen M. Individual Genetic Heterogeneity. Genes (Basel) 2022; 13:genes13091626. [PMID: 36140794 PMCID: PMC9498725 DOI: 10.3390/genes13091626] [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: 08/12/2022] [Revised: 08/25/2022] [Accepted: 09/08/2022] [Indexed: 11/28/2022] Open
Abstract
Genetic variation has been widely covered in literature, however, not from the perspective of an individual in any species. Here, a synthesis of genetic concepts and variations relevant for individual genetic constitution is provided. All the different levels of genetic information and variation are covered, ranging from whether an organism is unmixed or hybrid, has variations in genome, chromosomes, and more locally in DNA regions, to epigenetic variants or alterations in selfish genetic elements. Genetic constitution and heterogeneity of microbiota are highly relevant for health and wellbeing of an individual. Mutation rates vary widely for variation types, e.g., due to the sequence context. Genetic information guides numerous aspects in organisms. Types of inheritance, whether Mendelian or non-Mendelian, zygosity, sexual reproduction, and sex determination are covered. Functions of DNA and functional effects of variations are introduced, along with mechanism that reduce and modulate functional effects, including TARAR countermeasures and intraindividual genetic conflict. TARAR countermeasures for tolerance, avoidance, repair, attenuation, and resistance are essential for life, integrity of genetic information, and gene expression. The genetic composition, effects of variations, and their expression are considered also in diseases and personalized medicine. The text synthesizes knowledge and insight on individual genetic heterogeneity and organizes and systematizes the central concepts.
Collapse
Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, BMC B13, Lund University, SE-22184 Lund, Sweden
| |
Collapse
|
36
|
Liu Z, Xing L, Huang W, Liu B, Wan F, Raffa KF, Hofstetter RW, Qian W, Sun J. Chromosome-level genome assembly and population genomic analyses provide insights into adaptive evolution of the red turpentine beetle, Dendroctonus valens. BMC Biol 2022; 20:190. [PMID: 36002826 PMCID: PMC9400205 DOI: 10.1186/s12915-022-01388-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 08/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biological invasions are responsible for substantial environmental and economic losses. The red turpentine beetle (RTB), Dendroctonus valens LeConte, is an important invasive bark beetle from North America that has caused substantial tree mortality in China. The lack of a high-quality reference genome seriously limits deciphering the extent to which genetic adaptions resulted in a secondary pest becoming so destructive in its invaded area. RESULTS Here, we present a 322.41 Mb chromosome-scale reference genome of RTB, of which 98% of assembled sequences are anchored onto fourteen linkage groups including the X chromosome with a N50 size of 24.36 Mb, which is significantly greater than other Coleoptera species. Repetitive sequences make up 45.22% of the genome, which is higher than four other Coleoptera species, i.e., Mountain pine beetle Dendroctonus ponderosae, red flour beetle Tribolium castaneum, blister beetle Hycleus cichorii, and Colorado potato beetle Leptinotarsa decemlineata. We identify rapidly expanded gene families and positively selected genes in RTB, which may be responsible for its rapid environmental adaptation. Population genetic structure of RTB was revealed by genome resequencing of geographic populations in native and invaded regions, suggesting substantial divergence of the North American population and illustrates the possible invasion and spread route in China. Selective sweep analysis highlighted the enhanced ability of Chinese populations in environmental adaptation. CONCLUSIONS Overall, our high-quality reference genome represents an important resource for genomics study of invasive bark beetles, which will facilitate the functional study and decipher mechanism underlying invasion success of RTB by integrating the Pinus tabuliformis genome.
