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Choi SR, Lee J, Seo YJ, Jin HS, Ahn HB, Go Y, Kim NK, Ryu KS, Lee JH. Molecular basis of facilitated target search and sequence discrimination of TALE homeodomain transcription factor Meis1. Nat Commun 2024; 15:6984. [PMID: 39143123 PMCID: PMC11325038 DOI: 10.1038/s41467-024-51297-7] [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: 02/22/2023] [Accepted: 08/05/2024] [Indexed: 08/16/2024] Open
Abstract
Transcription factors specifically bind to their consensus sequence motifs and regulate transcription efficiency. Transcription factors are also able to non-specifically contact the phosphate backbone of DNA through electrostatic interaction. The homeodomain of Meis1 TALE human transcription factor (Meis1-HD) recognizes its target DNA sequences via two DNA contact regions, the L1-α1 region and the α3 helix (specific binding mode). This study demonstrates that the non-specific binding mode of Meis1-HD is the energetically favored process during DNA binding, achieved by the interaction of the L1-α1 region with the phosphate backbone. An NMR dynamics study suggests that non-specific binding might set up an intermediate structure which can then rapidly and easily find the consensus region on a long section of genomic DNA in a facilitated binding process. Structural analysis using NMR and molecular dynamics shows that key structural distortions in the Meis1-HD-DNA complex are induced by various single nucleotide mutations in the consensus sequence, resulting in decreased DNA binding affinity. Collectively, our results elucidate the detailed molecular mechanism of how Meis1-HD recognizes single nucleotide mutations within its consensus sequence: (i) through the conformational features of the α3 helix; and (ii) by the dynamic features (rigid or flexible) of the L1 loop and the α3 helix. These findings enhance our understanding of how single nucleotide mutations in transcription factor consensus sequences lead to dysfunctional transcription and, ultimately, human disease.
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Affiliation(s)
- Seo-Ree Choi
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongsangnam-do, 52828, Republic of Korea
- Advanced Analysis Data Center, Korea Institute of Science and Technology, Seoul, 02456, Republic of Korea
| | - Juyong Lee
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
- Research Institute of Pharmaceutical Science, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
- Arontier Co., Seoul, 06735, Republic of Korea.
| | - Yeo-Jin Seo
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongsangnam-do, 52828, Republic of Korea
| | - Ho-Seong Jin
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongsangnam-do, 52828, Republic of Korea
| | - Hye-Bin Ahn
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongsangnam-do, 52828, Republic of Korea
| | - Youyeon Go
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongsangnam-do, 52828, Republic of Korea
| | - Nak-Kyoon Kim
- Advanced Analysis Data Center, Korea Institute of Science and Technology, Seoul, 02456, Republic of Korea
| | - Kyoung-Seok Ryu
- Protein Structure Research Team, Korea Basic Science Institute, Cheongju, Chungcheongbuk-do, 28119, Republic of Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongsangnam-do, 52828, Republic of Korea
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2
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Webb JA, Farrow E, Cain B, Yuan Z, Yarawsky A, Schoch E, Gagliani E, Herr A, Gebelein B, Kovall R. Cooperative Gsx2-DNA binding requires DNA bending and a novel Gsx2 homeodomain interface. Nucleic Acids Res 2024; 52:7987-8002. [PMID: 38874471 PMCID: PMC11260452 DOI: 10.1093/nar/gkae522] [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: 12/11/2023] [Revised: 05/28/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024] Open
Abstract
The conserved Gsx homeodomain (HD) transcription factors specify neural cell fates in animals from flies to mammals. Like many HD proteins, Gsx factors bind A/T-rich DNA sequences prompting the following question: How do HD factors that bind similar DNA sequences in vitro regulate specific target genes in vivo? Prior studies revealed that Gsx factors bind DNA both as a monomer on individual A/T-rich sites and as a cooperative homodimer to two sites spaced precisely 7 bp apart. However, the mechanistic basis for Gsx-DNA binding and cooperativity is poorly understood. Here, we used biochemical, biophysical, structural and modeling approaches to (i) show that Gsx factors are monomers in solution and require DNA for cooperative complex formation, (ii) define the affinity and thermodynamic binding parameters of Gsx2/DNA interactions, (iii) solve a high-resolution monomer/DNA structure that reveals that Gsx2 induces a 20° bend in DNA, (iv) identify a Gsx2 protein-protein interface required for cooperative DNA binding and (v) determine that flexible spacer DNA sequences enhance Gsx2 cooperativity on dimer sites. Altogether, our results provide a mechanistic basis for understanding the protein and DNA structural determinants that underlie cooperative DNA binding by Gsx factors.
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Affiliation(s)
- Jordan A Webb
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Edward Farrow
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children’s Hospital Research Foundation, Cincinnati, OH 45229, USA
- Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Brittany Cain
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 7007, Cincinnati, OH 45229, USA
| | - Zhenyu Yuan
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Alexander E Yarawsky
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Emma Schoch
- Department of Medical Education, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Ellen K Gagliani
- Department of Chemistry, Xavier University, Cincinnati, OH 45207, USA
| | - Andrew B Herr
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 7007, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Rhett A Kovall
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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3
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David OG, Arce AV, Costa-da-Silva AL, Bellantuono AJ, DeGennaro M. Fertility decline in Aedes aegypti (Diptera: Culicidae) mosquitoes is associated with reduced maternal transcript deposition and does not depend on female age. JOURNAL OF MEDICAL ENTOMOLOGY 2024; 61:1064-1070. [PMID: 38757780 PMCID: PMC11239790 DOI: 10.1093/jme/tjae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 05/18/2024]
Abstract
Female mosquitoes undergo multiple rounds of reproduction known as gonotrophic cycles (GC). A gonotrophic cycle spans the period from blood meal intake to egg laying. Nutrients from vertebrate host blood are necessary for completing egg development. During oogenesis, a female prepackages mRNA into her oocytes, and these maternal transcripts drive the first 2 h of embryonic development prior to zygotic genome activation. In this study, we profiled transcriptional changes in 1-2 h of Aedes aegypti (Diptera: Culicidae) embryos across 2 GC. We found that homeotic genes which are regulators of embryogenesis are downregulated in embryos from the second gonotrophic cycle. Interestingly, embryos produced by Ae. aegypti females progressively reduced their ability to hatch as the number of GC increased. We show that this fertility decline is due to increased reproductive output and not the mosquitoes' age. Moreover, we found a similar decline in fertility and fecundity across 3 GC in Aedes albopictus. Our results are useful for predicting mosquito population dynamics to inform vector control efforts.
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Affiliation(s)
- Olayinka G David
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Andrea V Arce
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Andre Luis Costa-da-Silva
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Anthony J Bellantuono
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Matthew DeGennaro
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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4
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Birkholz N, Kamata K, Feussner M, Wilkinson ME, Cuba Samaniego C, Migur A, Kimanius D, Ceelen M, Went SC, Usher B, Blower TR, Brown CM, Beisel CL, Weinberg Z, Fagerlund RD, Jackson SA, Fineran PC. Phage anti-CRISPR control by an RNA- and DNA-binding helix-turn-helix protein. Nature 2024; 631:670-677. [PMID: 38987591 DOI: 10.1038/s41586-024-07644-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/31/2024] [Indexed: 07/12/2024]
Abstract
In all organisms, regulation of gene expression must be adjusted to meet cellular requirements and frequently involves helix-turn-helix (HTH) domain proteins1. For instance, in the arms race between bacteria and bacteriophages, rapid expression of phage anti-CRISPR (acr) genes upon infection enables evasion from CRISPR-Cas defence; transcription is then repressed by an HTH-domain-containing anti-CRISPR-associated (Aca) protein, probably to reduce fitness costs from excessive expression2-5. However, how a single HTH regulator adjusts anti-CRISPR production to cope with increasing phage genome copies and accumulating acr mRNA is unknown. Here we show that the HTH domain of the regulator Aca2, in addition to repressing Acr synthesis transcriptionally through DNA binding, inhibits translation of mRNAs by binding conserved RNA stem-loops and blocking ribosome access. The cryo-electron microscopy structure of the approximately 40 kDa Aca2-RNA complex demonstrates how the versatile HTH domain specifically discriminates RNA from DNA binding sites. These combined regulatory modes are widespread in the Aca2 family and facilitate CRISPR-Cas inhibition in the face of rapid phage DNA replication without toxic acr overexpression. Given the ubiquity of HTH-domain-containing proteins, it is anticipated that many more of them elicit regulatory control by dual DNA and RNA binding.
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MESH Headings
- Bacteriophages/chemistry
- Bacteriophages/genetics
- Bacteriophages/metabolism
- Bacteriophages/ultrastructure
- Binding Sites
- Clustered Regularly Interspaced Short Palindromic Repeats/genetics
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems
- Cryoelectron Microscopy
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- DNA-Binding Proteins/ultrastructure
- Gene Expression Regulation, Viral
- Genes, Viral
- Helix-Turn-Helix Motifs
- Models, Molecular
- Nucleic Acid Conformation
- Pectobacterium carotovorum/virology
- Protein Biosynthesis/genetics
- Protein Domains
- Ribosomes/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Messenger/ultrastructure
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- RNA, Viral/ultrastructure
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/ultrastructure
- Substrate Specificity
- Transcription, Genetic
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Proteins/metabolism
- Viral Proteins/ultrastructure
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Affiliation(s)
- Nils Birkholz
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Kotaro Kamata
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
| | - Maximilian Feussner
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Max E Wilkinson
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Angela Migur
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | | | - Marijn Ceelen
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute for Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Sam C Went
- Department of Biosciences, Durham University, Durham, UK
| | - Ben Usher
- Department of Biosciences, Durham University, Durham, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, Durham, UK
| | - Chris M Brown
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand.
- Genetics Otago, University of Otago, Dunedin, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand.
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5
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Zhou K, Wang T, Zhang J, Zhang J, Liu X, Guan J, Su P, Wu L, Yang X, Hu R, Sun Q, Fan Z, Yang S, Chu X, Song W, Shang Y, Zhou S, Hao X, Zhang X, Sun Q, Liu X, Miao YL. LEUTX regulates porcine embryonic genome activation in somatic cell nuclear transfer embryos. Cell Rep 2024; 43:114372. [PMID: 38878289 DOI: 10.1016/j.celrep.2024.114372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/06/2024] [Accepted: 05/31/2024] [Indexed: 07/02/2024] Open
Abstract
Emerging evidence highlights the regulatory role of paired-like (PRD-like) homeobox transcription factors (TFs) in embryonic genome activation (EGA). However, the majority of PRD-like genes are lost in rodents, thus prompting an investigation into PRD-like TFs in other mammals. Here, we showed that PRD-like TFs were transiently expressed during EGA in human, monkey, and porcine fertilized embryos, yet they exhibited inadequate expression in their cloned embryos. This study, using pig as the research model, identified LEUTX as a key PRD-like activator of porcine EGA through genomic profiling and found that LEUTX overexpression restored EGA failure and improved preimplantation development and cloning efficiency in porcine cloned embryos. Mechanistically, LEUTX opened EGA-related genomic regions and established histone acetylation via recruiting acetyltransferases p300 and KAT2A. These findings reveal the regulatory mechanism of LEUTX to govern EGA in pigs, which may provide valuable insights into the study of early embryo development for other non-rodent mammals.
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Affiliation(s)
- Kai Zhou
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Tingting Wang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Jingjing Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Jingcheng Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Xingchen Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiaqi Guan
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Peng Su
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Linhui Wu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Xin Yang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Ruifeng Hu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Qiaoran Sun
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Zhengang Fan
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Shichun Yang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Xiaoyu Chu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Wenting Song
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Yan Shang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Songxian Zhou
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Xingkun Hao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Xia Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Qiang Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Xin Liu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China.
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China.
