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Haghani V, Goyal A, Zhang A, Sharifi O, Mariano N, Yasui D, Korf I, LaSalle J. Improving rigor and reproducibility in chromatin immunoprecipitation assay data analysis workflows with Rocketchip. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602975. [PMID: 39071274 PMCID: PMC11275724 DOI: 10.1101/2024.07.10.602975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
As genome sequencing technologies advance, the accumulation of sequencing data in public databases necessitates more robust and adaptable data analysis workflows. Here, we present Rocketchip, which aims to offer a solution to this problem by allowing researchers to easily compare and swap out different components of ChIP-seq, CUT&RUN, and CUT&Tag data analysis, thereby facilitating the identification of reliable analysis methodologies. Rocketchip enables researchers to efficiently process large datasets while ensuring reproducibility and allowing for the reanalysis of existing data. By supporting comparative analyses across different datasets and methodologies, Rocketchip contributes to the rigor and reproducibility of scientific findings. Furthermore, Rocketchip serves as a platform for benchmarking algorithms, allowing researchers to identify the most accurate and efficient analytical approaches to be applied to their data. In emphasizing reproducibility and adaptability, Rocketchip represents a significant step towards fostering robust scientific research practices.
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Affiliation(s)
- Viktoria Haghani
- Department of Medical Microbiology and Immunology, Genome Center, University of California, Davis. Davis, CA, USA
- Department of Molecular and Cellular Biology, Genome Center, University of California, Davis. Davis, CA, USA
| | - Aditi Goyal
- Department of Molecular and Cellular Biology, Genome Center, University of California, Davis. Davis, CA, USA
| | - Alan Zhang
- Department of Molecular and Cellular Biology, Genome Center, University of California, Davis. Davis, CA, USA
| | - Osman Sharifi
- Department of Medical Microbiology and Immunology, Genome Center, University of California, Davis. Davis, CA, USA
- Department of Molecular and Cellular Biology, Genome Center, University of California, Davis. Davis, CA, USA
| | - Natasha Mariano
- Department of Molecular and Cellular Biology, Genome Center, University of California, Davis. Davis, CA, USA
| | - Dag Yasui
- Department of Medical Microbiology and Immunology, Genome Center, University of California, Davis. Davis, CA, USA
| | - Ian Korf
- Department of Molecular and Cellular Biology, Genome Center, University of California, Davis. Davis, CA, USA
| | - Janine LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, University of California, Davis. Davis, CA, USA
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2
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Ko SR, Lee S, Koo H, Seo H, Yu J, Kim YM, Kwon SY, Shin AY. High-quality chromosome-level genome assembly of Nicotiana benthamiana. Sci Data 2024; 11:386. [PMID: 38627408 PMCID: PMC11021556 DOI: 10.1038/s41597-024-03232-0] [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: 12/18/2023] [Accepted: 04/05/2024] [Indexed: 04/19/2024] Open
Abstract
Nicotiana benthamiana is a fundamental model organism in plant research. Recent advancements in genomic sequencing have revealed significant intraspecific genetic variations. This study addresses the pressing need for a precise genome sequence specific to its geographic origin by presenting a comprehensive genome assembly of the N. benthamiana LAB strain from the Republic of Korea (NbKLAB). We compare this assembly with the widely used NbLAB360 strain, shedding light on essential genomic differences between them. The outcome is a high-quality, chromosome-level genome assembly comprising 19 chromosomes, spanning 2,762 Mb, with an N50 of 142.6 Mb. Comparative analyses revealed notable variations, including 46,215 protein-coding genes, with an impressive 99.5% BUSCO completeness score. Furthermore, the NbKLAB assembly substantially improved the QV from 33% for NbLAB360 to 49%. This refined chromosomal genome assembly for N. benthamiana, in conjunction with comparative insights, provides a valuable resource for genomics research and molecular biology. This accomplishment forms a strong foundation for in-depth exploration into the intricacies of plant genetics and genomics, improved precision, and a comparative framework.
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Affiliation(s)
- Seo-Rin Ko
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Sanghee Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Biosystems and Bioengineering Program, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Hyunjin Koo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | | | | | - Yong-Min Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
- Digital Biotech Innovation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Biosystems and Bioengineering Program, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Korea.
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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3
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Nikonova E, DeCata J, Canela M, Barz C, Esser A, Bouterwek J, Roy A, Gensler H, Heß M, Straub T, Forne I, Spletter ML. Bruno 1/CELF regulates splicing and cytoskeleton dynamics to ensure correct sarcomere assembly in Drosophila flight muscles. PLoS Biol 2024; 22:e3002575. [PMID: 38683844 PMCID: PMC11081514 DOI: 10.1371/journal.pbio.3002575] [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: 06/24/2023] [Revised: 05/09/2024] [Accepted: 03/04/2024] [Indexed: 05/02/2024] Open
Abstract
Muscles undergo developmental transitions in gene expression and alternative splicing that are necessary to refine sarcomere structure and contractility. CUG-BP and ETR-3-like (CELF) family RNA-binding proteins are important regulators of RNA processing during myogenesis that are misregulated in diseases such as Myotonic Dystrophy Type I (DM1). Here, we report a conserved function for Bruno 1 (Bru1, Arrest), a CELF1/2 family homolog in Drosophila, during early muscle myogenesis. Loss of Bru1 in flight muscles results in disorganization of the actin cytoskeleton leading to aberrant myofiber compaction and defects in pre-myofibril formation. Temporally restricted rescue and RNAi knockdown demonstrate that early cytoskeletal defects interfere with subsequent steps in sarcomere growth and maturation. Early defects are distinct from a later requirement for bru1 to regulate sarcomere assembly dynamics during myofiber maturation. We identify an imbalance in growth in sarcomere length and width during later stages of development as the mechanism driving abnormal radial growth, myofibril fusion, and the formation of hollow myofibrils in bru1 mutant muscle. Molecularly, we characterize a genome-wide transition from immature to mature sarcomere gene isoform expression in flight muscle development that is blocked in bru1 mutants. We further demonstrate that temporally restricted Bru1 rescue can partially alleviate hypercontraction in late pupal and adult stages, but it cannot restore myofiber function or correct structural deficits. Our results reveal the conserved nature of CELF function in regulating cytoskeletal dynamics in muscle development and demonstrate that defective RNA processing due to misexpression of CELF proteins causes wide-reaching structural defects and progressive malfunction of affected muscles that cannot be rescued by late-stage gene replacement.
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Affiliation(s)
- Elena Nikonova
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Jenna DeCata
- School of Science and Engineering, Division of Biological and Biomedical Systems, Kansas City, Missouri, United States of America
| | - Marc Canela
- Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
| | - Christiane Barz
- Muscle Dynamics Group, Max Planck Institute of Biochemistry, München, Germany
| | - Alexandra Esser
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Jessica Bouterwek
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Akanksha Roy
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Heidemarie Gensler
- Department of Systematic Zoology, Biocenter, Faculty of Biology, Ludwig-Maximilians-Universität München, München, Germany
| | - Martin Heß
- Department of Systematic Zoology, Biocenter, Faculty of Biology, Ludwig-Maximilians-Universität München, München, Germany
| | - Tobias Straub
- Biomedical Center, Bioinformatics Core Unit, Ludwig-Maximilians-Universität München, München, Germany
| | - Ignasi Forne
- Biomedical Center, Protein Analysis Unit, Ludwig-Maximilians-Universität München, München, Germany
| | - Maria L. Spletter
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, München, Germany
- School of Science and Engineering, Division of Biological and Biomedical Systems, Kansas City, Missouri, United States of America
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Brovkina MV, Chapman MA, Holding ML, Clowney EJ. Emergence and influence of sequence bias in evolutionarily malleable, mammalian tandem arrays. BMC Biol 2023; 21:179. [PMID: 37612705 PMCID: PMC10463633 DOI: 10.1186/s12915-023-01673-4] [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: 04/25/2023] [Accepted: 08/01/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND The radiation of mammals at the extinction of the dinosaurs produced a plethora of new forms-as diverse as bats, dolphins, and elephants-in only 10-20 million years. Behind the scenes, adaptation to new niches is accompanied by extensive innovation in large families of genes that allow animals to contact the environment, including chemosensors, xenobiotic enzymes, and immune and barrier proteins. Genes in these "outward-looking" families are allelically diverse among humans and exhibit tissue-specific and sometimes stochastic expression. RESULTS Here, we show that these tandem arrays of outward-looking genes occupy AT-biased isochores and comprise the "tissue-specific" gene class that lack CpG islands in their promoters. Models of mammalian genome evolution have not incorporated the sharply different functions and transcriptional patterns of genes in AT- versus GC-biased regions. To examine the relationship between gene family expansion, sequence content, and allelic diversity, we use population genetic data and comparative analysis. First, we find that AT bias can emerge during evolutionary expansion of gene families in cis. Second, human genes in AT-biased isochores or with GC-poor promoters experience relatively low rates of de novo point mutation today but are enriched for non-synonymous variants. Finally, we find that isochores containing gene clusters exhibit low rates of recombination. CONCLUSIONS Our analyses suggest that tolerance of non-synonymous variation and low recombination are two forces that have produced the depletion of GC bases in outward-facing gene arrays. In turn, high AT content exerts a profound effect on their chromatin organization and transcriptional regulation.
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Affiliation(s)
- Margarita V Brovkina
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Margaret A Chapman
- Neurosciences Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - E Josephine Clowney
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA.
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5
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Klonaros D, Dresch JM, Drewell RA. Transcriptome profile in Drosophila Kc and S2 embryonic cell lines. G3 (BETHESDA, MD.) 2023; 13:jkad054. [PMID: 36869676 PMCID: PMC10151398 DOI: 10.1093/g3journal/jkad054] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/04/2023] [Accepted: 02/22/2023] [Indexed: 03/05/2023]
Abstract
Drosophila melanogaster cell lines are an important resource for a range of studies spanning genomics, molecular genetics, and cell biology. Amongst these valuable lines are Kc167 (Kc) and Schneider 2 (S2) cells, which were originally isolated in the late 1960s from embryonic sources and have been used extensively to investigate a broad spectrum of biological activities including cell-cell signaling and immune system function. Whole-genome tiling microarray analysis of total RNA from these two cell types was performed as part of the modENCODE project over a decade ago and revealed that they share a number of gene expression features. Here, we expand on these earlier studies by using deep-coverage RNA-sequencing approaches to investigate the transcriptional profile in Kc and S2 cells in detail. Comparison of the transcriptomes reveals that ∼75% of the 13,919 annotated genes are expressed at a detectable level in at least one of the cell lines, with the majority of these genes expressed at high levels in both cell lines. Despite the overall similarity of the transcriptional landscape in the two cell types, 2,588 differentially expressed genes are identified. Many of the genes with the largest fold change are known only by their "CG" designations, indicating that the molecular control of Kc and S2 cell identity may be regulated in part by a cohort of relatively uncharacterized genes. Our data also indicate that both cell lines have distinct hemocyte-like identities, but share active signaling pathways and express a number of genes in the network responsible for dorsal-ventral patterning of the early embryo.
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Affiliation(s)
- Daniel Klonaros
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Jacqueline M Dresch
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Robert A Drewell
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
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6
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Xue J, Ma T, Zhang X. TRA2: The dominant power of alternative splicing in tumors. Heliyon 2023; 9:e15516. [PMID: 37151663 PMCID: PMC10161706 DOI: 10.1016/j.heliyon.2023.e15516] [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: 01/06/2023] [Revised: 03/30/2023] [Accepted: 04/12/2023] [Indexed: 05/09/2023] Open
Abstract
The dysregulation of alternative splicing (AS) is frequently found in cancer and considered as key markers for cancer progression and therapy. Transformer 2 (TRA2), a nuclear RNA binding protein, consists of transformer 2 alpha homolog (TRA2A) and transformer 2 beta homolog (TRA2B), and plays a role in the regulation of pre-mRNA splicing. Growing evidence has been provided that TRA2A and TRA2B are dysregulated in several types of tumors, and participate in the regulation of proliferation, migration, invasion, and chemotherapy resistance in cancer cells through alteration of AS of cancer-related genes. In this review, we highlight the role of TRA2 in tumorigenesis and metastasis, and discuss potential molecular mechanisms how TRA2 influences tumorigenesis and metastasis via controlling AS of pre-mRNA. We propose that TRA2Ais a novel biomarker and therapeutic target for cancer progression and therapy.