Collapse
Affiliation(s)
- Zhudong Liu
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China.,State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 1000101, China
| | - Longsheng Xing
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China.,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | | | - Bo Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Fanghao Wan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Kenneth F Raffa
- Department of Entomology, University of Wisconsin, Madison, WI, 53706, USA
| | | | - Wanqiang Qian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Jianghua Sun
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China. .,State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 1000101, China.
| |
Collapse
|
37
|
Ma WJ, Knoles EM, Patch KB, Shoaib MM, Unckless RL. Hoisted with his own petard: How sex-ratio meiotic drive in Drosophila affinis creates resistance alleles that limit its spread. J Evol Biol 2022; 35:1765-1776. [PMID: 35997297 DOI: 10.1111/jeb.14077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/20/2022] [Accepted: 07/14/2022] [Indexed: 11/28/2022]
Abstract
Meiotic drivers are selfish genetic elements that tinker with gametogenesis to bias their own transmission into the next generation of offspring. Such tinkering can have significant consequences on gametogenesis and end up hampering the spread of the driver. In Drosophila affinis, sex-ratio meiotic drive is caused by an X-linked complex that, when in males with a susceptible Y chromosome, results in broods that are typically more than 95% female. Interestingly, D. affinis males lacking a Y chromosome (XO) are fertile and males with the meiotic drive X and no Y produce only sons-effectively reversing the sex-ratio effect. Here, we show that meiotic drive dramatically increases the rate of nondisjunction of the Y chromosome (at least 750X), meaning that the driver is creating resistant alleles through the process of driving. We then model how the O might influence the spread, dynamics and equilibrium of the sex-ratio X chromosome. We find that the O can prevent the spread or reduce the equilibrium frequency of the sex-ratio X chromosome, and it can even lead to oscillations in frequency. Finally, with reasonable parameters, the O is unlikely to lead to the loss of the Y chromosome, but we discuss how it might lead to sex-chromosome turnover indirectly.
Collapse
Affiliation(s)
- Wen-Juan Ma
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Emma M Knoles
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Kistie B Patch
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Murtaza M Shoaib
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Robert L Unckless
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| |
Collapse
|
38
|
Bourrat P, Doulcier G, Rose CJ, Rainey PB, Hammerschmidt K. Tradeoff breaking as model of evolutionary transitions in individuality and the limits of the fitness-decoupling metaphor. eLife 2022; 11:73715. [PMID: 35975712 PMCID: PMC9470156 DOI: 10.7554/elife.73715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 06/28/2022] [Indexed: 11/22/2022] Open
Abstract
Evolutionary transitions in individuality (ETIs) involve the formation of Darwinian collectives from Darwinian particles. The transition from cells to multicellular life is a prime example. During an ETI, collectives become units of selection in their own right. However, the underlying processes are poorly understood. One observation used to identify the completion of an ETI is an increase in collective-level performance accompanied by a decrease in particle-level performance, for example measured by growth rate. This seemingly counterintuitive dynamic has been referred to as fitness decoupling and has been used to interpret both models and experimental data. Extending and unifying results from the literature, we show that fitness of particles and collectives can never decouple because calculations of fitness performed over appropriate and equivalent time intervals are necessarily the same provided the population reaches a stable collective size distribution. By way of solution, we draw attention to the value of mechanistic approaches that emphasise traits, and tradeoffs among traits, as opposed to fitness. This trait-based approach is sufficient to capture dynamics that underpin evolutionary transitions. In addition, drawing upon both experimental and theoretical studies, we show that while early stages of transitions might often involve tradeoffs among particle traits, later—and critical—stages are likely to involve the rupture of such tradeoffs. Thus, when observed in the context of ETIs, tradeoff-breaking events stand as a useful marker of these transitions.
Collapse
Affiliation(s)
| | | | - Caroline J Rose
- Centre d'Écologie Fonctionnelle et Évolutive, CNRS, Montpellier, France
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | | |
Collapse
|
39
|
Melesse Vergara M, Labbé J, Tannous J. Reflection on the Challenges, Accomplishments, and New Frontiers of Gene Drives. BIODESIGN RESEARCH 2022; 2022:9853416. [PMID: 37850135 PMCID: PMC10521683 DOI: 10.34133/2022/9853416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/19/2022] [Indexed: 10/19/2023] Open
Abstract
Ongoing pest and disease outbreaks pose a serious threat to human, crop, and animal lives, emphasizing the need for constant genetic discoveries that could serve as mitigation strategies. Gene drives are genetic engineering approaches discovered decades ago that may allow quick, super-Mendelian dissemination of genetic modifications in wild populations, offering hopes for medicine, agriculture, and ecology in combating diseases. Following its first discovery, several naturally occurring selfish genetic elements were identified and several gene drive mechanisms that could attain relatively high threshold population replacement have been proposed. This review provides a comprehensive overview of the recent advances in gene drive research with a particular emphasis on CRISPR-Cas gene drives, the technology that has revolutionized the process of genome engineering. Herein, we discuss the benefits and caveats of this technology and place it within the context of natural gene drives discovered to date and various synthetic drives engineered. Later, we elaborate on the strategies for designing synthetic drive systems to address resistance issues and prevent them from altering the entire wild populations. Lastly, we highlight the major applications of synthetic CRISPR-based gene drives in different living organisms, including plants, animals, and microorganisms.