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6
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Ezura K, Lu Y, Suzuki Y, Mitsuda N, Ariizumi T. Class II knotted-like homeodomain protein SlKN5 with BEL1-like homeodomain proteins suppresses fruit greening in tomato fruit. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2037-2054. [PMID: 38577750 DOI: 10.1111/tpj.16727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 03/01/2024] [Accepted: 03/10/2024] [Indexed: 04/06/2024]
Abstract
Knotted1-like homeodomain (KNOX) proteins are essential in regulating plant organ differentiation. Land plants, including tomato (Solanum lycopersicum), have two classes of the KNOX protein family, namely, class I (KNOX I) and class II KNOX (KNOX II). While tomato KNOX I proteins are known to stimulate chloroplast development in fruit, affecting fruit coloration, the role of KNOX II proteins in this context remains unclear. In this study, we employ CRISPR/Cas9 to generate knockout mutants of the KNOX II member, SlKN5. These mutants display increased leaf complexity, a phenotype commonly associated with reduced KNOX II activity, as well as enhanced accumulation of chloroplasts and chlorophylls in smaller cells within young, unripe fruit. RNA-seq data analyses indicate that SlKN5 suppresses the transcriptions of genes involved in chloroplast biogenesis, chlorophyll biosynthesis, and gibberellin catabolism. Furthermore, protein-protein interaction assays reveal that SlKN5 physically interacts with three transcriptional repressors from the BLH1-clade of BEL1-like homeodomain (BLH) protein family, SlBLH4, SlBLH5, and SlBLH7, with SlBLH7 showing the strongest interaction. CRISPR/Cas9-mediated knockout of these SlBLH genes confirmed their overlapping roles in suppressing chloroplast biogenesis, chlorophyll biosynthesis, and lycopene cyclization. Transient assays further demonstrate that the SlKN5-SlBLH7 interaction enhances binding capacity to regulatory regions of key chloroplast- and chlorophyll-related genes, including SlAPRR2-like1, SlCAB-1C, and SlGUN4. Collectively, our findings elucidate that the KNOX II SlKN5-SlBLH regulatory modules serve to inhibit fruit greening and subsequently promote lycopene accumulation, thereby fine-tuning the color transition from immature green fruit to mature red fruit.
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Affiliation(s)
- Kentaro Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
- Japan Society for Promotion of Science (JSPS), Kojimachi, Tokyo, 102-0083, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8566, Japan
| | - Yu Lu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8566, Japan
| | - Tohru Ariizumi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
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7
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Singh A, Acharya B, Mukherjee B, Boorla VS, Boral S, Maiti S, De S. Stability and dynamics of extradenticle modulates its function. Curr Res Struct Biol 2024; 7:100150. [PMID: 38784963 PMCID: PMC11112286 DOI: 10.1016/j.crstbi.2024.100150] [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: 12/30/2023] [Revised: 04/03/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Extradenticle (EXD) is a partner protein of the HOX transcription factors and plays an important role in the development of Drosophila. It confers increased affinity and specificity of DNA-binding to the HOX proteins. However, the DNA-binding homeodomain of EXD has a significantly weaker affinity to DNA compared to the HOX homeodomains. Here, we show that a glycine residue (G290) in the middle of the EXD DNA-binding helix primarily results in this weaker binding. Glycine destabilizes helices. To probe its role in the stability and function of the protein, G290 was mutated to alanine. The intrinsic stability of the DNA-binding helix increased in the G290A mutant as observed by NMR studies and molecular dynamics (MD) simulation. Also, NMR dynamics and MD simulation show that dynamic motions present in the wild-type protein are quenched in the mutant. This in turn resulted in increased stability of the entire homeodomain (ΔΔGG→A of -2.6 kcal/mol). Increased protein stability resulted in three-fold better DNA-binding affinity of the mutant as compared to the wild-type protein. Molecular mechanics with generalized Born and surface area solvation (MMGBSA) analysis of our MD simulation on DNA-bound models of both wild-type and mutant proteins shows that the contribution to binding is enhanced for most of the interface residues in the mutant compared to the wild-type. Interestingly, the flexible N-terminal arm makes more stable contact with the DNA minor groove in the mutant. We found that the two interaction sites i.e. the DNA-binding helix and the unstructured N-terminal arm influence each other via the bound DNA. These results provide an interesting conundrum: alanine at position 290 enhances both the stability and the DNA-binding affinity of the protein, however, evolution prefers glycine at this position. We have provided several plausible explanations for this apparent conundrum. The function of the EXD as a HOX co-factor requires its ability to discriminate similar DNA sequences, which is most likely comprom.
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Affiliation(s)
- Aakanksha Singh
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Bidisha Acharya
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Beas Mukherjee
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | | | | | | | - Soumya De
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
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8
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Pandey M, Sarkar S, Ghosh SK. Ancestral TALE homeobox protein transcription factor regulates actin dynamics and cellular activities of protozoan parasite Entamoeba invadens. Mol Microbiol 2024. [PMID: 38654540 DOI: 10.1111/mmi.15266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024]
Abstract
Entamoeba histolytica causes invasive amoebiasis, an important neglected tropical disease with a significant global health impact. The pathogenicity and survival of E. histolytica and its reptilian equivalent, Entamoeba invadens, relies on its ability to exhibit efficient motility, evade host immune responses, and exploit host resources, all of which are governed by the actin cytoskeleton remodeling. Our study demonstrates the early origin and the regulatory role of TALE homeobox protein EiHbox1 in actin-related cellular processes. Several genes involved in different biological pathways, including actin dynamics are differentially expressed in EiHbox1 silenced cells. EiHbox1 silenced parasites showed disrupted F-actin organization and loss of cellular polarity. EiHbox1's presence in the anterior region of migrating cells further suggests its involvement in maintaining cellular polarity. Loss of polarized morphology of EiHbox1 silenced parasites leads to altered motility from fast, directionally persistent, and highly chemotactic to slow, random, and less chemotactic, which subsequently leads to defective aggregation during encystation. EiHbox1 knockdown also resulted in a significant reduction in phagocytic capacity and poor capping response. These findings highlight the importance of EiHbox1 of E. invadens in governing cellular processes crucial for their survival, pathogenicity, and evasion of the host immune system.
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Affiliation(s)
- Meenakshi Pandey
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Shilpa Sarkar
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Sudip K Ghosh
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
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9
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Gao Y, Zhu L, An M, Wang Y, Li S, Dong Y, Yang S, Shi K, Fan S, Chen X, Ren H, Liu X. Zinc Finger-Homeodomain Transcriptional Factors (ZHDs) in Cucumber ( Cucumis sativus L.): Identification, Evolution, Expression Profiles, and Function under Abiotic Stresses. Int J Mol Sci 2024; 25:4408. [PMID: 38673993 PMCID: PMC11050092 DOI: 10.3390/ijms25084408] [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: 03/13/2024] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Cucumber (Cucumis sativus L.) is a globally prevalent and extensively cultivated vegetable whose yield is significantly influenced by various abiotic stresses, including drought, heat, and salinity. Transcription factors, such as zinc finger-homeodomain proteins (ZHDs), a plant-specific subgroup of Homeobox, play a crucial regulatory role in stress resistance. In this study, we identified 13 CsZHDs distributed across all six cucumber chromosomes except chromosome 7. Phylogenetic analysis classified these genes into five clades (ZHDI-IV and MIF) with different gene structures but similar conserved motifs. Collinearity analysis revealed that members of clades ZHD III, IV, and MIF experienced amplification through segmental duplication events. Additionally, a closer evolutionary relationship was observed between the ZHDs in Cucumis sativus (C. sativus) and Arabidopsis thaliana (A. thaliana) compared to Oryza sativa (O. sativa). Quantitative real-time PCR (qRT-PCR) analysis demonstrated the general expression of CsZHD genes across all tissues, with notable expression in leaf and flower buds. Moreover, most of the CsZHDs, particularly CsZHD9-11, exhibited varying responses to drought, heat, and salt stresses. Virus-induced gene silencing (VIGS) experiments highlighted the potential functions of CsZHD9 and CsZHD10, suggesting their positive regulation of stomatal movement and responsiveness to drought stress. In summary, these findings provide a valuable resource for future analysis of potential mechanisms underlying CsZHD genes in response to stresses.
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Affiliation(s)
- Yiming Gao
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Liyan Zhu
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Menghang An
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yaru Wang
- Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Sen Li
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yuming Dong
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Songlin Yang
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Kexin Shi
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Shanshan Fan
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xiaofeng Chen
- College of Ocean and Agricultural Engineering, Yantai Institute of China Agricultural University, Yantai 264670, China
| | - Huazhong Ren
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Xingwang Liu
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Sanya 572025, China
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10
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Kock KH, Kimes PK, Gisselbrecht SS, Inukai S, Phanor SK, Anderson JT, Ramakrishnan G, Lipper CH, Song D, Kurland JV, Rogers JM, Jeong R, Blacklow SC, Irizarry RA, Bulyk ML. DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues. Nat Commun 2024; 15:3110. [PMID: 38600112 PMCID: PMC11006913 DOI: 10.1038/s41467-024-47396-0] [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: 08/16/2023] [Accepted: 03/29/2024] [Indexed: 04/12/2024] Open
Abstract
Homeodomains (HDs) are the second largest class of DNA binding domains (DBDs) among eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with the largest number of disease-associated mutations in the Human Gene Mutation Database (HGMD). Despite numerous structural studies and large-scale analyses of HD DNA binding specificity, HD-DNA recognition is still not fully understood. Here, we analyze 92 human HD mutants, including disease-associated variants and variants of uncertain significance (VUS), for their effects on DNA binding activity. Many of the variants alter DNA binding affinity and/or specificity. Detailed biochemical analysis and structural modeling identifies 14 previously unknown specificity-determining positions, 5 of which do not contact DNA. The same missense substitution at analogous positions within different HDs often exhibits different effects on DNA binding activity. Variant effect prediction tools perform moderately well in distinguishing variants with altered DNA binding affinity, but poorly in identifying those with altered binding specificity. Our results highlight the need for biochemical assays of TF coding variants and prioritize dozens of variants for further investigations into their pathogenicity and the development of clinical diagnostics and precision therapies.
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Affiliation(s)
- Kian Hong Kock
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA
| | - Patrick K Kimes
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stephen S Gisselbrecht
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Sachi Inukai
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Sabrina K Phanor
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - James T Anderson
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Gayatri Ramakrishnan
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
- Boston Bangalore Biosciences Beginnings Program, Harvard University, Cambridge, MA, USA
| | - Colin H Lipper
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Dongyuan Song
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jesse V Kurland
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Julia M Rogers
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
- Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, USA
| | - Raehoon Jeong
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
- Bioinformatics and Integrative Genomics Graduate Program, Harvard University, Cambridge, MA, USA
| | - Stephen C Blacklow
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
- Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, USA
| | - Rafael A Irizarry
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA.
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA.
- Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, USA.
- Bioinformatics and Integrative Genomics Graduate Program, Harvard University, Cambridge, MA, USA.
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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11
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Calvo AM, Dabholkar A, Wyman EM, Lohmar JM, Cary JW. Regulatory functions of homeobox domain transcription factors in fungi. Appl Environ Microbiol 2024; 90:e0220823. [PMID: 38421174 PMCID: PMC10952592 DOI: 10.1128/aem.02208-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
Homeobox domain (HD) proteins present a crucial involvement in morphological differentiation and other functions in eukaryotes. Most HD genes encode transcription factors (TFs) that orchestrate a regulatory role in cellular and developmental decisions. In fungi, multiple studies have increased our understanding of these important HD regulators in recent years. These reports have revealed their role in fungal development, both sexual and asexual, as well as their importance in governing other biological processes in these organisms, including secondary metabolism, pathogenicity, and sensitivity to environmental stresses. Here, we provide a comprehensive review of the current knowledge on the regulatory roles of HD-TFs in fungi, with a special focus on Aspergillus species.
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Affiliation(s)
- A. M. Calvo
- Department of Biological Sciences, Northern Illinois University, Dekalb, Illinois, USA
| | - A. Dabholkar
- Department of Biological Sciences, Northern Illinois University, Dekalb, Illinois, USA
| | - E. M. Wyman
- Department of Biological Sciences, Northern Illinois University, Dekalb, Illinois, USA
| | - J. M. Lohmar
- Food and Feed Safety Research Unit, USDA/ARS, Southern Regional Research Center, New Orleans, Louisiana, USA
| | - J. W. Cary
- Food and Feed Safety Research Unit, USDA/ARS, Southern Regional Research Center, New Orleans, Louisiana, USA
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12
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Zheng Y, Stormo GD, Chen S. Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584677. [PMID: 38559186 PMCID: PMC10979960 DOI: 10.1101/2024.03.12.584677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Paired-class homeodomain transcription factors (HD TFs) play essential roles in vertebrate development, and their mutations are linked to human diseases. One unique feature of paired-class HD is cooperative dimerization on specific palindrome DNA sequences. Yet, the functional significance of HD cooperative dimerization in animal development and its dysregulation in diseases remain elusive. Using the retinal TF Cone-rod Homeobox (CRX) as a model, we have studied how blindness-causing mutations in the paired HD, p.E80A and p.K88N, alter CRX's cooperative dimerization, lead to gene misexpression and photoreceptor developmental deficits in dominant manners. CRXE80A maintains binding at monomeric WT CRX motifs but is deficient in cooperative binding at dimeric motifs. CRXE80A's cooperativity defect impacts the exponential increase of photoreceptor gene expression in terminal differentiation and produces immature, non-functional photoreceptors in the CrxE80A retinas. CRXK88N is highly cooperative and localizes to ectopic genomic sites with strong enrichment of dimeric HD motifs. CRXK88N's altered biochemical properties disrupt CRX's ability to direct dynamic chromatin remodeling during development to activate photoreceptor differentiation programs and silence progenitor programs. Our study here provides in vitro and in vivo molecular evidence that paired-class HD cooperative dimerization regulates neuronal development and dysregulation of cooperative binding contributes to severe dominant blinding retinopathies.