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Affiliation(s)
- Jiancheng Xue
- Medical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Research and Application of Animal Model for Environmental and Metabolic Diseases, Shenyang, China
| | - Tie Ma
- Department of Pathology, Shengjing Hospital of China Medical University, Shenyang, China
- Corresponding author.
| | - Xiaowen Zhang
- Medical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Research and Application of Animal Model for Environmental and Metabolic Diseases, Shenyang, China
- Corresponding author. Medical Research Center, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004, China.
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7
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Zhang Z, Bae B, Cuddleston WH, Miura P. Coordination of Alternative Splicing and Alternative Polyadenylation revealed by Targeted Long-Read Sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533999. [PMID: 36993601 PMCID: PMC10055423 DOI: 10.1101/2023.03.23.533999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Nervous system development is associated with extensive regulation of alternative splicing (AS) and alternative polyadenylation (APA). AS and APA have been extensively studied in isolation, but little is known about how these processes are coordinated. Here, the coordination of cassette exon (CE) splicing and APA in Drosophila was investigated using a targeted long-read sequencing approach we call Pull-a-Long-Seq (PL-Seq). This cost-effective method uses cDNA pulldown and Nanopore sequencing combined with an analysis pipeline to resolve the connectivity of alternative exons to alternative 3' ends. Using PL-Seq, we identified genes that exhibit significant differences in CE splicing depending on connectivity to short versus long 3'UTRs. Genomic long 3'UTR deletion was found to alter upstream CE splicing in short 3'UTR isoforms and ELAV loss differentially affected CE splicing depending on connectivity to alternative 3'UTRs. This work highlights the importance of considering connectivity to alternative 3'UTRs when monitoring AS events.
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Affiliation(s)
- Zhiping Zhang
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
| | - Bongmin Bae
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | | | - Pedro Miura
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
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8
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Wang D, Hu X, Ye H, Wang Y, Yang Q, Liang X, Wang Z, Zhou Y, Wen M, Yuan X, Zheng X, Ye W, Guo B, Yusuyin M, Russinova E, Zhou Y, Wang K. Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton. Genome Biol 2023; 24:49. [PMID: 36918913 PMCID: PMC10012527 DOI: 10.1186/s13059-023-02886-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/26/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND The epidermis of cotton ovule produces fibers, the most important natural cellulose source for the global textile industry. However, the molecular mechanism of fiber cell growth is still poorly understood. RESULTS Here, we develop an optimized protoplasting method, and integrate single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) to systematically characterize the cells of the outer integument of ovules from wild type and fuzzless/lintless (fl) cotton (Gossypium hirsutum). By jointly analyzing the scRNA-seq data from wildtype and fl, we identify five cell populations including the fiber cell type and construct the development trajectory for fiber lineage cells. Interestingly, by time-course diurnal transcriptomic analysis, we demonstrate that the primary growth of fiber cells is a highly regulated circadian rhythmic process. Moreover, we identify a small peptide GhRALF1 that circadian rhythmically controls fiber growth possibly through oscillating auxin signaling and proton pump activity in the plasma membrane. Combining with scATAC-seq, we further identify two cardinal cis-regulatory elements (CREs, TCP motif, and TCP-like motif) which are bound by the trans factors GhTCP14s to modulate the circadian rhythmic metabolism of mitochondria and protein translation through regulating approximately one third of genes that are highly expressed in fiber cells. CONCLUSIONS We uncover a fiber-specific circadian clock-controlled gene expression program in regulating fiber growth. This study unprecedentedly reveals a new route to improve fiber traits by engineering the circadian clock of fiber cells.
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Affiliation(s)
- Dehe Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiao Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Hanzhe Ye
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Yue Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Qian Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaodong Liang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Zilin Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Yifan Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Hubei Hongshan Laboratory, Wuhan, China
| | - Miaomiao Wen
- Institute for Advanced Studies, Wuhan University, Wuhan, China.,TaiKang Center for Life and Medical Sciences, RNA Institute, Remin Hospital, Wuhan University, Wuhan, China
| | - Xueyan Yuan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaomin Zheng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wen Ye
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, School of Medicine, Wuhan University, Wuhan, China
| | - Boyu Guo
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Mayila Yusuyin
- Research Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Yu Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China. .,Institute for Advanced Studies, Wuhan University, Wuhan, China. .,TaiKang Center for Life and Medical Sciences, RNA Institute, Remin Hospital, Wuhan University, Wuhan, China. .,Medical Research Institute, Frontier Science Center for Immunology and Metabolism, School of Medicine, Wuhan University, Wuhan, China.
| | - Kun Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China. .,Hubei Hongshan Laboratory, Wuhan, China. .,Institute for Advanced Studies, Wuhan University, Wuhan, China.
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9
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Francis A, Ghosh S, Tyagi K, Prakasam V, Rani M, Singh NP, Pradhan A, Sundaram RM, Priyanka C, Laha GS, Kannan C, Prasad MS, Chattopadhyay D, Jha G. Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations. BMC Biol 2023; 21:15. [PMID: 36721195 PMCID: PMC9890813 DOI: 10.1186/s12915-023-01526-0] [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: 02/09/2022] [Accepted: 01/23/2023] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood. RESULTS We report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato. CONCLUSIONS Our study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control.
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Affiliation(s)
- Aleena Francis
- grid.419632.b0000 0001 2217 5846National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Srayan Ghosh
- grid.419632.b0000 0001 2217 5846National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India ,grid.8250.f0000 0000 8700 0572Present address: Department of Biosciences, Durham University, Durham, UK
| | - Kriti Tyagi
- grid.419632.b0000 0001 2217 5846National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - V. Prakasam
- grid.464820.cICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500 030 India
| | - Mamta Rani
- grid.419632.b0000 0001 2217 5846National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Nagendra Pratap Singh
- grid.419632.b0000 0001 2217 5846National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Amrita Pradhan
- grid.419632.b0000 0001 2217 5846National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - R. M. Sundaram
- grid.464820.cICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500 030 India
| | - C. Priyanka
- grid.464820.cICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500 030 India
| | - G. S. Laha
- grid.464820.cICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500 030 India
| | - C. Kannan
- grid.464820.cICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500 030 India
| | - M. S. Prasad
- grid.464820.cICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500 030 India
| | - Debasis Chattopadhyay
- grid.419632.b0000 0001 2217 5846National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Gopaljee Jha
- grid.419632.b0000 0001 2217 5846National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
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10
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Schöck F, González-Morales N. The insect perspective on Z-disc structure and biology. J Cell Sci 2022; 135:277280. [PMID: 36226637 DOI: 10.1242/jcs.260179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Myofibrils are the intracellular structures formed by actin and myosin filaments. They are paracrystalline contractile cables with unusually well-defined dimensions. The sliding of actin past myosin filaments powers contractions, and the entire system is held in place by a structure called the Z-disc, which anchors the actin filaments. Myosin filaments, in turn, are anchored to another structure called the M-line. Most of the complex architecture of myofibrils can be reduced to studying the Z-disc, and recently, important advances regarding the arrangement and function of Z-discs in insects have been published. On a very small scale, we have detailed protein structure information. At the medium scale, we have cryo-electron microscopy maps, super-resolution microscopy and protein-protein interaction networks, while at the functional scale, phenotypic data are available from precise genetic manipulations. All these data aim to answer how the Z-disc works and how it is assembled. Here, we summarize recent data from insects and explore how it fits into our view of the Z-disc, myofibrils and, ultimately, muscles.
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Affiliation(s)
- Frieder Schöck
- Department of Biology, McGill University, Montreal, Quebec, H3A 1B1, Canada
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11
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Identification, Phylogenetic and Expression Analyses of the AAAP Gene Family in Liriodendron chinense Reveal Their Putative Functions in Response to Organ and Multiple Abiotic Stresses. Int J Mol Sci 2022; 23:ijms23094765. [PMID: 35563155 PMCID: PMC9100865 DOI: 10.3390/ijms23094765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/21/2022] [Accepted: 04/23/2022] [Indexed: 12/10/2022] Open
Abstract
In this study, 52 AAAP genes were identified in the L. chinense genome and divided into eight subgroups based on phylogenetic relationships, gene structure, and conserved motif. A total of 48 LcAAAP genes were located on the 14 chromosomes, and the remaining four genes were mapped in the contigs. Multispecies phylogenetic tree and codon usage bias analysis show that the LcAAAP gene family is closer to the AAAP of Amborella trichopoda, indicating that the LcAAAP gene family is relatively primitive in angiosperms. Gene duplication events revealed six pairs of segmental duplications and one pair of tandem duplications, in which many paralogous genes diverged in function before monocotyledonous and dicotyledonous plants differentiation and were strongly purification selected. Gene expression pattern analysis showed that the LcAAAP gene plays a certain role in the development of Liriodendron nectary and somatic embryogenesis. Low temperature, drought, and heat stresses may activate some WRKY/MYB transcription factors to positively regulate the expression of LcAAAP genes to achieve long-distance transport of amino acids in plants to resist the unfavorable external environment. In addition, the GAT and PorT subgroups could involve gamma-aminobutyric acid (GABA) transport under aluminum poisoning. These findings could lay a solid foundation for further study of the biological role of LcAAAP and improvement of the stress resistance of Liriodendron.
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12
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Abstract
Small nucleolar RNAs (snoRNAs) are non-coding RNAs vital for ribosomal RNA (rRNA) maturation. The U8 snoRNA, encoded by the SNORD118 gene in humans, is an atypical C/D box snoRNA as it promotes rRNA cleavage rather than 2′–O–methylation and is unique to vertebrates. The U8 snoRNA is critical for cleavage events that produce the mature 5.8S and 28S rRNAs of the large ribosomal subunit. Unexpectedly, single nucleotide polymorphisms (SNPs) in the SNORD118 gene were recently found causal to the neurodegenerative disease leukoencephalopathy, brain calcifications, and cysts (LCC; aka Labrune syndrome), but its molecular pathogenesis is unclear. Here, we will review current knowledge on the function of the U8 snoRNA in ribosome biogenesis, and connect it to the preservation of brain function in humans as well as to its dysregulation in inherited white matter disease.
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Affiliation(s)
- Emily J McFadden
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Susan J Baserga
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
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13
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Karki P, Carney TD, Maracci C, Yatsenko AS, Shcherbata HR, Rodnina MV. Tissue-specific regulation of translational readthrough tunes functions of the traffic jam transcription factor. Nucleic Acids Res 2021; 50:6001-6019. [PMID: 34897510 PMCID: PMC9226519 DOI: 10.1093/nar/gkab1189] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/05/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Translational readthrough (TR) occurs when the ribosome decodes a stop codon as a sense codon, resulting in two protein isoforms synthesized from the same mRNA. TR has been identified in several eukaryotic organisms; however, its biological significance and mechanism remain unclear. Here, we quantify TR of several candidate genes in Drosophila melanogaster and characterize the regulation of TR in the large Maf transcription factor Traffic jam (Tj). Using CRISPR/Cas9-generated mutant flies, we show that the TR-generated Tj isoform is expressed in a subset of neural cells of the central nervous system and is excluded from the somatic cells of gonads. Control of TR in Tj is critical for preservation of neuronal integrity and maintenance of reproductive health. The tissue-specific distribution of a release factor splice variant, eRF1H, plays a critical role in modulating differential TR of leaky stop codon contexts. Fine-tuning of gene regulatory functions of transcription factors by TR provides a potential mechanism for cell-specific regulation of gene expression.