Collapse
Affiliation(s)
| | - Jesse Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Invaio Sciences, Cambridge, MA 02138USA
| | - Joanna Tannous
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| |
Collapse
|
40
|
Kumon T, Lampson MA. Evolution of eukaryotic centromeres by drive and suppression of selfish genetic elements. Semin Cell Dev Biol 2022; 128:51-60. [PMID: 35346579 PMCID: PMC9232976 DOI: 10.1016/j.semcdb.2022.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/20/2022] [Accepted: 03/20/2022] [Indexed: 10/18/2022]
Abstract
Despite the universal requirement for faithful chromosome segregation, eukaryotic centromeres are rapidly evolving. It is hypothesized that rapid centromere evolution represents an evolutionary arms race between selfish genetic elements that drive, or propagate at the expense of organismal fitness, and mechanisms that suppress fitness costs. Selfish centromere DNA achieves preferential inheritance in female meiosis by recruiting more effector proteins that alter spindle microtubule interaction dynamics. Parallel pathways for effector recruitment are adaptively evolved to suppress functional differences between centromeres. Opportunities to drive are not limited to female meiosis, and selfish transposons, plasmids and B chromosomes also benefit by maximizing their inheritance. Rapid evolution of selfish genetic elements can diversify suppressor mechanisms in different species that may cause hybrid incompatibility.
Collapse
Affiliation(s)
- Tomohiro Kumon
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Michael A Lampson
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
41
|
Komluski J, Stukenbrock EH, Habig M. Non-Mendelian transmission of accessory chromosomes in fungi. Chromosome Res 2022; 30:241-253. [PMID: 35881207 PMCID: PMC9508043 DOI: 10.1007/s10577-022-09691-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/15/2022] [Accepted: 04/11/2022] [Indexed: 11/27/2022]
Abstract
Non-Mendelian transmission has been reported for various genetic elements, ranging from small transposons to entire chromosomes. One prime example of such a transmission pattern are B chromosomes in plants and animals. Accessory chromosomes in fungi are similar to B chromosomes in showing presence/absence polymorphism and being non-essential. How these chromosomes are transmitted during meiosis is however poorly understood—despite their often high impact on the fitness of the host. For several fungal organisms, a non-Mendelian transmission or a mechanistically unique meiotic drive of accessory chromosomes have been reported. In this review, we provide an overview of the possible mechanisms that can cause the non-Mendelian transmission or meiotic drives of fungal accessory chromosomes. We compare processes responsible for the non-Mendelian transmission of accessory chromosomes for different fungal eukaryotes and discuss the structural traits of fungal accessory chromosomes affecting their meiotic transmission. We conclude that research on fungal accessory chromosomes, due to their small size, ease of sequencing, and epigenetic profiling, can complement the study of B chromosomes in deciphering factors that influence and regulate the non-Mendelian transmission of entire chromosomes.
Collapse
Affiliation(s)
- Jovan Komluski
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany.
- Max Planck Institute for Evolutionary Biology, Plön, Germany.
| | - Michael Habig
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany.