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Affiliation(s)
- Yiqiao Zheng
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
| | - Gary D. Stormo
- Department of Genetics, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
- Department of Developmental Biology, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
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13
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Nunes WVB, Oliveira DS, Dias GDR, Carvalho AB, Caruso ÍP, Biselli JM, Guegen N, Akkouche A, Burlet N, Vieira C, Carareto CMA. A comprehensive evolutionary scenario for the origin and neofunctionalization of the Drosophila speciation gene Odysseus (OdsH). G3 (BETHESDA, MD.) 2024; 14:jkad299. [PMID: 38156703 PMCID: PMC10917504 DOI: 10.1093/g3journal/jkad299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 11/22/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Odysseus (OdsH) was the first speciation gene described in Drosophila related to hybrid sterility in offspring of mating between Drosophila mauritiana and Drosophila simulans. Its origin is attributed to the duplication of the gene unc-4 in the subgenus Sophophora. By using a much larger sample of Drosophilidae species, we showed that contrary to what has been previously proposed, OdsH origin occurred 62 MYA. Evolutionary rates, expression, and transcription factor-binding sites of OdsH evidence that it may have rapidly experienced neofunctionalization in male sexual functions. Furthermore, the analysis of the OdsH peptide allowed the identification of mutations of D. mauritiana that could result in incompatibility in hybrids. In order to find if OdsH could be related to hybrid sterility, beyond Sophophora, we explored the expression of OdsH in Drosophila arizonae and Drosophila mojavensis, a pair of sister species with incomplete reproductive isolation. Our data indicated that OdsH expression is not atypical in their male-sterile hybrids. In conclusion, we have proposed that the origin of OdsH occurred earlier than previously proposed, followed by neofunctionalization. Our results also suggested that its role as a speciation gene might be restricted to D. mauritiana and D. simulans.
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Affiliation(s)
- William Vilas Boas Nunes
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Daniel Siqueira Oliveira
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Guilherme de Rezende Dias
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS sl A2-075, 373 Carlos Chagas Filho Avenue, 21941-971 Rio de Janeiro, Brazil
| | - Antonio Bernardo Carvalho
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS sl A2-075, 373 Carlos Chagas Filho Avenue, 21941-971 Rio de Janeiro, Brazil
| | - Ícaro Putinhon Caruso
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
| | - Joice Matos Biselli
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
| | - Nathalie Guegen
- Faculté de Médecine, iGReD, Université Clermont Auvergne, CNRS, INSERM, 4 Bd Claude Bernard, 63000 Clermont-Ferrande, France
| | - Abdou Akkouche
- Faculté de Médecine, iGReD, Université Clermont Auvergne, CNRS, INSERM, 4 Bd Claude Bernard, 63000 Clermont-Ferrande, France
| | - Nelly Burlet
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Claudia M A Carareto
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
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14
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Fu X, Zhu X. Key homeobox transcription factors regulate the development of the firefly's adult light organ and bioluminescence. Nat Commun 2024; 15:1736. [PMID: 38443352 PMCID: PMC10914744 DOI: 10.1038/s41467-024-45559-7] [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: 06/17/2023] [Accepted: 01/26/2024] [Indexed: 03/07/2024] Open
Abstract
Adult fireflies exhibit unique flashing courtship signals, emitted by specialized light organs, which develop mostly independently from larval light organs during the pupal stage. The mechanisms of adult light organ development have not been thoroughly studied until now. Here we show that key homeobox transcription factors AlABD-B and AlUNC-4 regulate the development of adult light organs and bioluminescence in the firefly Aquatica leii. Interference with the expression of AlAbd-B and AlUnc-4 genes results in undeveloped or non-luminescent adult light organs. AlABD-B regulates AlUnc-4, and they interact with each other. AlABD-B and AlUNC-4 activate the expression of the luciferase gene AlLuc1 and some peroxins. Four peroxins are involved in the import of AlLUC1 into peroxisomes. Our study provides key insights into the development of adult light organs and flash signal control in fireflies.
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Affiliation(s)
- Xinhua Fu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xinlei Zhu
- Firefly Conservation Research Centre, Wuhan, 430070, China
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15
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Nagel S, Rand U, Pommerenke C, Meyer C. Transcriptional Landscape of CUT-Class Homeobox Genes in Blastic Plasmacytoid Dendritic Cell Neoplasm. Int J Mol Sci 2024; 25:2764. [PMID: 38474011 DOI: 10.3390/ijms25052764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Homeobox genes encode developmental transcription factors regulating tissue-specific differentiation processes and drive cancerogenesis when deregulated. Dendritic cells (DCs) are myeloid immune cells occurring as two types, either conventional or plasmacytoid DCs. Recently, we showed that the expression of NKL-subclass homeobox gene VENTX is restricted to conventional DCs, regulating developmental genes. Here, we identified and investigated homeobox genes specifically expressed in plasmacytoid DCs (pDCs) and derived blastic plasmacytoid dendritic cell neoplasm (BPDCN). We analyzed gene expression data, performed RQ-PCR, protein analyses by Western blot and immuno-cytology, siRNA-mediated knockdown assays and subsequent RNA-sequencing and live-cell imaging. Screening of public gene expression data revealed restricted activity of the CUT-class homeobox gene CUX2 in pDCs. An extended analysis of this homeobox gene class in myelopoiesis showed that additional CUX2 activity was restricted to myeloid progenitors, while BPDCN patients aberrantly expressed ONECUT2, which remained silent in the complete myeloid compartment. ONECUT2 expressing BPDCN cell line CAL-1 served as a model to investigate its regulation and oncogenic activity. The ONECUT2 locus at 18q21 was duplicated and activated by IRF4, AUTS2 and TNF-signaling and repressed by BMP4-, TGFb- and IL13-signalling. Functional analyses of ONECUT2 revealed the inhibition of pDC differentiation and of CDKN1C and CASP1 expression, while SMAD3 and EPAS1 were activated. EPAS1 in turn enhanced survival under hypoxic conditions which thus may support dendritic tumor cells residing in hypoxic skin lesions. Collectively, we revealed physiological and aberrant activities of CUT-class homeobox genes in myelopoiesis including pDCs and in BPDCN, respectively. Our data may aid in the diagnosis of BPDCN patients and reveal novel therapeutic targets for this fatal malignancy.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, 38124 Braunschweig, Germany
| | - Ulfert Rand
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, 38124 Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, 38124 Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, 38124 Braunschweig, Germany
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16
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Zheng Y, Chen S. Transcriptional precision in photoreceptor development and diseases - Lessons from 25 years of CRX research. Front Cell Neurosci 2024; 18:1347436. [PMID: 38414750 PMCID: PMC10896975 DOI: 10.3389/fncel.2024.1347436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
The vertebrate retina is made up of six specialized neuronal cell types and one glia that are generated from a common retinal progenitor. The development of these distinct cell types is programmed by transcription factors that regulate the expression of specific genes essential for cell fate specification and differentiation. Because of the complex nature of transcriptional regulation, understanding transcription factor functions in development and disease is challenging. Research on the Cone-rod homeobox transcription factor CRX provides an excellent model to address these challenges. In this review, we reflect on 25 years of mammalian CRX research and discuss recent progress in elucidating the distinct pathogenic mechanisms of four CRX coding variant classes. We highlight how in vitro biochemical studies of CRX protein functions facilitate understanding CRX regulatory principles in animal models. We conclude with a brief discussion of the emerging systems biology approaches that could accelerate precision medicine for CRX-linked diseases and beyond.
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Affiliation(s)
- Yiqiao Zheng
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
| | - Shiming Chen
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
- Department of Developmental Biology, Washington University in St. Louis, Saint Louis, MO, United States
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17
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Kang J, Chung A, Suresh S, Bonzi LC, Sourisse JM, Ramirez‐Calero S, Romeo D, Petit‐Marty N, Pegueroles C, Schunter C. Long non-coding RNAs mediate fish gene expression in response to ocean acidification. Evol Appl 2024; 17:e13655. [PMID: 38357358 PMCID: PMC10866067 DOI: 10.1111/eva.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
The majority of the transcribed genome does not have coding potential but these non-coding transcripts play crucial roles in transcriptional and post-transcriptional regulation of protein-coding genes. Regulation of gene expression is important in shaping an organism's response to environmental changes, ultimately impacting their survival and persistence as population or species face global change. However, the roles of long non-coding RNAs (lncRNAs), when confronted with environmental changes, remain largely unclear. To explore the potential role of lncRNAs in fish exposed to ocean acidification (OA), we analyzed publicly available brain RNA-seq data from a coral reef fish Acanthochromis polyacanthus. We annotated the lncRNAs in its genome and examined the expression changes of intergenic lncRNAs (lincRNAs) between A. polyacanthus samples from a natural CO2 seep and a nearby control site. We identified 4728 lncRNAs, including 3272 lincRNAs in this species. Remarkably, 93.03% of these lincRNAs were species-specific. Among the 125 highly expressed lincRNAs and 403 differentially expressed lincRNAs in response to elevated CO2, we observed that lincRNAs were either neighboring or potentially trans-regulating differentially expressed coding genes associated with pH regulation, neural signal transduction, and ion transport, which are known to be important in the response to OA in fish. In summary, lncRNAs may facilitate fish acclimation and mediate the responses of fish to OA by modulating the expression of crucial coding genes, which offers insight into the regulatory mechanisms underlying fish responses to environmental changes.
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Affiliation(s)
- Jingliang Kang
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Arthur Chung
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Sneha Suresh
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Lucrezia C. Bonzi
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Jade M. Sourisse
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Sandra Ramirez‐Calero
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Daniele Romeo
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Natalia Petit‐Marty
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Cinta Pegueroles
- Department of Genetics, Microbiology and Statistics, Institute for Research on Biodiversity (IRBio)University of BarcelonaBarcelonaSpain
| | - Celia Schunter
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
- State Key Laboratory of Marine Pollution and Department of ChemistryCity University of Hong KongHong Kong SARChina
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18
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Bartold M, Ivanovski S. Biological processes and factors involved in soft and hard tissue healing. Periodontol 2000 2024. [PMID: 38243683 DOI: 10.1111/prd.12546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/12/2023] [Accepted: 11/23/2023] [Indexed: 01/21/2024]
Abstract
Wound healing is a complex and iterative process involving myriad cellular and biologic processes that are highly regulated to allow satisfactory repair and regeneration of damaged tissues. This review is intended to be an introductory chapter in a volume focusing on the use of platelet concentrates for tissue regeneration. In order to fully appreciate the clinical utility of these preparations, a sound understanding of the processes and factors involved in soft and hard tissue healing. This encompasses an appreciation of the cellular and biological mediators of both soft and hard tissues in general as well as specific consideration of the periodontal tissues. In light of good advances in this basic knowledge, there have been improvements in clinical strategies and therapeutic management of wound repair and regeneration. The use of platelet concentrates for tissue regeneration offers one such strategy and is based on the principles of cellular and biologic principles of wound repair discussed in this review.
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Affiliation(s)
- Mark Bartold
- University of Queensland, Brisbane, Queensland, Australia
| | - Saso Ivanovski
- University of Queensland, Brisbane, Queensland, Australia
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19
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Goswami R, Gupta A, Bednova O, Coulombe G, Patel D, Rotello VM, Leyton JV. Nuclear localization signal-tagged systems: relevant nuclear import principles in the context of current therapeutic design. Chem Soc Rev 2024; 53:204-226. [PMID: 38031452 PMCID: PMC10798298 DOI: 10.1039/d1cs00269d] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Nuclear targeting of therapeutics provides a strategy for enhancing efficacy of molecules active in the nucleus and minimizing off-target effects. 'Active' nuclear-directed transport and efficient translocations across nuclear pore complexes provide the most effective means of maximizing nuclear localization. Nuclear-targeting systems based on nuclear localization signal (NLS) motifs have progressed significantly since the beginning of the current millennium. Here, we offer a roadmap for understanding the basic mechanisms of nuclear import in the context of actionable therapeutic design for developing NLS-therapeutics with improved treatment efficacy.