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Affiliation(s)
- Prajwal Karki
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Travis D Carney
- Gene Expression and Signaling Group, Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
| | - Andriy S Yatsenko
- Gene Expression and Signaling Group, Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Halyna R Shcherbata
- Gene Expression and Signaling Group, Institute of Cell Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany
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14
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Mishra S, Sharma P, Singh R, Tiwari R, Singh GP. Genome-wide identification and expression analysis of sucrose nonfermenting-1-related protein kinase (SnRK) genes in Triticum aestivum in response to abiotic stress. Sci Rep 2021; 11:22477. [PMID: 34795369 PMCID: PMC8602265 DOI: 10.1038/s41598-021-99639-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/22/2021] [Indexed: 12/27/2022] Open
Abstract
The SnRK gene family is a key regulator that plays an important role in plant stress response by phosphorylating the target protein to regulate subsequent signaling pathways. This study was aimed to perform a genome-wide analysis of the SnRK gene family in wheat and the expression profiling of SnRKs in response to abiotic stresses. An in silico analysis identified 174 SnRK genes, which were then categorized into three subgroups (SnRK1/2/3) on the basis of phylogenetic analyses and domain types. The gene intron-exon structure and protein-motif composition of SnRKs were similar within each subgroup but different amongst the groups. Gene duplication and synteny between the wheat and Arabidopsis genomes was also investigated in order to get insight into the evolutionary aspects of the TaSnRK family genes. The result of cis-acting element analysis showed that there were abundant stress- and hormone-related cis-elements in the promoter regions of 129 SnRK genes. Furthermore, quantitative real-time PCR data revealed that heat, salt and drought treatments enhanced TaSnRK2.11 expression, suggesting that it might be a candidate gene for abiotic stress tolerance. We also identified eight microRNAs targeting 16 TaSnRK genes which are playing important role across abiotic stresses and regulation in different pathways. These findings will aid in the functional characterization of TaSnRK genes for further research.
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Affiliation(s)
- Shefali Mishra
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India.
| | - Rajender Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
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15
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Kao SY, Nikonova E, Chaabane S, Sabani A, Martitz A, Wittner A, Heemken J, Straub T, Spletter ML. A Candidate RNAi Screen Reveals Diverse RNA-Binding Protein Phenotypes in Drosophila Flight Muscle. Cells 2021; 10:2505. [PMID: 34685485 PMCID: PMC8534295 DOI: 10.3390/cells10102505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/14/2021] [Accepted: 09/18/2021] [Indexed: 12/30/2022] Open
Abstract
The proper regulation of RNA processing is critical for muscle development and the fine-tuning of contractile ability among muscle fiber-types. RNA binding proteins (RBPs) regulate the diverse steps in RNA processing, including alternative splicing, which generates fiber-type specific isoforms of structural proteins that confer contractile sarcomeres with distinct biomechanical properties. Alternative splicing is disrupted in muscle diseases such as myotonic dystrophy and dilated cardiomyopathy and is altered after intense exercise as well as with aging. It is therefore important to understand splicing and RBP function, but currently, only a small fraction of the hundreds of annotated RBPs expressed in muscle have been characterized. Here, we demonstrate the utility of Drosophila as a genetic model system to investigate basic developmental mechanisms of RBP function in myogenesis. We find that RBPs exhibit dynamic temporal and fiber-type specific expression patterns in mRNA-Seq data and display muscle-specific phenotypes. We performed knockdown with 105 RNAi hairpins targeting 35 RBPs and report associated lethality, flight, myofiber and sarcomere defects, including flight muscle phenotypes for Doa, Rm62, mub, mbl, sbr, and clu. Knockdown phenotypes of spliceosome components, as highlighted by phenotypes for A-complex components SF1 and Hrb87F (hnRNPA1), revealed level- and temporal-dependent myofibril defects. We further show that splicing mediated by SF1 and Hrb87F is necessary for Z-disc stability and proper myofibril development, and strong knockdown of either gene results in impaired localization of kettin to the Z-disc. Our results expand the number of RBPs with a described phenotype in muscle and underscore the diversity in myofibril and transcriptomic phenotypes associated with splicing defects. Drosophila is thus a powerful model to gain disease-relevant insight into cellular and molecular phenotypes observed when expression levels of splicing factors, spliceosome components and splicing dynamics are altered.
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Affiliation(s)
- Shao-Yen Kao
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, Germany; (S.-Y.K.); (E.N.); (S.C.); (A.W.); (J.H.)
| | - Elena Nikonova
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, Germany; (S.-Y.K.); (E.N.); (S.C.); (A.W.); (J.H.)
| | - Sabrina Chaabane
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, Germany; (S.-Y.K.); (E.N.); (S.C.); (A.W.); (J.H.)
| | - Albiona Sabani
- Department of Biology, University of Wisconsin at Madison, 1117 W. Johnson St., Madison, WI 53706, USA;
| | - Alexandra Martitz
- Molecular Nutrition Medicine, Else Kröner-Fresenius Center, Technical University of Munich, 85354 Freising, Germany;
| | - Anja Wittner
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, Germany; (S.-Y.K.); (E.N.); (S.C.); (A.W.); (J.H.)
| | - Jakob Heemken
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, Germany; (S.-Y.K.); (E.N.); (S.C.); (A.W.); (J.H.)
| | - Tobias Straub
- Biomedical Center, Bioinformatics Core Facility, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, Germany;
| | - Maria L. Spletter
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, Germany; (S.-Y.K.); (E.N.); (S.C.); (A.W.); (J.H.)
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16
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Manzoor MA, Manzoor MM, Li G, Abdullah M, Han W, Wenlong H, Shakoor A, Riaz MW, Rehman S, Cai Y. Genome-wide identification and characterization of bZIP transcription factors and their expression profile under abiotic stresses in Chinese pear (Pyrus bretschneideri). BMC PLANT BIOLOGY 2021; 21:413. [PMID: 34503442 PMCID: PMC8427902 DOI: 10.1186/s12870-021-03191-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 08/28/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND In plants, basic leucine zipper transcription factors (TFs) play important roles in multiple biological processes such as anthesis, fruit growth & development and stress responses. However, systematic investigation and characterization of bZIP-TFs remain unclear in Chinese white pear. Chinese white pear is a fruit crop that has important nutritional and medicinal values. RESULTS In this study, 62 bZIP genes were comprehensively identified from Chinese Pear, and 54 genes were distributed among 17 chromosomes. Frequent whole-genome duplication (WGD) and dispersed duplication (DSD) were the major driving forces underlying the bZIP gene family in Chinese white pear. bZIP-TFs are classified into 13 subfamilies according to the phylogenetic tree. Subsequently, purifying selection plays an important role in the evolution process of PbbZIPs. Synteny analysis of bZIP genes revealed that 196 orthologous gene pairs were identified between Pyrus bretschneideri, Fragaria vesca, Prunus mume, and Prunus persica. Moreover, cis-elements that respond to various stresses and hormones were found on the promoter regions of PbbZIP, which were induced by stimuli. Gene structure (intron/exon) and different compositions of motifs revealed that functional divergence among subfamilies. Expression pattern of PbbZIP genes differential expressed under hormonal treatment abscisic acid, salicylic acid, and methyl jasmonate in pear fruits by real-time qRT-PCR. CONCLUSIONS Collectively, a systematic analysis of gene structure, motif composition, subcellular localization, synteny analysis, and calculation of synonymous (Ks) and non-synonymous (Ka) was performed in Chinese white pear. Sixty-two bZIP-TFs in Chinese pear were identified, and their expression profiles were comprehensively analyzed under ABA, SA, and MeJa hormones, which respond to multiple abiotic stresses and fruit growth and development. PbbZIP gene occurred through Whole-genome duplication and dispersed duplication events. These results provide a basic framework for further elucidating the biological function characterizations under multiple developmental stages and abiotic stress responses.
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Affiliation(s)
| | | | - Guohui Li
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Muhammad Abdullah
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Wang Han
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Han Wenlong
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Awais Shakoor
- Department of Environment and Soil Sciences, University of Lleida, Avinguda Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | | | - Shamsur Rehman
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
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17
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Booysen E, Dicks LMT. Does the Future of Antibiotics Lie in Secondary Metabolites Produced by Xenorhabdus spp.? A Review. Probiotics Antimicrob Proteins 2021; 12:1310-1320. [PMID: 32844362 DOI: 10.1007/s12602-020-09688-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The over-prescription of antibiotics for treatment of infections is primarily to blame for the increase in bacterial resistance. Added to the problem is the slow rate at which novel antibiotics are discovered and the many processes that need to be followed to classify antimicrobials safe for medical use. Xenorhabdus spp. of the family Enterobacteriaceae, mutualistically associated with entomopathogenic nematodes of the genus Steinernema, produce a variety of antibacterial peptides, including bacteriocins, depsipeptides, xenocoumacins and PAX (peptide antimicrobial-Xenorhabdus) peptides, plus additional secondary metabolites with antibacterial and antifungal activity. The secondary metabolites of some strains are active against protozoa and a few have anti-carcinogenic properties. It is thus not surprising that nematodes invaded by a single strain of a Xenorhabdus species are not infected by other microorganisms. In this review, the antimicrobial compounds produced by Xenorhabdus spp. are listed and the gene clusters involved in synthesis of these secondary metabolites are discussed. We also review growth conditions required for increased production of antimicrobial compounds.
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Affiliation(s)
- E Booysen
- Department of Microbiology, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - L M T Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch, 7600, South Africa.
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18
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Myo T, Wei F, Zhang H, Hao J, Zhang B, Liu Z, Cao G, Tian B, Shi G. Genome-wide identification of the BASS gene family in four Gossypium species and functional characterization of GhBASSs against salt stress. Sci Rep 2021; 11:11342. [PMID: 34059742 PMCID: PMC8166867 DOI: 10.1038/s41598-021-90740-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 05/17/2021] [Indexed: 02/04/2023] Open
Abstract
Bile acid sodium symporter (BASS) family proteins encode a class of sodium/solute symporters. Even though the sodium transporting property of BASSs in mammals was well studied, their sodium transportability and functional roles in plant salt tolerance remained largely unknown. Here, BASS family members from 4 cotton species, as well as 30 other species were identified. Then, they were designated as members of BASS1 to BASS5 subfamilies according to their sequence similarity and phylogenetic relationships. There were 8, 11, 16 and 18 putative BASS genes in four cotton species. While whole-genome duplications (WGD) and segmental duplications rendered the expansion of the BASS gene family in cotton, BASS gene losses occurred in the tetraploid cotton during the evolution from diploids to allotetraploids. Concerning functional characterizations, the transcript profiling of GhBASSs revealed that they not only preferred tissue-specific expression but also were differently induced by various stressors and phytohormones. Gene silencing and overexpression experiments showed that GhBASS1 and GhBASS3 positively regulated, whereas GhBASS2, GhBASS4 and GhBASS5 negatively regulated plant salt tolerance. Taken together, BASS family genes have evolved before the divergence from the common ancestor of prokaryotes and eukaryotes, and GhBASSs are plastidial sodium-dependent metabolite co-transporters that can influence plant salt tolerance.
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Affiliation(s)
- Thwin Myo
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Fang Wei
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Honghao Zhang
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Jianfeng Hao
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Bin Zhang
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Zhixian Liu
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Gangqiang Cao
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Baoming Tian
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Gongyao Shi
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
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19
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Diaz F, Allan CW, Markow TA, Bono JM, Matzkin LM. Gene expression and alternative splicing dynamics are perturbed in female head transcriptomes following heterospecific copulation. BMC Genomics 2021; 22:359. [PMID: 34006224 PMCID: PMC8132402 DOI: 10.1186/s12864-021-07669-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/27/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Despite the growing interest in the female side of copulatory interactions, the roles played by differential expression and alternative splicing mechanisms of pre-RNA on tissues outside of the reproductive tract have remained largely unknown. Here we addressed these questions in the context of con- vs heterospecific matings between Drosophila mojavensis and its sister species, D. arizonae. We analyzed transcriptional responses in female heads using an integrated investigation of genome-wide patterns of gene expression, including differential expression (DE), alternative splicing (AS) and intron retention (IR). RESULTS Our results indicated that early transcriptional responses were largely congruent between con- and heterospecific matings but are substantially perturbed over time. Conspecific matings induced functional pathways related to amino acid balance previously associated with the brain's physiology and female postmating behavior. Heterospecific matings often failed to activate regulation of some of these genes and induced expression of additional genes when compared with those of conspecifically-mated females. These mechanisms showed functional specializations with DE genes mostly linked to pathways of proteolysis and nutrient homeostasis, while AS genes were more related to photoreception and muscle assembly pathways. IR seems to play a more general role in DE regulation during the female postmating response. CONCLUSIONS We provide evidence showing that AS genes substantially perturbed by heterospecific matings in female heads evolve at slower evolutionary rates than the genome background. However, DE genes evolve at evolutionary rates similar, or even higher, than those of male reproductive genes, which highlights their potential role in sexual selection and the evolution of reproductive barriers.