- Max Planck Institute for Evolutionary Biology, Plön, Germany.
| |
Collapse
|
42
|
Asad M, Liu D, Li J, Chen J, Yang G. Development of CRISPR/Cas9-Mediated Gene-Drive Construct Targeting the Phenotypic Gene in Plutella xylostella. Front Physiol 2022; 13:938621. [PMID: 35845988 PMCID: PMC9277308 DOI: 10.3389/fphys.2022.938621] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
The gene-drive system can ensure that desirable traits are transmitted to the progeny more than the normal Mendelian segregation. The clustered regularly interspersed palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) mediated gene-drive system has been demonstrated in dipteran insect species, including Drosophila and Anopheles, not yet in other insect species. Here, we have developed a single CRISPR/Cas9-mediated gene-drive construct for Plutella xylostella, a highly-destructive lepidopteran pest of cruciferous crops. The gene-drive construct was developed containing a Cas9 gene, a marker gene (EGFP) and a gRNA sequence targeting the phenotypic marker gene (Pxyellow) and site-specifically inserted into the P. xylostella genome. This homing-based gene-drive copied ∼12 kb of a fragment containing Cas9 gene, gRNA, and EGFP gene along with their promoters to the target site. Overall, 6.67%–12.59% gene-drive efficiency due to homology-directed repair (HDR), and 80.93%–86.77% resistant-allele formation due to non-homologous-end joining (NHEJ) were observed. Furthermore, the transgenic progeny derived from male parents showed a higher gene-drive efficiency compared with transgenic progeny derived from female parents. This study demonstrates the feasibility of the CRISPR/Cas9-mediated gene-drive construct in P. xylostella that inherits the desired traits to the progeny. The finding of this study provides a foundation to develop an effective CRISPR/Cas9-mediated gene-drive system for pest control.
Collapse
Affiliation(s)
- Muhammad Asad
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Dan Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Jianwen Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Jing Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Guang Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Guang Yang,
| |
Collapse
|
43
|
Lakovic M, Rillig MC. A Nuclei-Based Conceptual Model of (Eco)evolutionary Dynamics in Fungal Heterokaryons. Front Microbiol 2022; 13:914040. [PMID: 35711750 PMCID: PMC9194903 DOI: 10.3389/fmicb.2022.914040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/10/2022] [Indexed: 11/21/2022] Open
Abstract
Filamentous fungi are characterised by specific features, such as multinuclearity, coexistence of genetically different nuclei and nuclear movement across the mycelial network. These attributes make them an interesting, yet rather underappreciated, system for studying (eco)evolutionary dynamics. This is especially noticeable among theoretical studies, where rather few consider nuclei and their role in (eco)evolutionary dynamics. To encourage such theoretical approaches, we here provide an overview of existing research on nuclear genotype heterogeneity (NGH) and its sources, such as mutations and vegetative non-self-fusion. We then discuss the resulting intra-mycelial nuclear dynamics and the potential consequences for fitness and adaptation. Finally, we formulate a nuclei-based conceptual framework, which considers three levels of selection: a single nucleus, a subpopulation of nuclei and the mycelium. We compare this framework to other concepts, for example those that consider only the mycelium as the level of selection, and outline the benefits of our approach for studying (eco)evolutionary dynamics. Our concept should serve as a baseline for modelling approaches, such as individual-based simulations, which will contribute greatly to our understanding of multilevel selection and (eco)evolutionary dynamics in filamentous fungi.
Collapse
Affiliation(s)
- Milica Lakovic
- Institut für Biologie, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Matthias C Rillig
- Institut für Biologie, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| |
Collapse
|
44
|
Pilla G, Arcari G, Tang CM, Carattoli A. Virulence plasmid pINV as a genetic signature for Shigella flexneri phylogeny. Microb Genom 2022; 8. [PMID: 35759406 PMCID: PMC9455713 DOI: 10.1099/mgen.0.000846] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Shigella flexneri is a major health burden in low- and middle-income countries, where it is a leading cause of mortality associated with diarrhoea in children, and shows an increasing incidence among travellers and men having sex with men. Like all Shigella spp., S. flexneri has evolved from commensal Escherichia coli following the acquisition of a large plasmid pINV, which contains genes essential for virulence. Current sequence typing schemes of Shigella are based on combinations of chromosomal genetic loci, since pINV-encoded virulence genes are often lost during growth in the laboratory, making these elements inappropriate for sequence typing. By performing comparative analysis of pINVs from S. flexneri strains isolated from different geographical regions and belonging to different serotypes, we found that in contrast to plasmid-encoded virulence genes, plasmid maintenance genes are highly stable pINV-encoded elements. For the first time, to our knowledge, we have developed a S. flexneri plasmid multilocus sequence typing (pMLST) method based on different combinations of alleles of the vapBC and yacAB toxin–antitoxin (TA) systems, and the parAB partitioning system. This enables typing of S. flexneri pINV plasmids into distinct ‘virulence sequence types’ (vSTs). Furthermore, the phylogenies of vST alleles and bacterial host core genomes suggests an intimate co-evolution of pINV with the chromosome of its bacterial host, consistent with previous findings. This work demonstrates the potential of plasmid maintenance loci as genetic characteristics to study as well as to trace the molecular phylogenesis of S. flexneri pINV and the phylogenetic relationship of this plasmid with its bacterial host.