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Affiliation(s)
- Ritabrita Goswami
- Department of Chemistry, University of Massachusetts, Massachusetts, USA.
| | - Aarohi Gupta
- Department of Chemistry, University of Massachusetts, Massachusetts, USA.
| | - Olga Bednova
- Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Québec, Canada
| | - Gaël Coulombe
- Service des stages et du développement professionnel, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Dipika Patel
- Service des stages et du développement professionnel, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts, Massachusetts, USA.
| | - Jeffrey V Leyton
- École des sciences pharmaceutiques, Université d'Ottawa, Ottawa, Ontario, Canada.
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
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20
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Blanc-Mathieu R, Dumas R, Turchi L, Lucas J, Parcy F. Plant-TFClass: a structural classification for plant transcription factors. TRENDS IN PLANT SCIENCE 2024; 29:40-51. [PMID: 37482504 DOI: 10.1016/j.tplants.2023.06.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023]
Abstract
Transcription factors (TFs) bind DNA at specific sequences to regulate gene expression. This universal process is achieved via their DNA-binding domain (DBD). In mammals, the vast diversity of DBD structural conformations and the way in which they contact DNA has been used to organize TFs in the TFClass hierarchical classification. However, the numerous DBD types present in plants but absent from mammalian genomes were missing from this classification. We reviewed DBD 3D structures and models available for plant TFs to classify most of the 56 recognized plant TF types within the TFClass framework. This extended classification adds eight new classes and 37 new families corresponding to DBD structures absent in mammals. Plant-TFClass provides a unique resource for TF comparison across families and organisms.
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Affiliation(s)
- Romain Blanc-Mathieu
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - Renaud Dumas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - Laura Turchi
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - Jérémy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France.
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21
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Miller A, Dasen JS. Establishing and maintaining Hox profiles during spinal cord development. Semin Cell Dev Biol 2024; 152-153:44-57. [PMID: 37029058 PMCID: PMC10524138 DOI: 10.1016/j.semcdb.2023.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/18/2023] [Accepted: 03/30/2023] [Indexed: 04/09/2023]
Abstract
The chromosomally-arrayed Hox gene family plays central roles in embryonic patterning and the specification of cell identities throughout the animal kingdom. In vertebrates, the relatively large number of Hox genes and pervasive expression throughout the body has hindered understanding of their biological roles during differentiation. Studies on the subtype diversification of spinal motor neurons (MNs) have provided a tractable system to explore the function of Hox genes during differentiation, and have provided an entry point to explore how neuronal fate determinants contribute to motor circuit assembly. Recent work, using both in vitro and in vivo models of MN subtype differentiation, have revealed how patterning morphogens and regulation of chromatin structure determine cell-type specific programs of gene expression. These studies have not only shed light on basic mechanisms of rostrocaudal patterning in vertebrates, but also have illuminated mechanistic principles of gene regulation that likely operate in the development and maintenance of terminal fates in other systems.
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Affiliation(s)
- Alexander Miller
- NYU Neuroscience Institute and Developmental Genetics Programs, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA.
| | - Jeremy S Dasen
- NYU Neuroscience Institute and Developmental Genetics Programs, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA.
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22
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Smith JJ, Kratsios P. Hox gene functions in the C. elegans nervous system: From early patterning to maintenance of neuronal identity. Semin Cell Dev Biol 2024; 152-153:58-69. [PMID: 36496326 PMCID: PMC10244487 DOI: 10.1016/j.semcdb.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/14/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
The nervous system emerges from a series of genetic programs that generate a remarkable array of neuronal cell types. Each cell type must acquire a distinct anatomical position, morphology, and function, enabling the generation of specialized circuits that drive animal behavior. How are these diverse cell types and circuits patterned along the anterior-posterior (A-P) axis of the animal body? Hox genes encode transcription factors that regulate cell fate and patterning events along the A-P axis of the nervous system. While most of our understanding of Hox-mediated control of neuronal development stems from studies in segmented animals like flies, mice, and zebrafish, important new themes are emerging from work in a non-segmented animal: the nematode Caenorhabditis elegans. Studies in C. elegans support the idea that Hox genes are needed continuously and across different life stages in the nervous system; they are not only required in dividing progenitor cells, but also in post-mitotic neurons during development and adult life. In C. elegans embryos and young larvae, Hox genes control progenitor cell specification, cell survival, and neuronal migration, consistent with their neural patterning roles in other animals. In late larvae and adults, C. elegans Hox genes control neuron type-specific identity features critical for neuronal function, thereby extending the Hox functional repertoire beyond early patterning. Here, we provide a comprehensive review of Hox studies in the C. elegans nervous system. To relate to readers outside the C. elegans community, we highlight conserved roles of Hox genes in patterning the nervous system of invertebrate and vertebrate animals. We end by calling attention to new functions in adult post-mitotic neurons for these paradigmatic regulators of cell fate.
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Affiliation(s)
- Jayson J Smith
- Department of Neurobiology, University of Chicago, 947 East 58th Street, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, 947 East 58th Street, Chicago, IL 60637, USA.
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, 947 East 58th Street, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, 947 East 58th Street, Chicago, IL 60637, USA.
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23
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Bobola N, Sagerström CG. TALE transcription factors: Cofactors no more. Semin Cell Dev Biol 2024; 152-153:76-84. [PMID: 36509674 DOI: 10.1016/j.semcdb.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/27/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
Exd/PBX, Hth/MEIS and PREP proteins belong to the TALE (three-amino-acid loop extension) superclass of transcription factors (TFs) with an atypical homedomain (HD). Originally discovered as "cofactors" to HOX proteins, revisiting their traditional role in light of genome-wide experiments reveals a strong and reproducible pattern of HOX and TALE co-occupancy across diverse embryonic tissues. While confirming that TALE increases HOX specificity and selectivity in vivo, this wider outlook also reveals novel aspects of HOX:TALE collaboration, namely that HOX TFs generally require pre-bound TALE factors to access their functional binding sites in vivo. In contrast to the restricted expression domains of HOX TFs, TALE factors are largely ubiquitous, and PBX and PREP are expressed at the earliest developmental stages. PBX and MEIS control development of many organs and tissues and their dysregulation is associated with congenital disease and cancer. Accordingly, many instances of TALE cooperation with non HOX TFs have been documented in various systems. The model that emerges from these studies is that TALE TFs create a permissive chromatin platform that is selected by tissue-restricted TFs for binding. In turn, HOX and other tissue-restricted TFs selectively convert a ubiquitous pool of low affinity TALE binding events into high confidence, tissue-restricted binding events associated with transcriptional activation. As a result, TALE:TF complexes are associated with active chromatin and domain/lineage-specific gene activity. TALE ubiquitous expression and broad genomic occupancy, as well as the increasing examples of TALE tissue-specific partners, reveal a universal and obligatory role for TALE in the control of tissue and lineage-specific transcriptional programs, beyond their initial discovery as HOX co-factors.
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Affiliation(s)
- Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester, UK.
| | - Charles G Sagerström
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical School, Aurora, CO, USA.
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24
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Salomone J, Farrow E, Gebelein B. Homeodomain complex formation and biomolecular condensates in Hox gene regulation. Semin Cell Dev Biol 2024; 152-153:93-100. [PMID: 36517343 PMCID: PMC10258226 DOI: 10.1016/j.semcdb.2022.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/21/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022]
Abstract
Hox genes are a family of homeodomain transcription factors that regulate specialized morphological structures along the anterior-posterior axis of metazoans. Over the past few decades, researchers have focused on defining how Hox factors with similar in vitro DNA binding activities achieve sufficient target specificity to regulate distinct cell fates in vivo. In this review, we highlight how protein interactions with other transcription factors, many of which are also homeodomain proteins, result in the formation of transcription factor complexes with enhanced DNA binding specificity. These findings suggest that Hox-regulated enhancers utilize distinct combinations of homeodomain binding sites, many of which are low-affinity, to recruit specific Hox complexes. However, low-affinity sites can only yield reproducible responses with high transcription factor concentrations. To overcome this limitation, recent studies revealed how transcription factors, including Hox factors, use intrinsically disordered domains (IDRs) to form biomolecular condensates that increase protein concentrations. Moreover, Hox factors with altered IDRs have been associated with altered transcriptional activity and human disease states, demonstrating the importance of IDRs in mediating essential Hox output. Collectively, these studies highlight how Hox factors use their DNA binding domains, protein-protein interaction domains, and IDRs to form specific transcription factor complexes that yield accurate gene expression.
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Affiliation(s)
- Joseph Salomone
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA; Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Edward Farrow
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA; Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
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25
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Webb JA, Farrow E, Cain B, Yuan Z, Yarawsky AE, Schoch E, Gagliani EK, Herr AB, Gebelein B, Kovall RA. Cooperative Gsx2-DNA Binding Requires DNA Bending and a Novel Gsx2 Homeodomain Interface. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570805. [PMID: 38106145 PMCID: PMC10723402 DOI: 10.1101/2023.12.08.570805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The conserved Gsx homeodomain (HD) transcription factors specify neural cell fates in animals from flies to mammals. Like many HD proteins, Gsx factors bind A/T-rich DNA sequences prompting the question - how do HD factors that bind similar DNA sequences in vitro regulate specific target genes in vivo? Prior studies revealed that Gsx factors bind DNA both as a monomer on individual A/T-rich sites and as a cooperative homodimer to two sites spaced precisely seven base pairs apart. However, the mechanistic basis for Gsx DNA binding and cooperativity are poorly understood. Here, we used biochemical, biophysical, structural, and modeling approaches to (1) show that Gsx factors are monomers in solution and require DNA for cooperative complex formation; (2) define the affinity and thermodynamic binding parameters of Gsx2/DNA interactions; (3) solve a high-resolution monomer/DNA structure that reveals Gsx2 induces a 20° bend in DNA; (4) identify a Gsx2 protein-protein interface required for cooperative DNA binding; and (5) determine that flexible spacer DNA sequences enhance Gsx2 cooperativity on dimer sites. Altogether, our results provide a mechanistic basis for understanding the protein and DNA structural determinants that underlie cooperative DNA binding by Gsx factors, thereby providing a deeper understanding of HD specificity.
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Affiliation(s)
- Jordan A. Webb
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Edward Farrow
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children’s Hospital Research Foundation, Cincinnati, OH 45229, USA
- Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Brittany Cain
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
| | - Zhenyu Yuan
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Alexander E. Yarawsky
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, 3333, Burnet Ave, Cincinnati, OH 45229, USA
| | - Emma Schoch
- Department of Medical Education, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Ellen K. Gagliani
- Department of Chemistry, Xavier University, Cincinnati, OH 45207, USA
| | - Andrew B. Herr
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, 3333, Burnet Ave, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Rhett A. Kovall
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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26
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Lv Z, Zhao W, Kong S, Li L, Lin S. Overview of molecular mechanisms of plant leaf development: a systematic review. FRONTIERS IN PLANT SCIENCE 2023; 14:1293424. [PMID: 38146273 PMCID: PMC10749370 DOI: 10.3389/fpls.2023.1293424] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/22/2023] [Indexed: 12/27/2023]
Abstract
Leaf growth initiates in the peripheral region of the meristem at the apex of the stem, eventually forming flat structures. Leaves are pivotal organs in plants, serving as the primary sites for photosynthesis, respiration, and transpiration. Their development is intricately governed by complex regulatory networks. Leaf development encompasses five processes: the leaf primordium initiation, the leaf polarity establishment, leaf size expansion, shaping of leaf, and leaf senescence. The leaf primordia starts from the side of the growth cone at the apex of the stem. Under the precise regulation of a series of genes, the leaf primordia establishes adaxial-abaxial axes, proximal-distal axes and medio-lateral axes polarity, guides the primordia cells to divide and differentiate in a specific direction, and finally develops into leaves of a certain shape and size. Leaf senescence is a kind of programmed cell death that occurs in plants, and as it is the last stage of leaf development. Each of these processes is meticulously coordinated through the intricate interplay among transcriptional regulatory factors, microRNAs, and plant hormones. This review is dedicated to examining the regulatory influences of major regulatory factors and plant hormones on these five developmental aspects of leaves.