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Affiliation(s)
- Fernando Diaz
- Department of Entomology, University of Arizona, Tucson, AZ, USA.
| | - Carson W Allan
- Department of Entomology, University of Arizona, Tucson, AZ, USA
| | - Therese Ann Markow
- Cinvestav UGA-Langebio, Irapuato, Guanajuato, Mexico
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, California, USA
| | - Jeremy M Bono
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, USA.
| | - Luciano M Matzkin
- Department of Entomology, University of Arizona, Tucson, AZ, USA.
- BIO5 Institute, University of Arizona, Tucson, AZ, USA.
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
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20
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Healey AL, Shepherd M, King GJ, Butler JB, Freeman JS, Lee DJ, Potts BM, Silva-Junior OB, Baten A, Jenkins J, Shu S, Lovell JT, Sreedasyam A, Grimwood J, Furtado A, Grattapaglia D, Barry KW, Hundley H, Simmons BA, Schmutz J, Vaillancourt RE, Henry RJ. Pests, diseases, and aridity have shaped the genome of Corymbia citriodora. Commun Biol 2021; 4:537. [PMID: 33972666 PMCID: PMC8110574 DOI: 10.1038/s42003-021-02009-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/05/2021] [Indexed: 02/03/2023] Open
Abstract
Corymbia citriodora is a member of the predominantly Southern Hemisphere Myrtaceae family, which includes the eucalypts (Eucalyptus, Corymbia and Angophora; ~800 species). Corymbia is grown for timber, pulp and paper, and essential oils in Australia, South Africa, Asia, and Brazil, maintaining a high-growth rate under marginal conditions due to drought, poor-quality soil, and biotic stresses. To dissect the genetic basis of these desirable traits, we sequenced and assembled the 408 Mb genome of Corymbia citriodora, anchored into eleven chromosomes. Comparative analysis with Eucalyptus grandis reveals high synteny, although the two diverged approximately 60 million years ago and have different genome sizes (408 vs 641 Mb), with few large intra-chromosomal rearrangements. C. citriodora shares an ancient whole-genome duplication event with E. grandis but has undergone tandem gene family expansions related to terpene biosynthesis, innate pathogen resistance, and leaf wax formation, enabling their successful adaptation to biotic/abiotic stresses and arid conditions of the Australian continent.
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Affiliation(s)
- Adam L Healey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
- University of Queensland/QAAFI, Brisbane, QLD, Australia.
| | - Mervyn Shepherd
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Jakob B Butler
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Jules S Freeman
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, TAS, Australia
- Scion, Rotorua, New Zealand
| | - David J Lee
- Forest Industries Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Brad M Potts
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, TAS, Australia
| | | | - Abdul Baten
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
- Institute of Precision Medicine & Bioinformatics, Camperdown, NSW, Australia
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Agnelo Furtado
- University of Queensland/QAAFI, Brisbane, QLD, Australia
| | - Dario Grattapaglia
- EMBRAPA Genetic Resources and Biotechnology, Brasília, Brazil
- Genomic Science Program, Universidade Catolica de Brasilia, Taguatinga, Brazil
| | - Kerrie W Barry
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Hope Hundley
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Blake A Simmons
- University of Queensland/QAAFI, Brisbane, QLD, Australia
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - René E Vaillancourt
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, TAS, Australia
| | - Robert J Henry
- University of Queensland/QAAFI, Brisbane, QLD, Australia
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21
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Youlten SE, Kemp JP, Logan JG, Ghirardello EJ, Sergio CM, Dack MRG, Guilfoyle SE, Leitch VD, Butterfield NC, Komla-Ebri D, Chai RC, Corr AP, Smith JT, Mohanty ST, Morris JA, McDonald MM, Quinn JMW, McGlade AR, Bartonicek N, Jansson M, Hatzikotoulas K, Irving MD, Beleza-Meireles A, Rivadeneira F, Duncan E, Richards JB, Adams DJ, Lelliott CJ, Brink R, Phan TG, Eisman JA, Evans DM, Zeggini E, Baldock PA, Bassett JHD, Williams GR, Croucher PI. Osteocyte transcriptome mapping identifies a molecular landscape controlling skeletal homeostasis and susceptibility to skeletal disease. Nat Commun 2021; 12:2444. [PMID: 33953184 PMCID: PMC8100170 DOI: 10.1038/s41467-021-22517-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 03/11/2021] [Indexed: 12/17/2022] Open
Abstract
Osteocytes are master regulators of the skeleton. We mapped the transcriptome of osteocytes from different skeletal sites, across age and sexes in mice to reveal genes and molecular programs that control this complex cellular-network. We define an osteocyte transcriptome signature of 1239 genes that distinguishes osteocytes from other cells. 77% have no previously known role in the skeleton and are enriched for genes regulating neuronal network formation, suggesting this programme is important in osteocyte communication. We evaluated 19 skeletal parameters in 733 knockout mouse lines and reveal 26 osteocyte transcriptome signature genes that control bone structure and function. We showed osteocyte transcriptome signature genes are enriched for human orthologs that cause monogenic skeletal disorders (P = 2.4 × 10-22) and are associated with the polygenic diseases osteoporosis (P = 1.8 × 10-13) and osteoarthritis (P = 1.6 × 10-7). Thus, we reveal the molecular landscape that regulates osteocyte network formation and function and establish the importance of osteocytes in human skeletal disease.
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Affiliation(s)
- Scott E Youlten
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - John P Kemp
- University of Queensland Diamantina Institute, UQ, Brisbane, QLD, Australia
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - John G Logan
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Elena J Ghirardello
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Claudio M Sergio
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - Michael R G Dack
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Siobhan E Guilfoyle
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Victoria D Leitch
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- RMIT Centre for Additive Manufacturing, School of Engineering, RMIT University, Melbourne, VIC, UK
| | - Natalie C Butterfield
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Davide Komla-Ebri
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Ryan C Chai
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - Alexander P Corr
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- Faculty of Science, University of Bath, Bath, UK
| | - James T Smith
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- Faculty of Science, University of Bath, Bath, UK
| | - Sindhu T Mohanty
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - John A Morris
- New York Genome Center, New York, NY, USA
- Faculty of Arts and Science, Department of Biology, New York University, New York, NY, USA
| | - Michelle M McDonald
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Julian M W Quinn
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - Amelia R McGlade
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - Nenad Bartonicek
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, Sydney, NSW, Australia
| | - Matt Jansson
- Viapath Genetics Laboratory, Viapath Analytics LLP, Guy's Hospital, London, UK
- Department of Clinical Genetics, Guy's Hospital, London, UK
| | - Konstantinos Hatzikotoulas
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Phoenix, AZ, USA
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Melita D Irving
- Department of Clinical Genetics, Guy's and St Thomas' NHS Trust, London, UK
| | | | | | - Emma Duncan
- Faculty of Life Sciences and Medicine, Department of Twin Research & Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
- Australian Translational Genomics Centre, Institute of Health and Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, St Lucia, QLD, Australia
| | - J Brent Richards
- Faculty of Life Sciences and Medicine, Department of Twin Research & Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
- Faculty of Medicine, McGill University, Quebec, Canada
| | | | | | - Robert Brink
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- Division of Immunology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - Tri Giang Phan
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- Division of Immunology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - John A Eisman
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- School of Medicine Sydney, University of Notre Dame Australia, Fremantle, Australia
| | - David M Evans
- University of Queensland Diamantina Institute, UQ, Brisbane, QLD, Australia
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Phoenix, AZ, USA
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Paul A Baldock
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - J H Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - Graham R Williams
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - Peter I Croucher
- Bone Biology, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia.
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia.
- School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, Australia.
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22
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Li Y, Sun P, Lu Z, Chen J, Wang Z, Du X, Zheng Z, Wu Y, Hu H, Yang J, Ma J, Liu J, Yang Y. The Corylus mandshurica genome provides insights into the evolution of Betulaceae genomes and hazelnut breeding. HORTICULTURE RESEARCH 2021; 8:54. [PMID: 33642584 PMCID: PMC7917096 DOI: 10.1038/s41438-021-00495-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 01/11/2021] [Accepted: 01/20/2021] [Indexed: 05/04/2023]
Abstract
Hazelnut is popular for its flavor, and it has also been suggested that hazelnut is beneficial to cardiovascular health because it is rich in oleic acid. Here, we report the first high-quality chromosome-scale genome for the hazelnut species Corylus mandshurica (2n = 22), which has a high concentration of oleic acid in its nuts. The assembled genome is 367.67 Mb in length, and the contig N50 is 14.85 Mb. All contigs were assembled into 11 chromosomes, and 28,409 protein-coding genes were annotated. We reconstructed the evolutionary trajectories of the genomes of Betulaceae species and revealed that the 11 chromosomes of the hazelnut genus were derived from the most ancestral karyotype in Betula pendula, which has 14 protochromosomes, by inferring homology among five Betulaceae genomes. We identified 96 candidate genes involved in oleic acid biosynthesis, and 10 showed rapid evolution or positive selection. These findings will help us to understand the mechanisms of lipid synthesis and storage in hazelnuts. Several gene families related to salicylic acid metabolism and stress responses experienced rapid expansion in this hazelnut species, which may have increased its stress tolerance. The reference genome presented here constitutes a valuable resource for molecular breeding and genetic improvement of the important agronomic properties of hazelnut.
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Affiliation(s)
- Ying Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Pengchuan Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhiqiang Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303, Mengla, Yunnan, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, 666303, Mengla, Yunnan, China
| | - Jinyuan Chen
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhenyue Wang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xin Du
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zeyu Zheng
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ying Wu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Hongyin Hu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jiao Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jianxiang Ma
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.
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23
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The mitochondrial aspartate/glutamate carrier (AGC or Aralar1) isoforms in D. melanogaster: biochemical characterization, gene structure, and evolutionary analysis. Biochim Biophys Acta Gen Subj 2021; 1865:129854. [PMID: 33497735 DOI: 10.1016/j.bbagen.2021.129854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND In man two mitochondrial aspartate/glutamate carrier (AGC) isoforms, known as aralar and citrin, are required to accomplish several metabolic pathways. In order to fill the existing gap of knowledge in Drosophila melanogaster, we have studied aralar1 gene, orthologue of human AGC-encoding genes in this organism. METHODS The blastp algorithm and the "reciprocal best hit" approach have been used to identify the human orthologue of AGCs in Drosophilidae and non-Drosophilidae. Aralar1 proteins have been overexpressed in Escherichia coli and functionally reconstituted into liposomes for transport assays. RESULTS The transcriptional organization of aralar1 comprises six isoforms, three constitutively expressed (aralar1-RA, RD and RF), and the remaining three distributed during the development or in different tissues (aralar1-RB, RC and RE). Aralar1-PA and Aralar1-PE, representative of all isoforms, have been biochemically characterized. Recombinant Aralar1-PA and Aralar1-PE proteins share similar efficiency to exchange glutamate against aspartate, and same substrate affinities than the human isoforms. Interestingly, although Aralar1-PA and Aralar1-PE diverge only in their EF-hand 8, they greatly differ in their specific activities and substrate specificity. CONCLUSIONS The tight regulation of aralar1 transcripts expression and the high request of aspartate and glutamate during early embryogenesis suggest a crucial role of Aralar1 in this Drosophila developmental stage. Furthermore, biochemical characterization and calcium sensitivity have identified Aralar1-PA and Aralar1-PE as the human aralar and citrin counterparts, respectively. GENERAL SIGNIFICANCE The functional characterization of the fruit fly mitochondrial AGC transporter represents a crucial step toward a complete understanding of the metabolic events acting during early embryogenesis.