Collapse
Affiliation(s)
- Giulia Pilla
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Gabriele Arcari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | |
Collapse
|
45
|
Aravind L, Iyer LM, Burroughs AM. Discovering Biological Conflict Systems Through Genome Analysis: Evolutionary Principles and Biochemical Novelty. Annu Rev Biomed Data Sci 2022; 5:367-391. [PMID: 35609893 DOI: 10.1146/annurev-biodatasci-122220-101119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biological replicators, from genes within a genome to whole organisms, are locked in conflicts. Comparative genomics has revealed a staggering diversity of molecular armaments and mechanisms regulating their deployment, collectively termed biological conflict systems. These encompass toxins used in inter- and intraspecific interactions, self/nonself discrimination, antiviral immune mechanisms, and counter-host effectors deployed by viruses and intragenomic selfish elements. These systems possess shared syntactical features in their organizational logic and a set of effectors targeting genetic information flow through the Central Dogma, certain membranes, and key molecules like NAD+. These principles can be exploited to discover new conflict systems through sensitive computational analyses. This has led to significant advances in our understanding of the biology of these systems and furnished new biotechnological reagents for genome editing, sequencing, and beyond. We discuss these advances using specific examples of toxins, restriction-modification, apoptosis, CRISPR/second messenger-regulated systems, and other enigmatic nucleic acid-targeting systems. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA;
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA;
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA;
| |
Collapse
|
46
|
Payne C, Bovio R, Powell DL, Gunn TR, Banerjee SM, Grant V, Rosenthal GG, Schumer M. Genomic insights into variation in thermotolerance between hybridizing swordtail fishes. Mol Ecol 2022. [PMID: 35510780 DOI: 10.1111/mec.16489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/22/2022] [Accepted: 04/19/2022] [Indexed: 11/30/2022]
Abstract
Understanding how organisms adapt to changing environments is a core focus of research in evolutionary biology. One common mechanism is adaptive introgression, which has received increasing attention as a potential route to rapid adaptation in populations struggling in the face of ecological change, particularly global climate change. However, hybridization can also result in deleterious genetic interactions that may limit the benefits of adaptive introgression. Here, we used a combination of genome-wide quantitative trait locus mapping and differential gene expression analyses between the swordtail fish species Xiphophorus malinche and X. birchmanni to study the consequences of hybridization on thermotolerance. While these two species are adapted to different thermal environments, we document a complicated architecture of thermotolerance in hybrids. We identify a region of the genome that contributes to reduced thermotolerance in individuals heterozygous for X. malinche and X. birchmanni ancestry, as well as widespread misexpression in hybrids of genes that respond to thermal stress in the parental species, particularly in the circadian clock pathway. We also show that a previously mapped hybrid incompatibility between X. malinche and X. birchmanni contributes to reduced thermotolerance in hybrids. Together, our results highlight the challenges of understanding the impact of hybridization on complex ecological traits and its potential impact on adaptive introgression.