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Affiliation(s)
- Zhuo Lv
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, China
- College of Life Science, Nanjing Forestry University, Nanjing, China
| | - Wanqi Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, China
- College of Life Science, Nanjing Forestry University, Nanjing, China
| | - Shuxin Kong
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, China
- College of Life Science, Nanjing Forestry University, Nanjing, China
| | - Long Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, China
- College of Life Science, Nanjing Forestry University, Nanjing, China
| | - Shuyan Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, China
- College of Life Science, Nanjing Forestry University, Nanjing, China
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27
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Lim Y. Transcription factors in microcephaly. Front Neurosci 2023; 17:1302033. [PMID: 38094004 PMCID: PMC10716367 DOI: 10.3389/fnins.2023.1302033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/06/2023] [Indexed: 02/01/2024] Open
Abstract
Higher cognition in humans, compared to other primates, is often attributed to an increased brain size, especially forebrain cortical surface area. Brain size is determined through highly orchestrated developmental processes, including neural stem cell proliferation, differentiation, migration, lamination, arborization, and apoptosis. Disruption in these processes often results in either a small (microcephaly) or large (megalencephaly) brain. One of the key mechanisms controlling these developmental processes is the spatial and temporal transcriptional regulation of critical genes. In humans, microcephaly is defined as a condition with a significantly smaller head circumference compared to the average head size of a given age and sex group. A growing number of genes are identified as associated with microcephaly, and among them are those involved in transcriptional regulation. In this review, a subset of genes encoding transcription factors (e.g., homeobox-, basic helix-loop-helix-, forkhead box-, high mobility group box-, and zinc finger domain-containing transcription factors), whose functions are important for cortical development and implicated in microcephaly, are discussed.
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Affiliation(s)
- Youngshin Lim
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Department of Biomedical Science Education, Charles R. Drew University of Medicine and Science, Los Angeles, CA, United States
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28
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Lukic B, Curik I, Drzaic I, Galić V, Shihabi M, Vostry L, Cubric-Curik V. Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds. J Anim Sci Biotechnol 2023; 14:142. [PMID: 37932811 PMCID: PMC10626677 DOI: 10.1186/s40104-023-00936-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/04/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations. Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production (carcass, wool and milk yield). Therefore, eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation (EAS), are generally considered as multipurpose breeds (milk, meat and wool), not specialised for a particular type of production, but known for their robustness and resistance to certain environmental conditions. Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures, decipher their biological and productive functionality, and provide a "genomic" characterization of EAS adaptation and determine its production type. RESULTS We identified positive selection signatures in EAS using several methods based on reduced local variation, linkage disequilibrium and site frequency spectrum (eROHi, iHS, nSL and CLR). Our analyses identified numerous genomic regions and genes (e.g., desmosomal cadherin and desmoglein gene families) associated with environmental adaptation and economically important traits. Most candidate genes were related to meat/production and health/immune response traits, while some of the candidate genes discovered were important for domestication and evolutionary processes (e.g., HOXa gene family and FSIP2). These results were also confirmed by GO and QTL enrichment analysis. CONCLUSIONS Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type, ultimately providing a new opportunity for future breeding programmes. At the same time, the numerous genes identified will improve our understanding of ruminant (sheep) robustness and resistance in the harsh and specific Mediterranean environment.
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Affiliation(s)
- Boris Lukic
- Faculty of Agrobiotechnical Sciences Osijek, J.J, Strossmayer University of Osijek, Vladimira Preloga 1, 31000, Osijek, Croatia.
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia.
| | - Ivana Drzaic
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia
| | - Vlatko Galić
- Department of Maize Breeding and Genetics, Agricultural Institute Osijek, Južno predgrađe 17, 31000, Osijek, Croatia
| | - Mario Shihabi
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia
| | - Luboš Vostry
- Czech University of Life Sciences Prague, Kamýcká 129, 165 00, Praque, Czech Republic
| | - Vlatka Cubric-Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia
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29
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Li Y, Xiong H, Guo H, Zhao L, Xie Y, Gu J, Zhao S, Ding Y, Li H, Zhou C, Fu M, Wang Q, Liu L. Genome-wide characterization of two homeobox families identifies key genes associated with grain-related traits in wheat. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111862. [PMID: 37716191 DOI: 10.1016/j.plantsci.2023.111862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/11/2023] [Accepted: 09/03/2023] [Indexed: 09/18/2023]
Abstract
Homeodomain proteins encoded by BEL1- and KNAT1-type genes are ubiquitously distributed across plant species and play important roles in growth and development, whereby a comprehensive investigation of their molecular interactions and potential functions in wheat is of great significance. In this study, we systematically investigated the phylogenetic relationships, gene structures, conserved domains, and cis-acting elements of 34 TaBEL and 34 TaKNAT genes in the wheat genome. Our analysis revealed these genes evolved under different selective pressures and showed variable transcript levels in different wheat tissues. Subcellular localization analysis further indicated the proteins encoded by these genes were either exclusively located in the nucleus or both in the nucleus and the cytoplasm. Additionally, a comprehensive protein-protein interaction network was constructed with representative genes in which each TaBEL or TaKNAT proteins interact with at least two partners. The evaluation of wheat mutants identified key genes, including TaBEL-5B, TaBEL-4A.4, and TaKNAT6, which are involved in grain-related traits. Finally, haplotype analysis suggests TaKNAT-6B is associated with grain-related traits and is preferentially selected among a large set of wheat accessions. Our study provides important information on BEL1- and KNAT1-type gene families in wheat, and lays the foundation for functional research in the future.
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Affiliation(s)
- Yuting Li
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongchun Xiong
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huijun Guo
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Linshu Zhao
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yongdun Xie
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiayu Gu
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shirong Zhao
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuping Ding
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huiyuan Li
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chunyun Zhou
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Meiyu Fu
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qingguo Wang
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Luxiang Liu
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Kuznetsova K, Efremova E, Dodueva I, Lebedeva M, Lutova L. Functional Modules in the Meristems: "Tinkering" in Action. PLANTS (BASEL, SWITZERLAND) 2023; 12:3661. [PMID: 37896124 PMCID: PMC10610496 DOI: 10.3390/plants12203661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND A feature of higher plants is the modular principle of body organisation. One of these conservative morphological modules that regulate plant growth, histogenesis and organogenesis is meristems-structures that contain pools of stem cells and are generally organised according to a common principle. Basic content: The development of meristems is under the regulation of molecular modules that contain conservative interacting components and modulate the expression of target genes depending on the developmental context. In this review, we focus on two molecular modules that act in different types of meristems. The WOX-CLAVATA module, which includes the peptide ligand, its receptor and the target transcription factor, is responsible for the formation and control of the activity of all meristem types studied, but it has its own peculiarities in different meristems. Another regulatory module is the so-called florigen-activated complex, which is responsible for the phase transition in the shoot vegetative meristem (e.g., from the vegetative shoot apical meristem to the inflorescence meristem). CONCLUSIONS The review considers the composition and functions of these two functional modules in different developmental programmes, as well as their appearance, evolution and use in plant breeding.
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Affiliation(s)
| | | | - Irina Dodueva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya Emb. 7/9, 199034 Saint Petersburg, Russia; (K.K.); (E.E.); (M.L.); (L.L.)
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31
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Xu A, Yang J, Wang S, Zheng L, Wang J, Zhang Y, Bi X, Wang H. Characterization and expression profiles of WUSCHEL-related homeobox (WOX) gene family in cultivated alfalfa (Medicago sativa L.). BMC PLANT BIOLOGY 2023; 23:471. [PMID: 37803258 PMCID: PMC10557229 DOI: 10.1186/s12870-023-04476-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/19/2023] [Indexed: 10/08/2023]
Abstract
The WUSCHEL-related homeobox (WOX) family members are plant-specific transcriptional factors, which function in meristem maintenance, embryogenesis, lateral organ development, as well as abiotic stress tolerance. In this study, 14 MsWOX transcription factors were identified and comprehensively analyzed in the cultivated alfalfa cv. Zhongmu No.1. Overall, 14 putative MsWOX members containing conserved structural regions were clustered into three clades according to phylogenetic analysis. Specific expression patterns of MsWOXs in different tissues at different levels indicated that the MsWOX genes play various roles in alfalfa. MsWUS, MsWOX3, MsWOX9, and MsWOX13-1 from the three subclades were localized in the nucleus, among which, MsWUS and MsWOX13-1 exhibited strong self-activations in yeast. In addition, various cis-acting elements related to hormone responses, plant growth, and stress responses were identified in the 3.0 kb promoter regions of MsWOXs. Expression detection of separated shoots and roots under hormones including auxin, cytokinin, GA, and ABA, as well as drought and cold stresses, showed that MsWOX genes respond to different hormones and abiotic stress treatments. Furthermore, transcript abundance of MsWOX3, and MsWOX13-2 were significantly increased after rhizobia inoculation. This study presented comprehensive data on MsWOX transcription factors and provided valuable insights into further studies of their roles in developmental processes and abiotic stress responses in alfalfa.
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Affiliation(s)
- Aijiao Xu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Jiaqi Yang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Siqi Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Lin Zheng
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Jing Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yunwei Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Xiaojing Bi
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Hui Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
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32
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Leyva-Díaz E. CUT homeobox genes: transcriptional regulation of neuronal specification and beyond. Front Cell Neurosci 2023; 17:1233830. [PMID: 37744879 PMCID: PMC10515288 DOI: 10.3389/fncel.2023.1233830] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
CUT homeobox genes represent a captivating gene class fulfilling critical functions in the development and maintenance of multiple cell types across a wide range of organisms. They belong to the larger group of homeobox genes, which encode transcription factors responsible for regulating gene expression patterns during development. CUT homeobox genes exhibit two distinct and conserved DNA binding domains, a homeodomain accompanied by one or more CUT domains. Numerous studies have shown the involvement of CUT homeobox genes in diverse developmental processes such as body axis formation, organogenesis, tissue patterning and neuronal specification. They govern these processes by exerting control over gene expression through their transcriptional regulatory activities, which they accomplish by a combination of classic and unconventional interactions with the DNA. Intriguingly, apart from their roles as transcriptional regulators, they also serve as accessory factors in DNA repair pathways through protein-protein interactions. They are highly conserved across species, highlighting their fundamental importance in developmental biology. Remarkably, evolutionary analysis has revealed that CUT homeobox genes have experienced an extraordinary degree of rearrangements and diversification compared to other classes of homeobox genes, including the emergence of a novel gene family in vertebrates. Investigating the functions and regulatory networks of CUT homeobox genes provides significant understanding into the molecular mechanisms underlying embryonic development and tissue homeostasis. Furthermore, aberrant expression or mutations in CUT homeobox genes have been associated with various human diseases, highlighting their relevance beyond developmental processes. This review will overview the well known roles of CUT homeobox genes in nervous system development, as well as their functions in other tissues across phylogeny.
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Waury K, de Wit R, Verberk IMW, Teunissen CE, Abeln S. Deciphering Protein Secretion from the Brain to Cerebrospinal Fluid for Biomarker Discovery. J Proteome Res 2023; 22:3068-3080. [PMID: 37606934 PMCID: PMC10476268 DOI: 10.1021/acs.jproteome.3c00366] [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: 06/19/2023] [Indexed: 08/23/2023]
Abstract
Cerebrospinal fluid (CSF) is an essential matrix for the discovery of neurological disease biomarkers. However, the high dynamic range of protein concentrations in CSF hinders the detection of the least abundant protein biomarkers by untargeted mass spectrometry. It is thus beneficial to gain a deeper understanding of the secretion processes within the brain. Here, we aim to explore if and how the secretion of brain proteins to the CSF can be predicted. By combining a curated CSF proteome and the brain elevated proteome of the Human Protein Atlas, brain proteins were classified as CSF or non-CSF secreted. A machine learning model was trained on a range of sequence-based features to differentiate between CSF and non-CSF groups and effectively predict the brain origin of proteins. The classification model achieves an area under the curve of 0.89 if using high confidence CSF proteins. The most important prediction features include the subcellular localization, signal peptides, and transmembrane regions. The classifier generalized well to the larger brain detected proteome and is able to correctly predict novel CSF proteins identified by affinity proteomics. In addition to elucidating the underlying mechanisms of protein secretion, the trained classification model can support biomarker candidate selection.