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24
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Dudhate A, Shinde H, Yu P, Tsugama D, Gupta SK, Liu S, Takano T. Comprehensive analysis of NAC transcription factor family uncovers drought and salinity stress response in pearl millet (Pennisetum glaucum). BMC Genomics 2021; 22:70. [PMID: 33478383 PMCID: PMC7818933 DOI: 10.1186/s12864-021-07382-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 01/12/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Pearl millet (Pennisetum glaucum) is a cereal crop that possesses the ability to withstand drought, salinity and high temperature stresses. The NAC [NAM (No Apical Meristem), ATAF1 (Arabidopsis thaliana Activation Factor 1), and CUC2 (Cup-shaped Cotyledon)] transcription factor family is one of the largest transcription factor families in plants. NAC family members are known to regulate plant growth and abiotic stress response. Currently, no reports are available on the functions of the NAC family in pearl millet. RESULTS Our genome-wide analysis found 151 NAC transcription factor genes (PgNACs) in the pearl millet genome. Thirty-eight and 76 PgNACs were found to be segmental and dispersed duplicated respectively. Phylogenetic analysis divided these NAC transcription factors into 11 groups (A-K). Three PgNACs (- 073, - 29, and - 151) were found to be membrane-associated transcription factors. Seventeen other conserved motifs were found in PgNACs. Based on the similarity of PgNACs to NAC proteins in other species, the functions of PgNACs were predicted. In total, 88 microRNA target sites were predicted in 59 PgNACs. A previously performed transcriptome analysis suggests that the expression of 30 and 42 PgNACs are affected by salinity stress and drought stress, respectively. The expression of 36 randomly selected PgNACs were examined by quantitative reverse transcription-PCR. Many of these genes showed diverse salt- and drought-responsive expression patterns in roots and leaves. These results confirm that PgNACs are potentially involved in regulating abiotic stress tolerance in pearl millet. CONCLUSION The pearl millet genome contains 151 NAC transcription factor genes that can be classified into 11 groups. Many of these genes are either upregulated or downregulated by either salinity or drought stress and may therefore contribute to establishing stress tolerance in pearl millet.
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Affiliation(s)
- Ambika Dudhate
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Nishitokyo-shi, Tokyo, 188-0002 Japan
- Department of Pharmaceutical Sciences, Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY USA
| | - Harshraj Shinde
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Nishitokyo-shi, Tokyo, 188-0002 Japan
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY USA
| | - Pei Yu
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Nishitokyo-shi, Tokyo, 188-0002 Japan
| | - Daisuke Tsugama
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Nishitokyo-shi, Tokyo, 188-0002 Japan
| | - Shashi Kumar Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana State India
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A and F University, Lin’an, Hangzhou China
| | - Tetsuo Takano
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, Nishitokyo-shi, Tokyo, 188-0002 Japan
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25
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Ameis D, Liu F, Kirby E, Patel D, Keijzer R. The RNA-binding protein Quaking regulates multiciliated and basal cell abundance in the developing lung. Am J Physiol Lung Cell Mol Physiol 2021; 320:L557-L567. [PMID: 33438508 DOI: 10.1152/ajplung.00481.2019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
RNA-binding proteins (RBPs) form complexes with RNA, changing how the RNA is processed and thereby regulating gene expression. RBPs are important sources of gene regulation during organogenesis, including the development of lungs. The RBP called Quaking (QK) is critical for embryogenesis, yet it has not been studied in the developing lung. Here, we show that QK is widely expressed during rat lung development and into adulthood. The QK isoforms QK5 and QK7 colocalize to the nuclei of nearly all lung cells. QK6 is present in the nuclei and cytoplasm of mesenchymal cells and is only present in the epithelium during branching morphogenesis. QK knockdown in embryonic lung explants caused a greater number of multiciliated cells to appear in the airways, at the expense of basal cells. The mRNA of multiciliated cell genes and the abundance of FOXJ1/SOX2+ cells increased after knockdown, whereas P63/SOX2+ cells decreased. The cytokine IL-6, a known regulator of multiciliated cell differentiation, had increased mRNA levels after QK knockdown, although protein levels remained unchanged. Further studies are necessary to confirm whether QK acts as a blocker for the IL-6-induced differentiation of basal cells into multiciliated cells, and a conditional QK knockout would likely lead to additional discoveries on QK's role during lung development.
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Affiliation(s)
- Dustin Ameis
- Departments of Surgery, Division of Pediatric Surgery, Pediatrics & Child Health and Physiology & Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Biology of Breathing Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Franklin Liu
- Departments of Surgery, Division of Pediatric Surgery, Pediatrics & Child Health and Physiology & Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Biology of Breathing Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Eimear Kirby
- Departments of Surgery, Division of Pediatric Surgery, Pediatrics & Child Health and Physiology & Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Biology of Breathing Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Daywin Patel
- Departments of Surgery, Division of Pediatric Surgery, Pediatrics & Child Health and Physiology & Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Biology of Breathing Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Richard Keijzer
- Departments of Surgery, Division of Pediatric Surgery, Pediatrics & Child Health and Physiology & Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Biology of Breathing Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
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26
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Lammens EM, Nikel PI, Lavigne R. Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria. Nat Commun 2020; 11:5294. [PMID: 33082347 PMCID: PMC7576135 DOI: 10.1038/s41467-020-19124-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/25/2020] [Indexed: 12/26/2022] Open
Abstract
Non-model bacteria like Pseudomonas putida, Lactococcus lactis and other species have unique and versatile metabolisms, offering unique opportunities for Synthetic Biology (SynBio). However, key genome editing and recombineering tools require optimization and large-scale multiplexing to unlock the full SynBio potential of these bacteria. In addition, the limited availability of a set of characterized, species-specific biological parts hampers the construction of reliable genetic circuitry. Mining of currently available, diverse bacteriophages could complete the SynBio toolbox, as they constitute an unexplored treasure trove for fully adapted metabolic modulators and orthogonally-functioning parts, driven by the longstanding co-evolution between phage and host.
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Affiliation(s)
- Eveline-Marie Lammens
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001, Leuven, BE, Belgium
| | - Pablo Ivan Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, DK, Denmark
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001, Leuven, BE, Belgium.
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Drosophila melanogaster Mitochondrial Carriers: Similarities and Differences with the Human Carriers. Int J Mol Sci 2020; 21:ijms21176052. [PMID: 32842667 PMCID: PMC7504413 DOI: 10.3390/ijms21176052] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial carriers are a family of structurally related proteins responsible for the exchange of metabolites, cofactors and nucleotides between the cytoplasm and mitochondrial matrix. The in silico analysis of the Drosophila melanogaster genome has highlighted the presence of 48 genes encoding putative mitochondrial carriers, but only 20 have been functionally characterized. Despite most Drosophila mitochondrial carrier genes having human homologs and sharing with them 50% or higher sequence identity, D. melanogaster genes display peculiar differences from their human counterparts: (1) in the fruit fly, many genes encode more transcript isoforms or are duplicated, resulting in the presence of numerous subfamilies in the genome; (2) the expression of the energy-producing genes in D. melanogaster is coordinated from a motif known as Nuclear Respiratory Gene (NRG), a palindromic 8-bp sequence; (3) fruit-fly duplicated genes encoding mitochondrial carriers show a testis-biased expression pattern, probably in order to keep a duplicate copy in the genome. Here, we review the main features, biological activities and role in the metabolism of the D. melanogaster mitochondrial carriers characterized to date, highlighting similarities and differences with their human counterparts. Such knowledge is very important for obtaining an integrated view of mitochondrial function in D. melanogaster metabolism.
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28
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Mitema A, Feto NA. Molecular and Vegetative Compatibility Groups Characterization of Aspergillus flavus Isolates from Kenya. AIMS Microbiol 2020; 6:231-249. [PMID: 33134742 PMCID: PMC7595839 DOI: 10.3934/microbiol.2020015] [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: 04/21/2020] [Accepted: 07/06/2020] [Indexed: 12/02/2022] Open
Abstract
The genus Aspergillus contains diverse species and the identification is complicated. Vegetative compatibility groups (VCGs) and molecular mechanisms were deployed to study the species. The study was randomly conducted in four counties in Kenya based on the history of aflatoxicosis and maize cultivation. Thirty-seven Aspergillus flavus isolates from Nandi, Kisumu, Homa Bay and Makueni were characterized to determine their taxonomic status based on their VCGs and genotypes. A phylogenetic analysis of ITS1 and ITS2 sequences of the isolates investigated revealed ITS primers discriminating some of the A. flavus isolates as 100% sequence identity to the RefSeq. Nit mutants' complementation test revealed strong heterokaryon incompatibility between isolates of Nandi region (67%) and Makueni (33%). The trend based on VCGs and molecular findings showed high incidence of toxigenic A. flavus in Makueni, which could be the reason why the region frequently experiences chronic aflatoxicosis incidences over the last few decades as compared to other regions. Interestingly, we have discovered all S and L-morphotypes including the rare S/L-morphotypes, which implies that Kenya is home to all morphotypes of A. flavus. Thus, the analysis provides a deeper understanding of the taxonomic relationship between the A. flavus isolates and could help contextualise the data obtained for each isolate with respect to VCG genetic diversity and genotypes. Determining the primary causal agents of aflatoxin contamination is critical for predicting risk of contamination events and designing and implementing effective management strategies.
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Affiliation(s)
- Alfred Mitema
- OMICS Research Group, Department of Biotechnology, Vaal University of Technology, Vanderbijlpark 1911, South Africa.,School of Biological Sciences, University of Nairobi, Nairobi, Kenya
| | - Naser Aliye Feto
- OMICS Research Group, Department of Biotechnology, Vaal University of Technology, Vanderbijlpark 1911, South Africa
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29
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Ghangal R, Rajkumar MS, Garg R, Jain M. Genome-wide analysis of glutathione S-transferase gene family in chickpea suggests its role during seed development and abiotic stress. Mol Biol Rep 2020; 47:2749-2761. [DOI: 10.1007/s11033-020-05377-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/12/2020] [Indexed: 01/01/2023]
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30
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Guo W, Chen J, Li J, Huang J, Wang Z, Lim KJ. Portal of Juglandaceae: A comprehensive platform for Juglandaceae study. HORTICULTURE RESEARCH 2020; 7:35. [PMID: 32194971 PMCID: PMC7072074 DOI: 10.1038/s41438-020-0256-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/25/2019] [Accepted: 01/15/2020] [Indexed: 05/22/2023]
Abstract
Juglandaceae species are plants of great economic value and have been cultivated, domesticated, and utilized by human society for a long time. Their edible, nutrient-rich nuts and tough, durable wood have attracted the attention of botanists and breeders. With the advent of the genomics era, genome sequencing of the Juglandaceae family has been greatly accelerated, and a large amount of data has been generated. In this paper, we introduce the Portal of Juglandaceae (PJU), a tool to bring all these data together. The PJU contains genomes, gene-coding sequences, protein sequences, various types of annotation information, expression data, and miRNA data, which are configured with BLAST, JBrowse, and our self-developed synteny analysis tool. The PJU has a user-friendly and straightforward interface that performs a variety of query tasks with a few simple operations. In the future, we hope that the PJU will serve as a hub for the study of the Juglandaceae family.
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Affiliation(s)
- Wenlei Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an District, 311300 Hangzhou, Zhejiang China
| | - Junhao Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an District, 311300 Hangzhou, Zhejiang China
| | - Jian Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an District, 311300 Hangzhou, Zhejiang China
| | - Jianqin Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an District, 311300 Hangzhou, Zhejiang China
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an District, 311300 Hangzhou, Zhejiang China
| | - Kean-Jin Lim
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an District, 311300 Hangzhou, Zhejiang China
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Evaluation of Rationally Designed Label-free Stem-loop DNA Probe Opening in the Presence of miR-21 by Circular Dichroism and Fluorescence Techniques. Sci Rep 2020; 10:4018. [PMID: 32132554 PMCID: PMC7055349 DOI: 10.1038/s41598-020-60157-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 02/03/2020] [Indexed: 01/02/2023] Open
Abstract
The characteristic features of stem-loop structured probes make them robust tools to detect targets with high sensitivity and selectivity. The basis of the hairpin based sensors operation is a conformational change that occurs upon hybridization of target with stem-loop probe. The design of the stem-loop probe has an important role in target recognition. Therefore, we designed a label-free stem loop probe for targeting miR-21 as a cancer biomarker investigated by web-based tools; its thermodynamic parameters obtained by thermal UV spectroscopy. The efficiency of stem-loop structure opening in the presence of target and non-target sequences was evaluated by fluorescence spectroscopy and circular dichroism spectro-polarimetry. The results showed that the target sequence opens the structure of hairpin efficiently in comparison to non-target sequences. To optimize the stem-loop hybridization to its target, the buffer ionic strength was changed by adding different concentrations of NaCl, KCl and MgCl2. It was shown that buffering conditions have a significant role in loop structure opening and its optimization, led to an increase in sensitivity detection and have improved LOD from 60 pM to 45 pM.