Collapse
Affiliation(s)
- Cheyenne Payne
- Department of Biology, Stanford University, Stanford, California, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
| | - Richard Bovio
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Daniel L Powell
- Department of Biology, Stanford University, Stanford, California, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
| | - Theresa R Gunn
- Department of Biology, Stanford University, Stanford, California, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
| | - Shreya M Banerjee
- Department of Biology, Stanford University, Stanford, California, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
| | - Victoria Grant
- Department of Biology, Stanford University, Stanford, California, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
- Department of Biology, Texas A&M University, College Station, Texas, USA
- Department of Biology, University of Padua, Italy
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
- Department of Biology, University of Padua, Italy
- Hanna H. Gray Fellow, Howard Hughes Medical Institute, Stanford, California, USA
| |
Collapse
|
47
|
Darwell CT, Souto‐Vilarós D, Michalek J, Boutsi S, Isua B, Sisol M, Kuyaiva T, Weiblen G, Křivan V, Novotny V, Segar ST. Predicting distributions of
Wolbachia
strains through host ecological contact—Who's manipulating whom? Ecol Evol 2022; 12:e8826. [PMID: 35432921 PMCID: PMC9006231 DOI: 10.1002/ece3.8826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/23/2022] [Indexed: 12/05/2022] Open
Abstract
Reproductive isolation in response to divergent selection is often mediated via third‐party interactions. Under these conditions, speciation is inextricably linked to ecological context. We present a novel framework for understanding arthropod speciation as mediated by Wolbachia, a microbial endosymbiont capable of causing host cytoplasmic incompatibility (CI). We predict that sympatric host sister‐species harbor paraphyletic Wolbachia strains that provide CI, while well‐defined congeners in ecological contact and recently diverged noninteracting congeners are uninfected due to Wolbachia redundancy. We argue that Wolbachia provides an adaptive advantage when coupled with reduced hybrid fitness, facilitating assortative mating between co‐occurring divergent phenotypes—the contact contingency hypothesis. To test this, we applied a predictive algorithm to empirical pollinating fig wasp data, achieving up to 91.60% accuracy. We further postulate that observed temporal decay of Wolbachia incidence results from adaptive host purging—adaptive decay hypothesis—but implementation failed to predict systematic patterns. We then account for post‐zygotic offspring mortality during CI mating, modeling fitness clines across developmental resources—the fecundity trade‐off hypothesis. This model regularly favored CI despite fecundity losses. We demonstrate that a rules‐based algorithm accurately predicts Wolbachia infection status. This has implications among other systems where closely related sympatric species encounter adaptive disadvantage through hybridization.
Collapse
Affiliation(s)
- Clive T. Darwell
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency Khlong Luang Thailand
| | - Daniel Souto‐Vilarós
- Biology Centre Institute of Entomology Czech Academy of Sciences Ceske Budejovice Czech Republic
- Faculty of Science University of South Bohemia in Ceske Budejovice Ceske Budejovice Czech Republic
| | - Jan Michalek
- Biology Centre Institute of Entomology Czech Academy of Sciences Ceske Budejovice Czech Republic
| | - Sotiria Boutsi
- Agriculture & Environment Department Harper Adams University Newport UK
| | - Brus Isua
- The New Guinea Binatang Research Center Madang Papua New Guinea
| | - Mentap Sisol
- The New Guinea Binatang Research Center Madang Papua New Guinea
| | - Thomas Kuyaiva
- The New Guinea Binatang Research Center Madang Papua New Guinea
| | - George Weiblen
- Department of Plant & Microbial Biology Bell Museum University of Minnesota Saint Paul Minnesota USA
| | - Vlastimil Křivan
- Faculty of Science University of South Bohemia in Ceske Budejovice Ceske Budejovice Czech Republic
| | - Vojtech Novotny
- Biology Centre Institute of Entomology Czech Academy of Sciences Ceske Budejovice Czech Republic
- Faculty of Science University of South Bohemia in Ceske Budejovice Ceske Budejovice Czech Republic
| | - Simon T. Segar
- Biology Centre Institute of Entomology Czech Academy of Sciences Ceske Budejovice Czech Republic
- Faculty of Science University of South Bohemia in Ceske Budejovice Ceske Budejovice Czech Republic
- Agriculture & Environment Department Harper Adams University Newport UK
| |
Collapse
|
48
|
Katlav A, Cook JM, Riegler M. Common endosymbionts affect host fitness and sex allocation via egg size provisioning. Proc Biol Sci 2022; 289:20212582. [PMID: 35350856 PMCID: PMC8965393 DOI: 10.1098/rspb.2021.2582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
It is hard to overemphasize the importance of endosymbionts in arthropod biology, ecology and evolution. Some endosymbionts can complement host metabolic function or provide defence against pathogens; others, such as ubiquitous Wolbachia and Cardinium, have evolved strategies to manipulate host reproduction. A common reproductive manipulation strategy is cytoplasmic incompatibility (CI) between differently infected individuals which can result in female mortality or male development of fertilized eggs in haplodiploid hosts. Recently, an additional role of endosymbionts has been recognized in the modification of sex allocation in sexually reproducing haplodiploids. This was theoretically expected due to the maternal inheritance of endosymbionts and natural selection for them to increase infected female production, yet the underlying mechanism remained unknown. Here, we tested whether and how Cardinium and Wolbachia causing different CI types interact to increase female production in a haplodiploid thrips species where sex allocation depends on both maternal condition and egg size provisioning. We found that Cardinium augmented female production by increasing maternal fitness and egg size, thereby boosting fertilization rate and offspring fitness. Wolbachia, in contrast, reduced the beneficial effects of Cardinium. Our results demonstrate different invasion strategies and antagonistic effects of endosymbiotic bacteria on host fitness and evolution of sex allocation.