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Affiliation(s)
- Katharina Waury
- Department
of Computer Science, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Renske de Wit
- Department
of Computer Science, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Inge M. W. Verberk
- Neurochemistry
Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands
| | - Charlotte E. Teunissen
- Neurochemistry
Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands
| | - Sanne Abeln
- Department
of Computer Science, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, The Netherlands
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34
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Parrillo L, Spinelli R, Longo M, Zatterale F, Santamaria G, Leone A, Campitelli M, Raciti GA, Beguinot F. The Transcription Factor HOXA5: Novel Insights into Metabolic Diseases and Adipose Tissue Dysfunction. Cells 2023; 12:2090. [PMID: 37626900 PMCID: PMC10453582 DOI: 10.3390/cells12162090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/03/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
The transcription factor HOXA5, from the HOX gene family, has long been studied due to its critical role in physiological activities in normal cells, such as organ development and body patterning, and pathological activities in cancer cells. Nonetheless, recent evidence supports the hypothesis of a role for HOXA5 in metabolic diseases, particularly in obesity and type 2 diabetes (T2D). In line with the current opinion that adipocyte and adipose tissue (AT) dysfunction belong to the group of primary defects in obesity, linking this condition to an increased risk of insulin resistance (IR) and T2D, the HOXA5 gene has been shown to regulate adipocyte function and AT remodeling both in humans and mice. Epigenetics adds complexity to HOXA5 gene regulation in metabolic diseases. Indeed, epigenetic mechanisms, specifically DNA methylation, influence the dynamic HOXA5 expression profile. In human AT, the DNA methylation profile at the HOXA5 gene is associated with hypertrophic obesity and an increased risk of developing T2D. Thus, an inappropriate HOXA5 gene expression may be a mechanism causing or maintaining an impaired AT function in obesity and potentially linking obesity to its associated disorders. In this review, we integrate the current evidence about the involvement of HOXA5 in regulating AT function, as well as its association with the pathogenesis of obesity and T2D. We also summarize the current knowledge on the role of DNA methylation in controlling HOXA5 expression. Moreover, considering the susceptibility of epigenetic changes to reversal through targeted interventions, we discuss the potential therapeutic value of targeting HOXA5 DNA methylation changes in the treatment of metabolic diseases.
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Affiliation(s)
- Luca Parrillo
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| | - Rosa Spinelli
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, 41345 Gothenburg, Sweden
| | - Michele Longo
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| | - Federica Zatterale
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| | - Gianluca Santamaria
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy;
| | - Alessia Leone
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| | - Michele Campitelli
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| | - Gregory Alexander Raciti
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| | - Francesco Beguinot
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
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Mahtha SK, Kumari K, Gaur V, Yadav G. Cavity architecture based modulation of ligand binding tunnels in plant START domains. Comput Struct Biotechnol J 2023; 21:3946-3963. [PMID: 37635766 PMCID: PMC10448341 DOI: 10.1016/j.csbj.2023.07.039] [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] [Indexed: 08/29/2023] Open
Abstract
The Steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain represents an evolutionarily conserved superfamily of lipid transfer proteins widely distributed across the tree of life. Despite significant expansion in plants, knowledge about this domain remains inadequate in plants. In this work, we explore the role of cavity architectural modulations in START protein evolution and functional diversity. We use deep-learning approaches to generate plant START domain models, followed by surface accessibility studies and a comprehensive structural investigation of the rice START family. We validate 28 rice START domain models, delineate binding cavities, measure pocket volumes, and compare these with mammalian counterparts to understand evolution of binding preferences. Overall, plant START domains retain the ancestral α/β helix-grip signature, but we find subtle variation in cavity architectures, resulting in significantly smaller ligand-binding tunnels in the plant kingdom. We identify cavity lining residues (CLRs) responsible for reduction in ancestral tunnel space, and these appear to be class specific, and unique to plants, providing a mechanism for the observed shift in domain function. For instance, mammalian cavity lining residues A135, G181 and A192 have evolved to larger CLRs across the plant kingdom, contributing to smaller sizes, minimal STARTs being the largest, while members of type-IV HD-Zip family show almost complete obliteration of lipid binding cavities, consistent with their present-day DNA binding functions. In summary, this work quantifies plant START structural & functional divergence, bridging current knowledge gaps.
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Affiliation(s)
| | - Kamlesh Kumari
- National Institute of Plant Genome Research, New Delhi 110067, India
| | - Vineet Gaur
- National Institute of Plant Genome Research, New Delhi 110067, India
| | - Gitanjali Yadav
- National Institute of Plant Genome Research, New Delhi 110067, India
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36
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Balbhim SS, Sarkar S, Vasudevan M, Ghosh SK. Three-amino acid loop extension homeodomain proteins regulate stress responses and encystation in Entamoeba. Mol Microbiol 2023. [PMID: 37424153 DOI: 10.1111/mmi.15121] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/11/2023]
Abstract
It is interesting to identify factors involved in the regulation of the encystation of Entamoeba histolytica that differentiate trophozoites into cysts. Evolutionarily conserved three amino acid loop extension (TALE) homeodomain proteins act as transcription factors and execute a variety of functions that are essential for life. A TALE homeodomain (EhHbox) protein-encoding gene has been identified in E. histolytica (Eh) that is highly upregulated during heat shock, glucose, and serum starvation. Its ortholog, EiHbox1, a putative homeobox protein in E. invadens (Ei), is also highly upregulated during the early hours of encystation, glucose starvation, and heat shock. They belong to the PBX family of TALE homeobox proteins and have conserved residues in the homeodomain that are essential for DNA binding. Both are localized in the nucleus during encystation and under different stress conditions. The electrophoretic mobility shift assay confirmed that the recombinant GST-EhHbox binds to the reported TGACAG and TGATTGAT motifs. Down-regulation of EiHbox1 by gene silencing reduced Chitin synthase, Jacob, and increased Jessie gene expression, resulting in defective cysts and decreased encystation efficiency and viability. Overall, our results suggest that the TALE homeobox family has been conserved during evolution and acts as a transcription factor to control the differentiation of Entamoeba by regulating the key encystation-induced genes.
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Affiliation(s)
- Sonar Shubham Balbhim
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Shilpa Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | | | - Sudip K Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
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37
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Cain B, Webb J, Yuan Z, Cheung D, Lim HW, Kovall R, Weirauch MT, Gebelein B. Prediction of cooperative homeodomain DNA binding sites from high-throughput-SELEX data. Nucleic Acids Res 2023; 51:6055-6072. [PMID: 37114997 PMCID: PMC10325903 DOI: 10.1093/nar/gkad318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/12/2023] [Accepted: 04/25/2023] [Indexed: 04/29/2023] Open
Abstract
Homeodomain proteins constitute one of the largest families of metazoan transcription factors. Genetic studies have demonstrated that homeodomain proteins regulate many developmental processes. Yet, biochemical data reveal that most bind highly similar DNA sequences. Defining how homeodomain proteins achieve DNA binding specificity has therefore been a long-standing goal. Here, we developed a novel computational approach to predict cooperative dimeric binding of homeodomain proteins using High-Throughput (HT) SELEX data. Importantly, we found that 15 of 88 homeodomain factors form cooperative homodimer complexes on DNA sites with precise spacing requirements. Approximately one third of the paired-like homeodomain proteins cooperatively bind palindromic sequences spaced 3 bp apart, whereas other homeodomain proteins cooperatively bind sites with distinct orientation and spacing requirements. Combining structural models of a paired-like factor with our cooperativity predictions identified key amino acid differences that help differentiate between cooperative and non-cooperative factors. Finally, we confirmed predicted cooperative dimer sites in vivo using available genomic data for a subset of factors. These findings demonstrate how HT-SELEX data can be computationally mined to predict cooperativity. In addition, the binding site spacing requirements of select homeodomain proteins provide a mechanism by which seemingly similar AT-rich DNA sequences can preferentially recruit specific homeodomain factors.
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Affiliation(s)
- Brittany Cain
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH 45221, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
| | - Jordan Webb
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Zhenyu Yuan
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - David Cheung
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Divisions of Human Genetics, Biomedical Informatics and Developmental Biology, Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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38
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Losa M, Barozzi I, Osterwalder M, Hermosilla-Aguayo V, Morabito A, Chacón BH, Zarrineh P, Girdziusaite A, Benazet JD, Zhu J, Mackem S, Capellini TD, Dickel D, Bobola N, Zuniga A, Visel A, Zeller R, Selleri L. A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2. Nat Commun 2023; 14:3993. [PMID: 37414772 PMCID: PMC10325989 DOI: 10.1038/s41467-023-39443-z] [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: 03/17/2022] [Accepted: 06/14/2023] [Indexed: 07/08/2023] Open
Abstract
A lingering question in developmental biology has centered on how transcription factors with widespread distribution in vertebrate embryos can perform tissue-specific functions. Here, using the murine hindlimb as a model, we investigate the elusive mechanisms whereby PBX TALE homeoproteins, viewed primarily as HOX cofactors, attain context-specific developmental roles despite ubiquitous presence in the embryo. We first demonstrate that mesenchymal-specific loss of PBX1/2 or the transcriptional regulator HAND2 generates similar limb phenotypes. By combining tissue-specific and temporally controlled mutagenesis with multi-omics approaches, we reconstruct a gene regulatory network (GRN) at organismal-level resolution that is collaboratively directed by PBX1/2 and HAND2 interactions in subsets of posterior hindlimb mesenchymal cells. Genome-wide profiling of PBX1 binding across multiple embryonic tissues further reveals that HAND2 interacts with subsets of PBX-bound regions to regulate limb-specific GRNs. Our research elucidates fundamental principles by which promiscuous transcription factors cooperate with cofactors that display domain-restricted localization to instruct tissue-specific developmental programs.
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Affiliation(s)
- Marta Losa
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, Switzerland
| | - Viviana Hermosilla-Aguayo
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Angela Morabito
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Brandon H Chacón
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Peyman Zarrineh
- School of Medical Sciences, University of Manchester, Manchester, UK
| | - Ausra Girdziusaite
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Jean Denis Benazet
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Jianjian Zhu
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Susan Mackem
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Diane Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester, UK
| | - Aimée Zuniga
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- School of Natural Sciences, University of California, Merced, Merced, CA, 95343, USA
| | - Rolf Zeller
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Licia Selleri
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA.
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39
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Vorel J, Kmentová N, Hahn C, Bureš P, Kašný M. An insight into the functional genomics and species classification of Eudiplozoon nipponicum (Monogenea, Diplozoidae), a haematophagous parasite of the common carp Cyprinus carpio. BMC Genomics 2023; 24:363. [PMID: 37380941 DOI: 10.1186/s12864-023-09461-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/16/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND Monogenea (Platyhelminthes, Neodermata) are the most species-rich class within the Neodermata superclass of primarily fish parasites. Despite their economic and ecological importance, monogenean research tends to focus on their morphological, phylogenetic, and population characteristics, while comprehensive omics analyses aimed at describing functionally important molecules are few and far between. We present a molecular characterisation of monogenean representative Eudiplozoon nipponicum, an obligate haematophagous parasite infecting the gills of the common carp. We report its nuclear and mitochondrial genomes, present a functional annotation of protein molecules relevant to the molecular and biochemical aspect of physiological processes involved in interactions with the fish hosts, and re-examinate the taxonomic position of Eudiplozoon species within the Diplozoidae family. RESULTS We have generated 50.81 Gbp of raw sequencing data (Illumina and Oxford Nanopore reads), bioinformatically processed, and de novo assembled them into a genome draft 0.94 Gbp long, consisting of 21,044 contigs (N50 = 87 kbp). The final assembly represents 57% of the estimated total genome size (~ 1.64 Gbp), whereby repetitive and low-complexity regions account for ~ 64% of the assembled length. In total, 36,626 predicted genes encode 33,031 proteins and homology-based annotation of protein-coding genes (PCGs) and proteins characterises 14,785 (44.76%) molecules. We have detected significant representation of functional proteins and known molecular functions. The numbers of peptidases and inhibitors (579 proteins), characterised GO terms (16,016 unique assigned GO terms), and identified KEGG Orthology (4,315 proteins) acting in 378 KEGG pathways demonstrate the variety of mechanisms by which the parasite interacts with hosts on a macromolecular level (immunomodulation, feeding, and development). Comparison between the newly assembled E. nipponicum mitochondrial genome (length of 17,038 bp) and other diplozoid monogeneans confirms the existence of two distinct Eudiplozoon species infecting different fish hosts: Cyprinus carpio and Carassius spp. CONCLUSIONS Although the amount of sequencing data and characterised molecules of monogenean parasites has recently increased, a better insight into their molecular biology is needed. The E. nipponicum nuclear genome presented here, currently the largest described genome of any monogenean parasite, represents a milestone in the study of monogeneans and their molecules but further omics research is needed to understand these parasites' biological nature.