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Nikonova E, Kao SY, Spletter ML. Contributions of alternative splicing to muscle type development and function. Semin Cell Dev Biol 2020; 104:65-80. [PMID: 32070639 DOI: 10.1016/j.semcdb.2020.02.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/30/2022]
Abstract
Animals possess a wide variety of muscle types that support different kinds of movements. Different muscles have distinct locations, morphologies and contractile properties, raising the question of how muscle diversity is generated during development. Normal aging processes and muscle disorders differentially affect particular muscle types, thus understanding how muscles normally develop and are maintained provides insight into alterations in disease and senescence. As muscle structure and basic developmental mechanisms are highly conserved, many important insights into disease mechanisms in humans as well as into basic principles of muscle development have come from model organisms such as Drosophila, zebrafish and mouse. While transcriptional regulation has been characterized to play an important role in myogenesis, there is a growing recognition of the contributions of alternative splicing to myogenesis and the refinement of muscle function. Here we review our current understanding of muscle type specific alternative splicing, using examples of isoforms with distinct functions from both vertebrates and Drosophila. Future exploration of the vast potential of alternative splicing to fine-tune muscle development and function will likely uncover novel mechanisms of isoform-specific regulation and a more holistic understanding of muscle development, disease and aging.
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Affiliation(s)
- Elena Nikonova
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, Germany
| | - Shao-Yen Kao
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, Germany
| | - Maria L Spletter
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, Germany; Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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Li J, Yu H, Wang W, Fu C, Zhang W, Han F, Wu H. Genomic and transcriptomic insights into molecular basis of sexually dimorphic nuptial spines in Leptobrachium leishanense. Nat Commun 2019; 10:5551. [PMID: 31804492 PMCID: PMC6895153 DOI: 10.1038/s41467-019-13531-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 11/13/2019] [Indexed: 12/21/2022] Open
Abstract
Sexually dimorphic (SD) traits are important in sexual selection and species survival, yet the molecular basis remains elusive, especially in amphibians where SD traits have evolved repeatedly. We focus on the Leishan moustache toad (Leptobrachium leishanense), in which males develop nuptial spines on their maxillary skin. Here we report a 3.5 Gb genome assembly with a contig N50 of 1.93 Mb. We find a specific expansion of the intermediate filament gene family including numerous keratin genes. Within these genes, a cluster of duplicated hair keratin genes exhibits male-biased and maxillary skin-specific expression, suggesting a role in developing nuptial spines. We identify a module of coexpressed genes significantly associated with spine formation. In addition, we find several hormones likely to be involved in regulating spine development. This study not only presents a high-quality anuran genome but also provides a reference for studying skin-derived SD traits in amphibians. The basis of sexual dimorphism in non-model species may be elusive, in part due to a lack of genomic and molecular resources. Here, Li et al. report a high-quality anuran genome and reveal candidate genes and pathways associated with shaping sexually dimorphic nuptial spines in a moustache toad.
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Affiliation(s)
- Jun Li
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China
| | - Haiyan Yu
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Wenxia Wang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China
| | - Chao Fu
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China
| | - Wei Zhang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China
| | - Fengming Han
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Hua Wu
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan, 430079, China.
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Wairich A, de Oliveira BHN, Arend EB, Duarte GL, Ponte LR, Sperotto RA, Ricachenevsky FK, Fett JP. The Combined Strategy for iron uptake is not exclusive to domesticated rice (Oryza sativa). Sci Rep 2019; 9:16144. [PMID: 31695138 PMCID: PMC6834603 DOI: 10.1038/s41598-019-52502-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/14/2019] [Indexed: 01/12/2023] Open
Abstract
Iron (Fe) is an essential micronutrient that is frequently inaccessible to plants. Rice (Oryza sativa L.) plants employ the Combined Strategy for Fe uptake, which is composed by all features of Strategy II, common to all Poaceae species, and some features of Strategy I, common to non-Poaceae species. To understand the evolution of Fe uptake mechanisms, we analyzed the root transcriptomic response to Fe deficiency in O. sativa and its wild progenitor O. rufipogon. We identified 622 and 2,017 differentially expressed genes in O. sativa and O. rufipogon, respectively. Among the genes up-regulated in both species, we found Fe transporters associated with Strategy I, such as IRT1, IRT2 and NRAMP1; and genes associated with Strategy II, such as YSL15 and IRO2. In order to evaluate the conservation of these Strategies among other Poaceae, we identified the orthologs of these genes in nine species from the Oryza genus, maize and sorghum, and evaluated their expression profile in response to low Fe condition. Our results indicate that the Combined Strategy is not specific to O. sativa as previously proposed, but also present in species of the Oryza genus closely related to domesticated rice, and originated around the same time the AA genome lineage within Oryza diversified. Therefore, adaptation to Fe2+ acquisition via IRT1 in flooded soils precedes O. sativa domestication.
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Affiliation(s)
- Andriele Wairich
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ben Hur Neves de Oliveira
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ezequiel Barth Arend
- Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Guilherme Leitão Duarte
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Lucas Roani Ponte
- Departamento de Biologia, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Raul Antonio Sperotto
- Programa de Pós-Graduação em Biotecnologia, Universidade do Vale do Taquari - Univates, Lajeado, Brazil
| | - Felipe Klein Ricachenevsky
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
- Departamento de Biologia, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil.
| | - Janette Palma Fett
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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35
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Moschall R, Rass M, Rossbach O, Lehmann G, Kullmann L, Eichner N, Strauss D, Meister G, Schneuwly S, Krahn MP, Medenbach J. Drosophila Sister-of-Sex-lethal reinforces a male-specific gene expression pattern by controlling Sex-lethal alternative splicing. Nucleic Acids Res 2019; 47:2276-2288. [PMID: 30590805 PMCID: PMC6411925 DOI: 10.1093/nar/gky1284] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/04/2018] [Accepted: 12/14/2018] [Indexed: 01/14/2023] Open
Abstract
In Drosophila, female development is governed by a single RNA-binding protein, Sex-lethal (Sxl), that controls the expression of key factors involved in dosage compensation, germline homeostasis and the establishment of female morphology and behaviour. Sxl expression in female flies is maintained by an auto-regulatory, positive feedback loop with Sxl controlling splicing of its own mRNA. Until now, it remained unclear how males prevent accidental triggering of the Sxl expression cascade and protect themselves against runaway protein production. Here, we identify the protein Sister-of-Sex-lethal (Ssx) as an inhibitor of Sxl auto-regulatory splicing. Sxl and Ssx have a comparable RNA-binding specificity and compete for binding to RNA regulatory elements present in the Sxl transcript. In cultured Drosophila cells, Sxl-induced changes to alternative splicing can be reverted by the expression of Ssx. Moreover, in adult male flies ablation of the ssx gene results in a low level of productive Sxl mRNA splicing and Sxl protein production in isolated, clonal cell populations. In sum, this demonstrates that Ssx safeguards male animals against Sxl protein production to reinforce a stable, male-specific gene expression pattern.
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Affiliation(s)
- Rebecca Moschall
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Mathias Rass
- Institute of Zoology, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Oliver Rossbach
- Institute of Biochemistry, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany
| | - Gerhard Lehmann
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Lars Kullmann
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Norbert Eichner
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Daniela Strauss
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Gunter Meister
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Stephan Schneuwly
- Institute of Zoology, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Michael P Krahn
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany.,Medical Clinic D, University of Muenster, Domagkstrasse 3, D-48149 Muenster, Germany
| | - Jan Medenbach
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
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Ke Y, Zhang J, Lv X, Zeng X, Ba X. Novel insights into PARPs in gene expression: regulation of RNA metabolism. Cell Mol Life Sci 2019; 76:3283-3299. [PMID: 31055645 PMCID: PMC6697709 DOI: 10.1007/s00018-019-03120-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 04/13/2019] [Accepted: 04/29/2019] [Indexed: 12/15/2022]
Abstract
Poly(ADP-ribosyl)ation (PARylation) is an important post-translational modification in which an ADP-ribose group is transferred to the target protein by poly(ADP-riboses) polymerases (PARPs). Since the discovery of poly-ADP-ribose (PAR) 50 years ago, its roles in cellular processes have been extensively explored. Although research initially focused on the functions of PAR and PARPs in DNA damage detection and repair, our understanding of the roles of PARPs in various nuclear and cytoplasmic processes, particularly in gene expression, has increased significantly. In this review, we discuss the current advances in understanding the roles of PARylation with a particular emphasis in gene expression through RNA biogenesis and processing. In addition to updating PARP's significance in transcriptional regulation, we specifically focus on how PARPs and PARylation affect gene expression, especially inflammation-related genes, at the post-transcriptional levels by modulating RNA processing and degrading. Increasing evidence suggests that PARP inhibition is a promising treatment for inflammation-related diseases besides conventional chemotherapy for cancer.
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Affiliation(s)
- Yueshuang Ke
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Institute of Genetics and Cytology, School of Life Science, Northeast Normal University, Changchun, 130024, Jilin, China
| | - Jing Zhang
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Institute of Genetics and Cytology, School of Life Science, Northeast Normal University, Changchun, 130024, Jilin, China
| | - Xueping Lv
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Institute of Genetics and Cytology, School of Life Science, Northeast Normal University, Changchun, 130024, Jilin, China
| | - Xianlu Zeng
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Institute of Genetics and Cytology, School of Life Science, Northeast Normal University, Changchun, 130024, Jilin, China
| | - Xueqing Ba
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Institute of Genetics and Cytology, School of Life Science, Northeast Normal University, Changchun, 130024, Jilin, China.
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China.
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Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae. Sci Rep 2019; 9:12122. [PMID: 31431676 PMCID: PMC6702216 DOI: 10.1038/s41598-019-47797-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 07/19/2019] [Indexed: 01/19/2023] Open
Abstract
Extensive transcriptional activity occurring in intergenic regions of genomes has raised the question whether intergenic transcription represents the activity of novel genes or noisy expression. To address this, we evaluated cross-species and post-duplication sequence and expression conservation of intergenic transcribed regions (ITRs) in four Poaceae species. Among 43,301 ITRs across the four species, 34,460 (80%) are species-specific. ITRs found across species tend to be more divergent in expression and have more recent duplicates compared to annotated genes. To assess if ITRs are functional (under selection), machine learning models were established in Oryza sativa (rice) that could accurately distinguish between phenotype genes and pseudogenes (area under curve-receiver operating characteristic = 0.94). Based on the models, 584 (8%) and 4391 (61%) rice ITRs are classified as likely functional and nonfunctional with high confidence, respectively. ITRs with conserved expression and ancient retained duplicates, features that were not part of the model, are frequently classified as likely-functional, suggesting these characteristics could serve as pragmatic rules of thumb for identifying candidate sequences likely to be under selection. This study also provides a framework to identify novel genes using comparative transcriptomic data to improve genome annotation that is fundamental for connecting genotype to phenotype in crop and model systems.
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38
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Wu S, Tong X, Li C, Lu K, Tan D, Hu H, Liu H, Dai F. Genome-wide identification and expression profiling of the C2H2-type zinc finger protein genes in the silkworm Bombyx mori. PeerJ 2019; 7:e7222. [PMID: 31316872 PMCID: PMC6613534 DOI: 10.7717/peerj.7222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 05/30/2019] [Indexed: 12/29/2022] Open
Abstract
Cys2-His2 zinc finger (C2H2-ZF) proteins comprise the largest class of putative eukaryotic transcription factors. The zinc finger motif array is highly divergent, indicating that most proteins will have distinctive binding sites and perform different functions. However, the binding sites and functions of the majority of C2H2-ZF proteins remain unknown. In this study, we identified 327 C2H2-ZF protein genes in the silkworm, 290 in the monarch butterfly, 243 in the fruit fly, 107 in elegans, 673 in mouse, and 1,082 in human. The C2H2-ZF protein genes of the silkworm were classified into three main grouping clades according to a phylogenetic classification, and 312 of these genes could be mapped onto 27 chromosomes. Most silkworm C2H2-ZF protein genes exhibited specific expression in larval tissues. Furthermore, several C2H2-ZF protein genes had sex-specific expression during metamorphosis. In addition, we found that some C2H2-ZF protein genes are involved in metamorphosis and female reproduction by using expression clustering and gene annotation analysis. Among them, five genes were selected, BGIBMGA002091 (CTCF), BGIBMGA006492 (fru), BGIBMGA006230 (wor), BGIBMGA004640 (lola), and BIGBMGA004569, for quantitative real-time PCR analysis from larvae to adult ovaries. The results showed that the five genes had different expression patterns in ovaries, among which BGIBMGA002091 (CTCF) gene expression level was the highest, and its expression level increased rapidly in late pupae and adult stages. These findings provide a basis for further investigation of the functions of C2H2-ZF protein genes in the silkworm, and the results offer clues for further research into the development of metamorphosis and female reproduction in the silkworm.
