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Fischer MD, Graham P, Pick L. The ftz upstream element drives late ftz stripes but is not required for regulation of Ftz target genes. Dev Biol 2024; 505:141-147. [PMID: 37977522 PMCID: PMC10843599 DOI: 10.1016/j.ydbio.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
The regulation of gene expression in precise, rapidly changing spatial patterns is essential for embryonic development. Multiple enhancers have been identified for the evolving expression patterns of the cascade of Drosophila segmentation genes that establish the basic body plan of the fly. Classic reporter transgene experiments identified multiple cis-regulatory elements (CREs) that are sufficient to direct various aspects of the evolving expression pattern of the pair-rule gene fushi tarazu (ftz). These include enhancers that coordinately activate expression in all seven stripes and stripe-specific elements that activate expression in one or more ftz stripes. Of the two 7-stripe enhancers, analysis of reporter transgenes demonstrated that the upstream element (UPS) is autoregulatory, requiring direct binding of Ftz protein to direct striped expression. Here, we asked about the endogenous role of the UPS by precisely deleting this 7-stripe enhancer. In ftzΔUPS7S homozygotes, ftz stripes appear in the same order as wildtype, and all but stripe 4 are expressed at wildtype levels by the end of the cellular blastoderm stage. This suggests that the zebra element and UPS harbor information to direct stripe 4 expression, although previous deletion analyses failed to identify a stripe-specific CRE within these two 7-stripe enhancers. However, the UPS is necessary for late ftz stripe expression, with all 7 stripes decaying earlier than wildtype in ftzΔUPS7S homozygotes. Despite this premature loss of ftz expression, downstream target gene regulation proceeds as in wildtype, and segmentation is unperturbed in the overwhelming majority of animals. We propose that this late-acting enhancer provides a buffer against perturbations in gene expression but is not required for establishment of Ftz cell fates. Overall, our results demonstrate that multiple enhancers, each directing distinct aspects of an overall gene expression pattern, contribute to fine-tuning the complex patterns necessary for embryonic development.
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Affiliation(s)
- Matthew D Fischer
- Department of Pathology and Laboratory Medicine, 3501 Civic Center Boulevard, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Patricia Graham
- Department of Entomology, 4291 Fieldhouse Drive, University of Maryland, College Park, MD, 20742, USA
| | - Leslie Pick
- Department of Entomology, 4291 Fieldhouse Drive, University of Maryland, College Park, MD, 20742, USA.
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2
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Sharma M, Larow VM, Dobychina N, Kessler DS, Krasilnikova MM, Yaklichkin S. The evolutionary loss of the Eh1 motif in FoxE1 in the lineage of placental mammals. PLoS One 2023; 18:e0296176. [PMID: 38150428 PMCID: PMC10752562 DOI: 10.1371/journal.pone.0296176] [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: 03/30/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
Abstract
Forkhead box E1 (FoxE1) protein is a transcriptional regulator known to play a major role in the development of the thyroid gland. By performing sequence alignments, we detected a deletion in FoxE1, which occurred in the evolution of mammals, near the point of divergence of placental mammals. This deletion led to the loss of the majority of the Eh1 motif, which was important for interactions with transcriptional corepressors. To investigate a potential mechanism for this deletion, we analyzed replication through the deletion area in mammalian cells with two-dimensional gel electrophoresis, and in vitro, using a primer extension reaction. We demonstrated that the area of the deletion presented an obstacle for replication in both assays. The exact position of polymerization arrest in primer extension indicated that it was most likely caused by a quadruplex DNA structure. The quadruplex structure hypothesis is also consistent with the exact borders of the deletion. The exact roles of these evolutionary changes in FoxE1 family proteins are still to be determined.
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Affiliation(s)
- Mahak Sharma
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, United States of America
| | - Victoria M. Larow
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, United States of America
| | - Nataliia Dobychina
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Daniel S. Kessler
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Maria M. Krasilnikova
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, United States of America
| | - Sergey Yaklichkin
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
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3
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Hox genes in spiders: Their significance for development and evolution. Semin Cell Dev Biol 2022:S1084-9521(22)00355-X. [PMID: 36522242 DOI: 10.1016/j.semcdb.2022.11.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/13/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022]
Abstract
Hox genes are known for their role in the specification of typical body plan features in animals. Evolutionary changes in Hox gene function are believed to be involved in the emergence of the diverse body plans we observe in animals today. Spiders share many body plan features with other arthropods, but also have numerous unique traits of their own. Studies of spider Hox genes have already provided insights into evolutionarily conserved and derived features of the spider body plan and their genetic basis. However, many aspects of Hox gene biology have been insufficiently studied in spiders so far. In this review, we highlight previous comparative studies of Hox genes in spiders and their significance for our understanding of the evolution of the spider body plan. We also identify aspects of Hox gene biology that need to be studied in greater detail. Many spider Hox genes have not been investigated beyond their mRNA expression patterns, and the role of Hox genes with apparently plesiomorphic or dual functions, like ftz and Hox3 is still unclear. Spiders have a duplicated Hox gene cluster, but possible sub- or neofunctionalisation of duplicates have not yet been studied systematically. Future research should therefore focus on these issues, in addition to the role of Polycomb and trithorax-mediated regulation, the identification of regulatory regions, cofactors or spider-specific target genes, and the significance of non-coding RNAs transcribed from within the Hox cluster and even from the antisense strand of particular Hox genes.