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Affiliation(s)
- Jiří Vorel
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic.
| | - Nikol Kmentová
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Agoralaan Gebouw D, Diepenbeek, B-3590, Belgium
| | - Christoph Hahn
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, A-8010, Austria
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Martin Kašný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
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Catta-Preta R, Lindtner S, Ypsilanti A, Price J, Abnousi A, Su-Feher L, Wang Y, Juric I, Jones IR, Akiyama JA, Hu M, Shen Y, Visel A, Pennacchio LA, Dickel D, Rubenstein JLR, Nord AS. Combinatorial transcription factor binding encodes cis-regulatory wiring of forebrain GABAergic neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.28.546894. [PMID: 37425940 PMCID: PMC10327028 DOI: 10.1101/2023.06.28.546894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Transcription factors (TFs) bind combinatorially to genomic cis-regulatory elements (cREs), orchestrating transcription programs. While studies of chromatin state and chromosomal interactions have revealed dynamic neurodevelopmental cRE landscapes, parallel understanding of the underlying TF binding lags. To elucidate the combinatorial TF-cRE interactions driving mouse basal ganglia development, we integrated ChIP-seq for twelve TFs, H3K4me3-associated enhancer-promoter interactions, chromatin and transcriptional state, and transgenic enhancer assays. We identified TF-cREs modules with distinct chromatin features and enhancer activity that have complementary roles driving GABAergic neurogenesis and suppressing other developmental fates. While the majority of distal cREs were bound by one or two TFs, a small proportion were extensively bound, and these enhancers also exhibited exceptional evolutionary conservation, motif density, and complex chromosomal interactions. Our results provide new insights into how modules of combinatorial TF-cRE interactions activate and repress developmental expression programs and demonstrate the value of TF binding data in modeling gene regulatory wiring.
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Affiliation(s)
- Rinaldo Catta-Preta
- Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA
- Current Address: Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Susan Lindtner
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Athena Ypsilanti
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - James Price
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Armen Abnousi
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44106, USA
- Current Address: NovaSignal, Los Angeles, CA 90064, USA
| | - Linda Su-Feher
- Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA
| | - Yurong Wang
- Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA
| | - Ivan Juric
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44106, USA
| | - Ian R Jones
- Institute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Neurology, University of California, San Francisco, CA 94143, USA
| | - Jennifer A Akiyama
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44106, USA
| | - Yin Shen
- Institute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Neurology, University of California, San Francisco, CA 94143, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- Comparative Biochemistry Program, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Diane Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John L R Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alex S Nord
- Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA
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Bai Y, Zhou Y, Lei Q, Wang Y, Pu G, Liu Z, Chen X, Liu Q. Analysis of the HD-Zip I transcription factor family in Salvia miltiorrhiza and functional research of SmHD-Zip12 in tanshinone synthesis. PeerJ 2023; 11:e15510. [PMID: 37397009 PMCID: PMC10312201 DOI: 10.7717/peerj.15510] [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: 11/22/2022] [Accepted: 05/15/2023] [Indexed: 07/04/2023] Open
Abstract
Background The homeodomain-leucine zipper I (HD-Zip I) transcription factor is a plant-specific protein that plays an essential role in the abiotic stress response of plants. Research on the HD-Zip I family in Salvia miltiorrhiza is still lacking. Methods and Results In this study, a total of 25 SmHD-Zip I proteins were identified. Their characterizations, phylogenetic relationships, conserved motifs, gene structures, and cis-elements were analyzed comprehensively using bioinformatics methods. Expression profiling revealed that SmHD-Zip I genes exhibited distinctive tissue-specific patterns and divergent responses to ABA, PEG, and NaCl stresses. SmHD-Zip12 responded the most strongly to ABA, PEG, and NaCl, so it was used for transgenic experiments. The overexpression of SmHD-Zip12 significantly increased the content of cryptotanshinone, dihydrotanshinone I, tanshinone I, and tanshinone IIA by 2.89-fold, 1.85-fold, 2.14-fold, and 8.91-fold compared to the wild type, respectively. Moreover, in the tanshinone biosynthetic pathways, the overexpression of SmHD-Zip12 up-regulated the expression levels of SmAACT, SmDXS, SmIDS, SmGGPPS, SmCPS1, SmCPS2, SmCYP76AH1, SmCYP76AH3, and SmCYP76AK1 compared with the wild type. Conclusions This study provides information the possible functions of the HD-Zip I family and lays a theoretical foundation for clarifying the functional mechanism of the SmHD-Zip12 gene in regulating the synthesis of tanshinone in S. miltiorrhiza.
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Affiliation(s)
- Yanhong Bai
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Ying Zhou
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Qiaoqi Lei
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Yu Wang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Gaobin Pu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Zhenhua Liu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Xue Chen
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Qian Liu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
- LiShizhen College of Traditional Chinese Medicine, Huanggang Normal University, Huanggang, Hubei, China
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42
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Santini S, Schenkelaars Q, Jourda C, Duchesne M, Belahbib H, Rocher C, Selva M, Riesgo A, Vervoort M, Leys SP, Kodjabachian L, Le Bivic A, Borchiellini C, Claverie JM, Renard E. The compact genome of the sponge Oopsacas minuta (Hexactinellida) is lacking key metazoan core genes. BMC Biol 2023; 21:139. [PMID: 37337252 DOI: 10.1186/s12915-023-01619-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/09/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Explaining the emergence of the hallmarks of bilaterians is a central focus of evolutionary developmental biology-evodevo-and evolutionary genomics. For this purpose, we must both expand and also refine our knowledge of non-bilaterian genomes, especially by studying early branching animals, in particular those in the metazoan phylum Porifera. RESULTS We present a comprehensive analysis of the first whole genome of a glass sponge, Oopsacas minuta, a member of the Hexactinellida. Studying this class of sponge is evolutionary relevant because it differs from the three other Porifera classes in terms of development, tissue organization, ecology, and physiology. Although O. minuta does not exhibit drastic body simplifications, its genome is among the smallest of animal genomes sequenced so far, and surprisingly lacks several metazoan core genes (including Wnt and several key transcription factors). Our study also provides the complete genome of a symbiotic Archaea dominating the associated microbial community: a new Thaumarchaeota species. CONCLUSIONS The genome of the glass sponge O. minuta differs from all other available sponge genomes by its compactness and smaller number of encoded proteins. The unexpected loss of numerous genes previously considered ancestral and pivotal for metazoan morphogenetic processes most likely reflects the peculiar syncytial tissue organization in this group. Our work further documents the importance of convergence during animal evolution, with multiple convergent evolution of septate-like junctions, electrical-signaling and multiciliated cells in metazoans.
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Affiliation(s)
- Sébastien Santini
- Aix Marseille Univ, CNRS, IGS, UMR 7256, IMM, IM2B, IOM, Marseille, France
| | - Quentin Schenkelaars
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Cyril Jourda
- Aix Marseille Univ, CNRS, IGS, UMR 7256, IMM, IM2B, IOM, Marseille, France
- CIRAD, UMR PVBMT, La Réunion, France
| | - Marc Duchesne
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Hassiba Belahbib
- Aix Marseille Univ, CNRS, IGS, UMR 7256, IMM, IM2B, IOM, Marseille, France
| | - Caroline Rocher
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
| | - Marjorie Selva
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
| | - Ana Riesgo
- Department of Biodiversity and Evolutionary Biology, Madrid, Spain
- Department of Life Sciences, Natural History Museum of London, London, SW7 5BD, UK
| | - Michel Vervoort
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Sally P Leys
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Laurent Kodjabachian
- Aix Marseille Univ, CNRS, IBDM, UMR 7288, Turing Center for Living Systems, Marseille, France
| | - André Le Bivic
- Aix Marseille Univ, CNRS, IBDM, UMR 7288, Marseille, France
| | | | | | - Emmanuelle Renard
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France.
- Aix Marseille Univ, CNRS, IBDM, UMR 7288, Marseille, France.
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Rajan A, Anhezini L, Rives-Quinto N, Chhabra JY, Neville MC, Larson ED, Goodwin SF, Harrison MM, Lee CY. Low-level repressive histone marks fine-tune gene transcription in neural stem cells. eLife 2023; 12:e86127. [PMID: 37314324 PMCID: PMC10344426 DOI: 10.7554/elife.86127] [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: 01/11/2023] [Accepted: 06/11/2023] [Indexed: 06/15/2023] Open
Abstract
Coordinated regulation of gene activity by transcriptional and translational mechanisms poise stem cells for a timely cell-state transition during differentiation. Although important for all stemness-to-differentiation transitions, mechanistic understanding of the fine-tuning of gene transcription is lacking due to the compensatory effect of translational control. We used intermediate neural progenitor (INP) identity commitment to define the mechanisms that fine-tune stemness gene transcription in fly neural stem cells (neuroblasts). We demonstrate that the transcription factor FruitlessC (FruC) binds cis-regulatory elements of most genes uniquely transcribed in neuroblasts. Loss of fruC function alone has no effect on INP commitment but drives INP dedifferentiation when translational control is reduced. FruC negatively regulates gene expression by promoting low-level enrichment of the repressive histone mark H3K27me3 in gene cis-regulatory regions. Identical to fruC loss-of-function, reducing Polycomb Repressive Complex 2 activity increases stemness gene activity. We propose low-level H3K27me3 enrichment fine-tunes gene transcription in stem cells, a mechanism likely conserved from flies to humans.
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Affiliation(s)
- Arjun Rajan
- Life Sciences Institute, University of Michigan-Ann ArborAnn ArborUnited States
| | - Lucas Anhezini
- Life Sciences Institute, University of Michigan-Ann ArborAnn ArborUnited States
| | - Noemi Rives-Quinto
- Life Sciences Institute, University of Michigan-Ann ArborAnn ArborUnited States
| | - Jay Y Chhabra
- Life Sciences Institute, University of Michigan-Ann ArborAnn ArborUnited States
| | - Megan C Neville
- Centre for Neural Circuits and Behaviour, University of OxfordOxfordUnited Kingdom
| | - Elizabeth D Larson
- Department of Biomolecular Chemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Stephen F Goodwin
- Centre for Neural Circuits and Behaviour, University of OxfordOxfordUnited Kingdom
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Cheng-Yu Lee
- Life Sciences Institute, University of Michigan-Ann ArborAnn ArborUnited States
- Department of Cell and Developmental Biology, University of Michigan Medical SchoolAnn ArborUnited States
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan Medical SchoolAnn ArborUnited States
- Rogel Cancer Center, University of Michigan Medical SchoolAnn ArborUnited States
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Pan A, Zeng Y, Liu J, Zhou M, Lai EC, Yu Y. Unanticipated broad phylogeny of BEN DNA-binding domains revealed by structural homology searches. Curr Biol 2023; 33:2270-2282.e2. [PMID: 37236184 PMCID: PMC10348805 DOI: 10.1016/j.cub.2023.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/07/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023]
Abstract
Organization of protein sequences into domain families is a foundation for cataloging and investigating protein functions. However, long-standing strategies based on primary amino acid sequences are blind to the possibility that proteins with dissimilar sequences could have comparable tertiary structures. Building on our recent findings that in silico structural predictions of BEN family DNA-binding domains closely resemble their experimentally determined crystal structures, we exploited the AlphaFold2 database for comprehensive identification of BEN domains. Indeed, we identified numerous novel BEN domains, including members of new subfamilies. For example, while no BEN domain factors had previously been annotated in C. elegans, this species actually encodes multiple BEN proteins. These include key developmental timing genes of orphan domain status, sel-7 and lin-14, the latter being the central target of the founding miRNA lin-4. We also reveal that the domain of unknown function 4806 (DUF4806), which is widely distributed across metazoans, is structurally similar to BEN and comprises a new subtype. Surprisingly, we find that BEN domains resemble both metazoan and non-metazoan homeodomains in 3D conformation and preserve characteristic residues, indicating that despite their inability to be aligned by conventional methods, these DNA-binding modules are probably evolutionarily related. Finally, we broaden the application of structural homology searches by revealing novel human members of DUF3504, which exists on diverse proteins with presumed or known nuclear functions. Overall, our work strongly expands this recently identified family of transcription factors and illustrates the value of 3D structural predictions to annotate protein domains and interpret their functions.
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Affiliation(s)
- Anyu Pan
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Yangfan Zeng
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Jingjing Liu
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Mengjie Zhou
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Yang Yu
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100005, China.