Collapse
Affiliation(s)
- Alihan Katlav
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, New South Wales 2751, Australia
| | - James M. Cook
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, New South Wales 2751, Australia
| | - Markus Riegler
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, New South Wales 2751, Australia
| |
Collapse
|
49
|
Saunders PA, Perez J, Ronce O, Veyrunes F. Multiple sex chromosome drivers in a mammal with three sex chromosomes. Curr Biol 2022; 32:2001-2010.e3. [PMID: 35381184 DOI: 10.1016/j.cub.2022.03.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/06/2022] [Accepted: 03/10/2022] [Indexed: 12/22/2022]
Abstract
Eukaryotes with separate males and females display a great diversity in the way they determine sex, but it is still unclear what evolutionary forces cause transitions between sex-determining systems. Rather that the lack of hypotheses, the problem is the scarcity of adequate biological systems to test them. Here, we take advantage of the recent evolution of a feminizing X chromosome (called X∗) in the African pygmy mouse Mus minutoides to investigate one of the evolutionary forces hypothesized to cause such transitions, namely sex chromosome drive (i.e., biased transmission of sex chromosomes to the next generation). Through extensive molecular sexing of pups at weaning, we reveal the existence of a remarkable male sex chromosome drive system in this species, whereby direction and strength of drive are conditional upon the genotype of males' partners: males transmit their Y at a rate close to 80% when mating with XX or XX∗ females and only 36% when mating with X∗Y females. Using mathematical modeling, we explore the joint evolution of these unusual sex-determining and drive systems, revealing that different sequences of events could have led to the evolution of this bizarre system and that the "conditional" nature of sex chromosome drive plays a crucial role in the short- and long-term maintenance of the three sex chromosomes.
Collapse
Affiliation(s)
- Paul A Saunders
- Institut des Sciences de l'Evolution de Montpellier, UMR 5554 (CNRS, Université de Montpellier, IRD, EPHE), 34090 Montpellier, France.
| | - Julie Perez
- Institut des Sciences de l'Evolution de Montpellier, UMR 5554 (CNRS, Université de Montpellier, IRD, EPHE), 34090 Montpellier, France
| | - Ophélie Ronce
- Institut des Sciences de l'Evolution de Montpellier, UMR 5554 (CNRS, Université de Montpellier, IRD, EPHE), 34090 Montpellier, France
| | - Frédéric Veyrunes
- Institut des Sciences de l'Evolution de Montpellier, UMR 5554 (CNRS, Université de Montpellier, IRD, EPHE), 34090 Montpellier, France
| |
Collapse
|
50
|
Hochstrasser M. Cytoplasmic incompatibility: A Wolbachia toxin-antidote mechanism comes into view. Curr Biol 2022; 32:R287-R289. [PMID: 35349818 DOI: 10.1016/j.cub.2022.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Wolbachia cidA and cidB genes promote bacterial endosymbiont inheritance through the host female germline. CidB is now shown to load into maturing sperm nuclei. Following fertilization, it disrupts paternal chromosome condensation, triggering embryonic arrest if not countered by CidA in Wolbachia-infected eggs.
Collapse
Affiliation(s)
- Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.
| |
Collapse
|