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Affiliation(s)
- SongYuan Wu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China.,College of Plant Protection, Southwest University, Chong Qing, China
| | - Xiaoling Tong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China
| | - ChunLin Li
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China
| | - KunPeng Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China
| | - Duan Tan
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China
| | - Hai Hu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China
| | - Huai Liu
- College of Plant Protection, Southwest University, Chong Qing, China
| | - FangYin Dai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China
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Slabaugh E, Desai JS, Sartor RC, Lawas LMF, Jagadish SVK, Doherty CJ. Analysis of differential gene expression and alternative splicing is significantly influenced by choice of reference genome. RNA (NEW YORK, N.Y.) 2019; 25:669-684. [PMID: 30872414 PMCID: PMC6521602 DOI: 10.1261/rna.070227.118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 03/06/2019] [Indexed: 05/19/2023]
Abstract
RNA-seq analysis has enabled the evaluation of transcriptional changes in many species including nonmodel organisms. However, in most species only a single reference genome is available and RNA-seq reads from highly divergent varieties are typically aligned to this reference. Here, we quantify the impacts of the choice of mapping genome in rice where three high-quality reference genomes are available. We aligned RNA-seq data from a popular productive rice variety to three different reference genomes and found that the identification of differentially expressed genes differed depending on which reference genome was used for mapping. Furthermore, the ability to detect differentially used transcript isoforms was profoundly affected by the choice of reference genome: Only 30% of the differentially used splicing features were detected when reads were mapped to the more commonly used, but more distantly related reference genome. This demonstrated that gene expression and splicing analysis varies considerably depending on the mapping reference genome, and that analysis of individuals that are distantly related to an available reference genome may be improved by acquisition of new genomic reference material. We observed that these differences in transcriptome analysis are, in part, due to the presence of single nucleotide polymorphisms between the sequenced individual and each respective reference genome, as well as annotation differences between the reference genomes that exist even between syntenic orthologs. We conclude that even between two closely related genomes of similar quality, using the reference genome that is most closely related to the species being sampled significantly improves transcriptome analysis.
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Affiliation(s)
- Erin Slabaugh
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Jigar S Desai
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Ryan C Sartor
- Crop and Soil Science Department, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Lovely Mae F Lawas
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam, Germany
| | - S V Krishna Jagadish
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- Department of Agronomy, Kansas State University, Manhattan, Kansas 66506, USA
| | - Colleen J Doherty
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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40
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Nikonova E, Kao SY, Ravichandran K, Wittner A, Spletter ML. Conserved functions of RNA-binding proteins in muscle. Int J Biochem Cell Biol 2019; 110:29-49. [PMID: 30818081 DOI: 10.1016/j.biocel.2019.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 02/21/2019] [Accepted: 02/23/2019] [Indexed: 12/13/2022]
Abstract
Animals require different types of muscle for survival, for example for circulation, motility, reproduction and digestion. Much emphasis in the muscle field has been placed on understanding how transcriptional regulation generates diverse types of muscle during development. Recent work indicates that alternative splicing and RNA regulation are as critical to muscle development, and altered function of RNA-binding proteins causes muscle disease. Although hundreds of genes predicted to bind RNA are expressed in muscles, many fewer have been functionally characterized. We present a cross-species view summarizing what is known about RNA-binding protein function in muscle, from worms and flies to zebrafish, mice and humans. In particular, we focus on alternative splicing regulated by the CELF, MBNL and RBFOX families of proteins. We discuss the systemic nature of diseases associated with loss of RNA-binding proteins in muscle, focusing on mis-regulation of CELF and MBNL in myotonic dystrophy. These examples illustrate the conservation of RNA-binding protein function and the marked utility of genetic model systems in understanding mechanisms of RNA regulation.
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Affiliation(s)
- Elena Nikonova
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Shao-Yen Kao
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Keshika Ravichandran
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Anja Wittner
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Maria L Spletter
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany; Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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Chalmers L, Vera LM, Taylor JF, Adams A, Migaud H. Comparative ploidy response to experimental hydrogen peroxide exposure in Atlantic salmon (Salmo salar). FISH & SHELLFISH IMMUNOLOGY 2018; 81:354-367. [PMID: 30012493 PMCID: PMC6115329 DOI: 10.1016/j.fsi.2018.07.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/04/2018] [Accepted: 07/10/2018] [Indexed: 05/05/2023]
Abstract
While research into the growth, survival, nutrition and, more recently, disease susceptibility of triploid Atlantic salmon has expanded, there remains an overall lack of studies assessing the response of triploids to chemical treatments. It is essential that the response of triploids to disease treatments be characterised to validate their suitability for commercial production. This study aimed to investigate and compare the stress and immune responses of triploid and diploid Atlantic salmon following an experimental treatment with hydrogen peroxide (H2O2). A dose response test was first undertaken to determine a suitable test dose for both diploid and triploid Atlantic salmon. Following this, diploids and triploids were exposed to H2O2 (1800 ppm) for 20 min, as per commercial practices, after which blood glucose and lactate, and plasma cortisol and lysozyme were measured, along with the expression of oxidative stress and immune-related genes. In the first 6 h post-exposure to H2O2, comparable mortalities occurred in both diploid and triploid Atlantic salmon. Cortisol, glucose and lactate were not significantly influenced by ploidy suggesting that, physiologically, triploid Atlantic salmon are able to cope with the stress associated with H2O2 exposure as well as their diploid counterparts. Exposure to H2O2 significantly elevated the expression of cat and sod2 in diploid livers and gr, il1β and crp/sap1b in diploid gills, while it significantly decreased the expression of saa5 and crp/sap1a in diploid gills. In triploids, the expression levels of cat, hsp70, sod1, saa5, crp/sap1a and crp/sap1b in liver was significantly higher in fish exposed to H2O2 compared to control fish. The expression of gr, sod1 and il1β in triploid gills was also elevated in response to H2O2 exposure. This study represents the first experimental evidence of the effects of H2O2 exposure on triploid Atlantic salmon and continues to support their application into commercial production.
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Affiliation(s)
- Lynn Chalmers
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Luisa M Vera
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - John F Taylor
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Alexandra Adams
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Herve Migaud
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK.
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Monedero Cobeta I, Stadler CB, Li J, Yu P, Thor S, Benito-Sipos J. Specification of Drosophila neuropeptidergic neurons by the splicing component brr2. PLoS Genet 2018; 14:e1007496. [PMID: 30133436 PMCID: PMC6122834 DOI: 10.1371/journal.pgen.1007496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 09/04/2018] [Accepted: 06/18/2018] [Indexed: 02/07/2023] Open
Abstract
During embryonic development, a number of genetic cues act to generate neuronal diversity. While intrinsic transcriptional cascades are well-known to control neuronal sub-type cell fate, the target cells can also provide critical input to specific neuronal cell fates. Such signals, denoted retrograde signals, are known to provide critical survival cues for neurons, but have also been found to trigger terminal differentiation of neurons. One salient example of such target-derived instructive signals pertains to the specification of the Drosophila FMRFamide neuropeptide neurons, the Tv4 neurons of the ventral nerve cord. Tv4 neurons receive a BMP signal from their target cells, which acts as the final trigger to activate the FMRFa gene. A recent FMRFa-eGFP genetic screen identified several genes involved in Tv4 specification, two of which encode components of the U5 subunit of the spliceosome: brr2 (l(3)72Ab) and Prp8. In this study, we focus on the role of RNA processing during target-derived signaling. We found that brr2 and Prp8 play crucial roles in controlling the expression of the FMRFa neuropeptide specifically in six neurons of the VNC (Tv4 neurons). Detailed analysis of brr2 revealed that this control is executed by two independent mechanisms, both of which are required for the activation of the BMP retrograde signaling pathway in Tv4 neurons: (1) Proper axonal pathfinding to the target tissue in order to receive the BMP ligand. (2) Proper RNA splicing of two genes in the BMP pathway: the thickveins (tkv) gene, encoding a BMP receptor subunit, and the Medea gene, encoding a co-Smad. These results reveal involvement of specific RNA processing in diversifying neuronal identity within the central nervous system. The nervous system displays daunting cellular diversity, largely generated through complex regulatory input operating on stem cells and their neural lineages during development. Most of the reported mechanisms acting to generate neural diversity pertain to transcriptional regulation. In contrast, little is known regarding the post-transcriptional mechanisms involved. Here, we use a specific group of neurons, Apterous neurons, in the ventral nerve cord of Drosophila melanogaster as our model, to analyze the function of two essential components of the spliceosome; Brr2 and Prp8. Apterous neurons require a BMP retrograde signal for terminal differentiation, and we find that brr2 and Prp8 play crucial roles during this process. brr2 is critical for two independent events; axon pathfinding and BMP signaling, both of which are required for the activation of the retrograde signaling pathway necessary for Apterous neurons. These results identify a post-transcriptional mechanism as key for specifying neuronal identity, by ensuring the execution of a retrograde signal.
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Affiliation(s)
- Ignacio Monedero Cobeta
- Dept. of Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- Dept. of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden
| | | | - Jin Li
- Department of Electrical and Computer Engineering Texas A&M University, College Station, Texas, United States of America
- TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Peng Yu
- Department of Electrical and Computer Engineering Texas A&M University, College Station, Texas, United States of America
| | - Stefan Thor
- Dept. of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden
| | - Jonathan Benito-Sipos
- Dept. of Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- * E-mail:
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43
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Jamek SB, Muschiol J, Holck J, Zeuner B, Busk PK, Mikkelsen JD, Meyer AS. Loop Protein Engineering for Improved Transglycosylation Activity of a β‐
N
‐Acetylhexosaminidase. Chembiochem 2018; 19:1858-1865. [DOI: 10.1002/cbic.201800181] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Indexed: 01/17/2023]
Affiliation(s)
- Shariza B. Jamek
- Center for Bioprocess EngineeringDepartment of Chemical and Biochemical EngineeringTechnical University of Denmark Søltofts Plads Building 229 2800 Kongens Lyngby Denmark
- Faculty of Chemical and Natural Resources EngineeringUniversity Malaysia Pahang Lebuhraya Tun Razak 26300 Gambang, Kuantan, Pahang Malaysia
| | - Jan Muschiol
- Center for Bioprocess EngineeringDepartment of Chemical and Biochemical EngineeringTechnical University of Denmark Søltofts Plads Building 229 2800 Kongens Lyngby Denmark
| | - Jesper Holck
- Center for Bioprocess EngineeringDepartment of Chemical and Biochemical EngineeringTechnical University of Denmark Søltofts Plads Building 229 2800 Kongens Lyngby Denmark
| | - Birgitte Zeuner
- Center for Bioprocess EngineeringDepartment of Chemical and Biochemical EngineeringTechnical University of Denmark Søltofts Plads Building 229 2800 Kongens Lyngby Denmark
| | - Peter K. Busk
- Center for Bioprocess EngineeringDepartment of Chemical and Biochemical EngineeringTechnical University of Denmark Søltofts Plads Building 229 2800 Kongens Lyngby Denmark
| | - Jørn D. Mikkelsen
- Center for Bioprocess EngineeringDepartment of Chemical and Biochemical EngineeringTechnical University of Denmark Søltofts Plads Building 229 2800 Kongens Lyngby Denmark
| | - Anne S. Meyer
- Center for Bioprocess EngineeringDepartment of Chemical and Biochemical EngineeringTechnical University of Denmark Søltofts Plads Building 229 2800 Kongens Lyngby Denmark
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44
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Streubel S, Fritz MA, Teltow M, Kappel C, Sicard A. Successive duplication-divergence mechanisms at the RCO locus contributed to leaf shape diversity in the Brassicaceae. Development 2018; 145:145/8/dev164301. [PMID: 29691226 DOI: 10.1242/dev.164301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 03/21/2018] [Indexed: 12/19/2022]
Abstract
Gene duplication is a major driver for the increase of biological complexity. The divergence of newly duplicated paralogs may allow novel functions to evolve, while maintaining the ancestral one. Alternatively, partitioning the ancestral function among paralogs may allow parts of that role to follow independent evolutionary trajectories. We studied the REDUCED COMPLEXITY (RCO) locus, which contains three paralogs that have evolved through two independent events of gene duplication, and which underlies repeated events of leaf shape evolution within the Brassicaceae. In particular, we took advantage of the presence of three potentially functional paralogs in Capsella to investigate the extent of functional divergence among them. We demonstrate that the RCO copies control growth in different areas of the leaf. Consequently, the copies that are retained active in the different Brassicaceae lineages contribute to define the leaf dissection pattern. Our results further illustrate how successive gene duplication events and subsequent functional divergence can increase trait evolvability by providing independent evolutionary trajectories to specialized functions that have an additive effect on a given trait.