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Kim DG, Joo K, Han J, Choi M, Kim SW, Park KH, Park SJ, Lee CS, Byeon SH, Woo SJ. Genotypic Profile and Clinical Characteristics of CRX-Associated Retinopathy in Koreans. Genes (Basel) 2023; 14:genes14051057. [PMID: 37239417 DOI: 10.3390/genes14051057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/26/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
This study aimed to investigate the clinical characteristics of Korean patients with retinal dystrophy associated with pathogenic variants of cone rod homeobox-containing gene (CRX). We retrospectively enrolled Korean patients with CRX-associated retinal dystrophy (CRX-RD) who visited two tertiary referral hospitals. Pathogenic variants were identified using targeted panel sequencing or whole-exome sequencing. We analyzed clinical features and phenotypic spectra according to genotype. Eleven patients with CRX-RD were included in this study. Six patients with cone-rod dystrophy (CORD), two with macular dystrophy (MD), two with Leber congenital amaurosis (LCA), and one with retinitis pigmentosa (RP) were included. One patient (9.1%) had autosomal recessive inheritance, and the other ten patients (90.9%) had autosomal dominant inheritance. Six patients (54.5%) were male, and the mean age of symptom onset was 27.0 ± 17.9 years. At the first presentation, the mean age was 39.4 ± 20.6 years, and best-corrected visual acuity (BCVA) (logMAR) was 0.76 ± 0.90 in the better eye. Negative electroretinography (ERG) was observed in seven (63.6%) patients. Nine pathogenic variants were identified, including two novel variants, c.101-1G>A and c.898T>C:p.(*300Glnext*118). Taken together with the variants reported in prior studies, all variants within the homeodomain are missense variants, whereas most variants downstream of the homeodomain are truncating variants (88%). The clinical features of pathogenic variants within the homeodomain are either CORD or MD with bull's eye maculopathy, whereas variants downstream of the homeodomain cause more diverse phenotypes, with CORD and MD in 36%, LCA in 40%, and RP in 24%. This is the first case series in Korea to investigate the CRX-RD genotype-phenotype correlation. Pathogenic variants downstream of the homeodomain of the CRX gene are present as RP, LCA, and CORD, whereas pathogenic variants within the homeodomain are mainly present as CORD or MD with bull's eye maculopathy. This trend was similar to previous genotype-phenotype analyses of CRX-RD. Further molecular biologic research on this correlation is required.
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Affiliation(s)
- Dong Geun Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea
- Department of Ophthalmology, Inje University College of Medicine, Busan Paik Hospital, Busan 47392, Republic of Korea
| | - Kwangsic Joo
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea
| | - Jinu Han
- Institute of Vision Research, Department of Ophthalmology, Yonsei University College of Medicine, Severance Hospital, Seoul 06273, Republic of Korea
| | - Mihyun Choi
- Department of Ophthalmology, Guro Hospital, Korea University College of Medicine, Seoul 08308, Republic of Korea
| | - Seong-Woo Kim
- Department of Ophthalmology, Guro Hospital, Korea University College of Medicine, Seoul 08308, Republic of Korea
| | - Kyu Hyung Park
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea
| | - Sang Jun Park
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea
| | - Christopher Seungkyu Lee
- Institute of Vision Research, Department of Ophthalmology, Yonsei University College of Medicine, Severance Hospital, Seoul 06273, Republic of Korea
| | - Suk Ho Byeon
- Institute of Vision Research, Department of Ophthalmology, Yonsei University College of Medicine, Severance Hospital, Seoul 06273, Republic of Korea
| | - Se Joon Woo
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea
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Haberkorn C, David J, Henri H, Delpuech J, Lasseur R, Vavre F, Varaldi J. A major 6 Mb superlocus is involved in pyrethroid resistance in the common bed bug Cimex lectularius. Evol Appl 2023; 16:1012-1028. [PMID: 37216030 PMCID: PMC10197226 DOI: 10.1111/eva.13550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/23/2023] [Accepted: 04/04/2023] [Indexed: 05/24/2023] Open
Abstract
In the last few years, the bed bug Cimex lectularius has been an increasing problem worldwide, mainly due to the development of insecticide resistance to pyrethroids. The characterization of resistance alleles is a prerequisite to improve surveillance and resistance management. To identify genomic variants associated with pyrethroid resistance in Cimex lectularius, we compared the genetic composition of two recent and resistant populations with that of two ancient-susceptible strains using a genome-wide pool-seq design. We identified a large 6 Mb "superlocus" showing particularly high genetic differentiation and association with the resistance phenotype. This superlocus contained several clustered resistance genes and was also characterized by a high density of structural variants (inversions, duplications). The possibility that this superlocus constitutes a resistance "supergene" that evolved after the clustering of alleles adapted to insecticide and after reduction in recombination is discussed.
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Affiliation(s)
- Chloé Haberkorn
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
- IZInovationLyonFrance
| | - Jean‐Philippe David
- Laboratoire d'Écologie AlpineUMR UGA‐USMB‐CNRS 5553 Université Grenoble Alpes CS 40700Grenoble cedex 9France
| | - Hélène Henri
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | - Jean‐Marie Delpuech
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | | | - Fabrice Vavre
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | - Julien Varaldi
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
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Guo AD, Yan KN, Hu H, Zhai L, Hu TF, Su H, Chi Y, Zha J, Xu Y, Zhao D, Lu X, Xu YJ, Zhang J, Tan M, Chen XH. Spatiotemporal and global profiling of DNA-protein interactions enables discovery of low-affinity transcription factors. Nat Chem 2023:10.1038/s41557-023-01196-z. [PMID: 37106095 DOI: 10.1038/s41557-023-01196-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/30/2023] [Indexed: 04/29/2023]
Abstract
Precise dissection of DNA-protein interactions is essential for elucidating the recognition basis, dynamics and gene regulation mechanism. However, global profiling of weak and dynamic DNA-protein interactions remains a long-standing challenge. Here, we establish the light-induced lysine (K) enabled crosslinking (LIKE-XL) strategy for spatiotemporal and global profiling of DNA-protein interactions. Harnessing unique abilities to capture weak and transient DNA-protein interactions, we demonstrate that LIKE-XL enables the discovery of low-affinity transcription-factor/DNA interactions via sequence-specific DNA baits, determining the binding sites for transcription factors that have been previously unknown. More importantly, we successfully decipher the dynamics of the transcription factor subproteome in response to drug treatment in a time-resolved manner, and find downstream target transcription factors from drug perturbations, providing insight into their dynamic transcriptional networks. The LIKE-XL strategy offers a complementary method to expand the DNA-protein profiling toolbox and map accurate DNA-protein interactomes that were previously inaccessible via non-covalent strategies, for better understanding of protein function in health and disease.
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Affiliation(s)
- An-Di Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ke-Nian Yan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Teng-Fei Hu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yijia Chi
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinyin Zha
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Dongxin Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yong-Jiang Xu
- School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
| | - Jian Zhang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
- College of Pharmacy, Jiangsu Ocean University, Lianyungang, China.
| | - Xiao-Hua Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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48
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Prathap V, Kumar S, Tyagi A. Comparative proteome analysis of phosphorus-responsive genotypes reveals the proteins differentially expressed under phosphorous starvation stress in rice. Int J Biol Macromol 2023; 234:123760. [PMID: 36812961 DOI: 10.1016/j.ijbiomac.2023.123760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/23/2023]
Abstract
Phosphorus (P)-deficiency is one of the major nutrient constraints for global rice production. P-deficiency tolerance in rice involves complex regulatory mechanisms. To gain insights into the proteins involved in phosphorus acquisition and use efficiency in rice, proteome analysis of a high-yielding rice cultivar Pusa-44 and its near-isogenic line (NIL)-23 harboring a major phosphorous uptake (Pup1) QTL, grown under control and P-starvation stress, was performed. Comparative proteome profiling of shoot and root tissues from the plants grown hydroponically with P (16 ppm, +P) or without P (0 ppm, -P) resulted in the identification of 681 and 567 differentially expressed proteins (DEPs) in shoot of Pusa-44 and NIL-23, respectively. Similarly, 66 and 93 DEPs were identified in root of Pusa-44 and NIL-23, respectively. These P-starvation responsive DEPs were annotated to be involved in metabolic processes like photosynthesis, starch-, sucrose-, energy-metabolism, transcription factors (mainly ARF, ZFP, HD-ZIP, MYB), and phytohormone signaling. Comparative analysis of the expression patterns observed by proteome analysis with that reported at the transcriptome level indicated the Pup1 QTL-mediated post-transcriptional regulation plays an important role under -P stress. Thus, the present study describes the molecular aspect of the regulatory functions of Pup1 QTL under P-starvation stress in rice, which might help develop an efficient rice cultivar with enhanced P acquisition and assimilation for better performance in P-deficient soil.
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Affiliation(s)
- V Prathap
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.
| | - Aruna Tyagi
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.
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49
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Yang Q, Cong T, Yao Y, Cheng T, Yuan C, Zhang Q. KNOX Genes Were Involved in Regulating Axillary Bud Formation of Chrysanthemum × morifolium. Int J Mol Sci 2023; 24:ijms24087081. [PMID: 37108245 PMCID: PMC10138332 DOI: 10.3390/ijms24087081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Branching is an important agronomic and economic trait in cut chrysanthemums. The axillary meristem (AM) formation of the axillary buds of cut chrysanthemums has a decisive role in its branching characteristics. However, little is known about the regulation mechanism of axillary meristem formation in chrysanthemums at the molecular level. Members of the Homeobox gene family especially genes belonging to the class I KNOX branch play a key role in regulating the axillary bud growth and development processes of plants. In this study, three genes belonging to the class I KNOX branch, CmKNAT1, CmKNAT6, and CmSTM were cloned from chrysanthemums, and their functions in regulating axillary bud formation were examined. The subcellular localization test showed that these three KNOX genes were expressed in the nucleus, so all of them might function as transcription factors. The results of the expression profile analysis showed that these three KNOX genes were highly expressed in the AM formation stage of axillary buds. Overexpression of KNOX genes result in a wrinkled leaf phenotype in tobacco and Arabidopsis, which may be related to the excessive division of leaf cells, resulting in the proliferation of leaf tissue. Furthermore, overexpression of these three KNOX genes enhances the regeneration ability of tobacco leaves, indicating that these three KNOX genes may participate in the regulation of cell meristematic ability, thus promoting the formation of buds. In addition, the results of fluorescence quantitative testing showed that these three KNOX genes may promote the formation of chrysanthemum axillary buds by promoting the cytokinin pathway while inhibiting the auxin and gibberellin pathways. In conclusion, this study demonstrated that CmKNAT1, CmKNAT6, and CmSTM genes were involved in regulating axillary bud formation of Chrysanthemum × morifolium and preliminarily revealed the molecular mechanism of their regulation of AM formation. These findings may provide a theoretical basis and candidate gene resources for genetic engineering breeding of new varieties of cut chrysanthemums without lateral branches.
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Affiliation(s)
- Qingqing Yang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Tianci Cong
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Yicen Yao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Cunquan Yuan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing 100083, China
- National Engineering Research Center for Floriculture, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing 100083, China
- Engineering Research Center of Landscape Environment of Ministry of Education, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing 100083, China
- School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
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50
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DelRosso N, Tycko J, Suzuki P, Andrews C, Aradhana, Mukund A, Liongson I, Ludwig C, Spees K, Fordyce P, Bassik MC, Bintu L. Large-scale mapping and mutagenesis of human transcriptional effector domains. Nature 2023; 616:365-372. [PMID: 37020022 PMCID: PMC10484233 DOI: 10.1038/s41586-023-05906-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 03/01/2023] [Indexed: 04/07/2023]
Abstract
Human gene expression is regulated by more than 2,000 transcription factors and chromatin regulators1,2. Effector domains within these proteins can activate or repress transcription. However, for many of these regulators we do not know what type of effector domains they contain, their location in the protein, their activation and repression strengths, and the sequences that are necessary for their functions. Here, we systematically measure the effector activity of more than 100,000 protein fragments tiling across most chromatin regulators and transcription factors in human cells (2,047 proteins). By testing the effect they have when recruited at reporter genes, we annotate 374 activation domains and 715 repression domains, roughly 80% of which are new and have not been previously annotated3-5. Rational mutagenesis and deletion scans across all the effector domains reveal aromatic and/or leucine residues interspersed with acidic, proline, serine and/or glutamine residues are necessary for activation domain activity. Furthermore, most repression domain sequences contain sites for small ubiquitin-like modifier (SUMO)ylation, short interaction motifs for recruiting corepressors or are structured binding domains for recruiting other repressive proteins. We discover bifunctional domains that can both activate and repress, some of which dynamically split a cell population into high- and low-expression subpopulations. Our systematic annotation and characterization of effector domains provide a rich resource for understanding the function of human transcription factors and chromatin regulators, engineering compact tools for controlling gene expression and refining predictive models of effector domain function.
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Affiliation(s)
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Peter Suzuki
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Cecelia Andrews
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Aradhana
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Adi Mukund
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Ivan Liongson
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Connor Ludwig
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Kaitlyn Spees
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Polly Fordyce
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H Institute, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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