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Affiliation(s)
- Susanna Streubel
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Michael André Fritz
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Melanie Teltow
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Christian Kappel
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Adrien Sicard
- Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany .,Uppsala Biocenter, Department of Plant Biology, BOX 7080, 750 07, Uppsala, Sweden
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45
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Lajkó DB, Valkai I, Domoki M, Ménesi D, Ferenc G, Ayaydin F, Fehér A. In silico identification and experimental validation of amino acid motifs required for the Rho-of-plants GTPase-mediated activation of receptor-like cytoplasmic kinases. PLANT CELL REPORTS 2018; 37:627-639. [PMID: 29340786 DOI: 10.1007/s00299-018-2256-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/08/2018] [Indexed: 06/07/2023]
Abstract
Several amino acid motifs required for Rop-dependent activity were found to form a common surface on RLCKVI_A kinases. This indicates a unique mechanism for Rho-type GTPase-mediated kinase activation in plants. Rho-of-plants (Rop) G-proteins are implicated in the regulation of various cellular processes, including cell growth, cell polarity, hormonal and pathogen responses. Our knowledge about the signalling pathways downstream of Rops is continuously increasing. However, there are still substantial gaps in this knowledge. One reason for this is that these pathways are considerably different from those described for yeast and/or animal Rho-type GTPases. Among others, plants lack all Rho/Rac/Cdc42-activated kinase families. Only a small group of plant-specific receptor-like cytoplasmic kinases (RLCK VI_A) has been shown to exhibit Rop-binding-dependent in vitro activity. These kinases do not carry any known GTPase-binding motifs. Based on the sequence comparison of the Rop-activated RLCK VI_A and the closely related but constitutively active RLCK VI_B kinases, several distinguishing amino acid residues/motifs were identified. All but one of these were found to be required for the Rop-mediated regulation of the in vitro activity of two RLCK VI_A kinases. Structural modelling indicated that these motifs might form a common Rop-binding surface. Based on in silico data mining, kinases that have the identified Rop-binding motifs are present in Embryophyta but not in unicellular green algae. It can, therefore, be supposed that Rops recruited these plant-specific kinases for signalling at an early stage of land plant evolution.
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Affiliation(s)
- Dézi Bianka Lajkó
- Biological Research Centre, Institute of Plant Biology, Hungarian Academy of Sciences, Temesvári krt. 62, P.O. Box 521, Szeged, 6701, Hungary
| | - Ildikó Valkai
- Biological Research Centre, Institute of Plant Biology, Hungarian Academy of Sciences, Temesvári krt. 62, P.O. Box 521, Szeged, 6701, Hungary
| | - Mónika Domoki
- Biological Research Centre, Institute of Plant Biology, Hungarian Academy of Sciences, Temesvári krt. 62, P.O. Box 521, Szeged, 6701, Hungary
| | - Dalma Ménesi
- Biological Research Centre, Institute of Plant Biology, Hungarian Academy of Sciences, Temesvári krt. 62, P.O. Box 521, Szeged, 6701, Hungary
| | - Györgyi Ferenc
- Biological Research Centre, Institute of Plant Biology, Hungarian Academy of Sciences, Temesvári krt. 62, P.O. Box 521, Szeged, 6701, Hungary
| | - Ferhan Ayaydin
- Biological Research Centre, Institute of Plant Biology, Hungarian Academy of Sciences, Temesvári krt. 62, P.O. Box 521, Szeged, 6701, Hungary
| | - Attila Fehér
- Biological Research Centre, Institute of Plant Biology, Hungarian Academy of Sciences, Temesvári krt. 62, P.O. Box 521, Szeged, 6701, Hungary.
- Department of Plant Biology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary.
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46
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Moschall R, Strauss D, García-Beyaert M, Gebauer F, Medenbach J. Drosophila Sister-of-Sex-lethal is a repressor of translation. RNA (NEW YORK, N.Y.) 2018; 24:149-158. [PMID: 29089381 PMCID: PMC5769743 DOI: 10.1261/rna.063776.117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
The RNA-binding protein Sex-lethal (Sxl) is an important post-transcriptional regulator of sex determination and dosage compensation in female Drosophila To prevent the assembly of the MSL dosage compensation complex in female flies, Sxl acts as a repressor of male-specific lethal-2 (msl-2) mRNA translation. It uses two distinct and mutually reinforcing blocks to translation that operate on the 5' and 3' untranslated regions (UTRs) of msl-2 mRNA, respectively. While 5' UTR-mediated translational control involves an upstream open reading frame, 3' UTR-mediated regulation strictly requires the co-repressor protein Upstream of N-ras (Unr), which is recruited to the transcript by Sxl. We have identified the protein Sister-of-Sex-lethal (Ssx) as a novel repressor of translation with Sxl-like activity. Both proteins have a comparable RNA-binding specificity and can associate with uracil-rich RNA regulatory elements present in msl-2 mRNA. Moreover, both repress translation when bound to the 5' UTR of msl-2 However, Ssx is inactive in 3' UTR-mediated regulation, as it cannot engage the co-repressor protein Unr. The difference in activity maps to the first RNA-recognition motif (RRM) of Ssx. Conversion of three amino acids within this domain into their Sxl counterpart results in a gain of function and repression via the 3' UTR, allowing detailed insights into the evolutionary origin of the two proteins and into the molecular requirements of an important translation regulatory pathway.
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Affiliation(s)
- Rebecca Moschall
- Institute of Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Daniela Strauss
- Institute of Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Marina García-Beyaert
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Jan Medenbach
- Institute of Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
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47
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Liu D, Hunt M, Tsai IJ. Inferring synteny between genome assemblies: a systematic evaluation. BMC Bioinformatics 2018; 19:26. [PMID: 29382321 PMCID: PMC5791376 DOI: 10.1186/s12859-018-2026-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 01/15/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Genome assemblies across all domains of life are being produced routinely. Initial analysis of a new genome usually includes annotation and comparative genomics. Synteny provides a framework in which conservation of homologous genes and gene order is identified between genomes of different species. The availability of human and mouse genomes paved the way for algorithm development in large-scale synteny mapping, which eventually became an integral part of comparative genomics. Synteny analysis is regularly performed on assembled sequences that are fragmented, neglecting the fact that most methods were developed using complete genomes. It is unknown to what extent draft assemblies lead to errors in such analysis. RESULTS We fragmented genome assemblies of model nematodes to various extents and conducted synteny identification and downstream analysis. We first show that synteny between species can be underestimated up to 40% and find disagreements between popular tools that infer synteny blocks. This inconsistency and further demonstration of erroneous gene ontology enrichment tests raise questions about the robustness of previous synteny analysis when gold standard genome sequences remain limited. In addition, assembly scaffolding using a reference guided approach with a closely related species may result in chimeric scaffolds with inflated assembly metrics if a true evolutionary relationship was overlooked. Annotation quality, however, has minimal effect on synteny if the assembled genome is highly contiguous. CONCLUSIONS Our results show that a minimum N50 of 1 Mb is required for robust downstream synteny analysis, which emphasizes the importance of gold standard genomes to the science community, and should be achieved given the current progress in sequencing technology.
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Affiliation(s)
- Dang Liu
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Martin Hunt
- Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, Oxford, OX1 1NF UK
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Isheng J Tsai
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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48
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Lee YCG, Yang Q, Chi W, Turkson SA, Du WA, Kemkemer C, Zeng ZB, Long M, Zhuang X. Genetic Architecture of Natural Variation Underlying Adult Foraging Behavior That Is Essential for Survival of Drosophila melanogaster. Genome Biol Evol 2018; 9:1357-1369. [PMID: 28472322 PMCID: PMC5452641 DOI: 10.1093/gbe/evx089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2017] [Indexed: 01/04/2023] Open
Abstract
Foraging behavior is critical for the fitness of individuals. However, the genetic basis of variation in foraging behavior and the evolutionary forces underlying such natural variation have rarely been investigated. We developed a systematic approach to assay the variation in survival rate in a foraging environment for adult flies derived from a wild Drosophila melanogaster population. Despite being such an essential trait, there is substantial variation of foraging behavior among D. melanogaster strains. Importantly, we provided the first evaluation of the potential caveats of using inbred Drosophila strains to perform genome-wide association studies on life-history traits, and concluded that inbreeding depression is unlikely a major contributor for the observed large variation in adult foraging behavior. We found that adult foraging behavior has a strong genetic component and, unlike larval foraging behavior, depends on multiple loci. Identified candidate genes are enriched in those with high expression in adult heads and, demonstrated by expression knock down assay, are involved in maintaining normal functions of the nervous system. Our study not only identified candidate genes for foraging behavior that is relevant to individual fitness, but also shed light on the initial stage underlying the evolution of the behavior.
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Affiliation(s)
- Yuh Chwen G Lee
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL.,Present address: Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory; Department of Molecular Biology and Cell Biology, University of California, Berkeley
| | - Qian Yang
- Department of Neurobiology, The University of Chicago, Chicago, IL
| | - Wanhao Chi
- Department of Neurobiology, The University of Chicago, Chicago, IL.,Present address: Committee on Genetics, Genomics & Systems Biology, The University of Chicago, Chicago, IL
| | - Susie A Turkson
- Department of Neurobiology, The University of Chicago, Chicago, IL
| | - Wei A Du
- Department of Biology, Wayne State University, Detroit, MI
| | - Claus Kemkemer
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL
| | - Zhao-Bang Zeng
- Department of Statistical Genetics and Bioinformatics, North Carolina State University, Raleigh, NC
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL
| | - Xiaoxi Zhuang
- Department of Neurobiology, The University of Chicago, Chicago, IL
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Abstract
In the present chapter, we present the protocols and guidelines to facilitate implementation of CRISPR-Cas9 technology in fungi where few or no genetic tools are in place. Hence, we firstly explain how to identify dominant markers for genetic transformation. Secondly, we provide a guide for construction of Cas9/sgRNA episomal expression vectors. Thirdly, we present how to mutagenize reporter genes to explore the efficiency of CRISPR-Cas9 in the relevant fungus and to ease subsequent CRISPR-mediated genetic engineering. Lastly, we describe how to make CRISPR-mediated marker-dependent and marker-free gene targeting.
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Affiliation(s)
- Jakob B Hoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs.Lyngby, Denmark
| | - Christina S Nødvig
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs.Lyngby, Denmark
| | - Uffe H Mortensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs.Lyngby, Denmark.
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50
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The Y Chromosome Modulates Splicing and Sex-Biased Intron Retention Rates in Drosophila. Genetics 2017; 208:1057-1067. [PMID: 29263027 DOI: 10.1534/genetics.117.300637] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/18/2017] [Indexed: 01/01/2023] Open
Abstract
The Drosophila Y chromosome is a 40-Mb segment of mostly repetitive DNA; it harbors a handful of protein-coding genes and a disproportionate amount of satellite repeats, transposable elements, and multicopy DNA arrays. Intron retention (IR) is a type of alternative splicing (AS) event by which one or more introns remain within the mature transcript. IR recently emerged as a deliberate cellular mechanism to modulate gene expression levels and has been implicated in multiple biological processes. However, the extent of sex differences in IR and the contribution of the Y chromosome to the modulation of AS and IR rates has not been addressed. Here we showed pervasive IR in the fruit fly Drosophila melanogaster with thousands of novel IR events, hundreds of which displayed extensive sex bias. The data also revealed an unsuspected role for the Y chromosome in the modulation of AS and IR. The majority of sex-biased IR events introduced premature termination codons and the magnitude of sex bias was associated with gene expression differences between the sexes. Surprisingly, an extra Y chromosome in males (X^YY genotype) or the presence of a Y chromosome in females (X^XY genotype) significantly modulated IR and recapitulated natural differences in IR between the sexes. Our results highlight the significance of sex-biased IR in tuning sex differences and the role of the Y chromosome as a source of variable IR rates between the sexes. Modulation of splicing and IR rates across the genome represent new and unexpected outcomes of the Drosophila Y chromosome.
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