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4
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Prazak L, Iwasaki Y, Kim AR, Kozlov K, King K, Gergen JP. A dual role for DNA binding by Runt in activation and repression of sloppy paired transcription. Mol Biol Cell 2021; 32:ar26. [PMID: 34432496 PMCID: PMC8693977 DOI: 10.1091/mbc.e20-08-0509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
This work investigates the role of DNA binding by Runt in regulating the sloppy paired 1 (slp1) gene and in particular two distinct cis-regulatory elements that mediate regulation by Runt and other pair-rule transcription factors during Drosophila segmentation. We find that a DNA-binding-defective form of Runt is ineffective at repressing both the distal (DESE) and proximal (PESE) early stripe elements of slp1 and is also compromised for DESE-dependent activation. The function of Runt-binding sites in DESE is further investigated using site-specific transgenesis and quantitative imaging techniques. When DESE is tested as an autonomous enhancer, mutagenesis of the Runt sites results in a clear loss of Runt-dependent repression but has little to no effect on Runt-dependent activation. Notably, mutagenesis of these same sites in the context of a reporter gene construct that also contains the PESE enhancer results in a significant reduction of DESE-dependent activation as well as the loss of repression observed for the autonomous mutant DESE enhancer. These results provide strong evidence that DNA binding by Runt directly contributes to the regulatory interplay of interactions between these two enhancers in the early embryo.
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Affiliation(s)
- Lisa Prazak
- Department of Biology, Farmingdale State College, Farmingdale, NY 11735-1021.,Department of Biochemistry and Cell Biology and Center for Developmental Genetics.,Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY 11794-5215
| | - Yasuno Iwasaki
- Department of Biochemistry and Cell Biology and Center for Developmental Genetics
| | - Ah-Ram Kim
- Graduate Program in Biochemistry and Structural Biology, and
| | - Konstantin Kozlov
- Department of Applied Mathematics, St. Petersburg State Polytechnical University, St. Petersburg, Russia 195251
| | - Kevin King
- Department of Biochemistry and Cell Biology and Center for Developmental Genetics.,Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY 11794-5215
| | - J Peter Gergen
- Department of Biochemistry and Cell Biology and Center for Developmental Genetics
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5
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Patkar S, Magen A, Sharan R, Hannenhalli S. A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer. PLoS Comput Biol 2017; 13:e1005793. [PMID: 29190299 PMCID: PMC5708603 DOI: 10.1371/journal.pcbi.1005793] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/27/2017] [Indexed: 11/18/2022] Open
Abstract
Guilt-by-association codifies the empirical observation that a gene's function is informed by its neighborhood in a biological network. This would imply that when a gene's network context is altered, for instance in disease condition, so could be the gene's function. Although context-specific changes in biological networks have been explored, the potential changes they may induce on the functional roles of genes are yet to be characterized. Here we analyze, for the first time, the network-induced potential functional changes in breast cancer. Using transcriptomic samples for 1047 breast tumors and 110 healthy breast tissues from TCGA, we derive sample-specific protein interaction networks and assign sample-specific functions to genes via a diffusion strategy. Testing for significant changes in the inferred functions between normal and cancer samples, we find several functions to have significantly gained or lost genes in cancer, not due to differential expression of genes known to perform the function, but rather due to changes in the network topology. Our predicted functional changes are supported by mutational and copy number profiles in breast cancers. Our diffusion-based functional assignment provides a novel characterization of a tumor that is complementary to the standard approach based on functional annotation alone. Importantly, this characterization is effective in predicting patient survival, as well as in predicting several known histopathological subtypes of breast cancer.
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Affiliation(s)
- Sushant Patkar
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Assaf Magen
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Roded Sharan
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Sridhar Hannenhalli
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
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6
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Percival-Smith A. Non-specificity of transcription factor function in Drosophila melanogaster. Dev Genes Evol 2016; 227:25-39. [PMID: 27848019 DOI: 10.1007/s00427-016-0566-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 11/03/2016] [Indexed: 10/20/2022]
Abstract
A major problem in developmental genetics is how HOX transcription factors, like Proboscipedia (PB) and Ultrabithorax (UBX), regulate distinct programs of gene expression to result in a proboscis versus a haltere, respectively, when the DNA-binding homeodomain (HD) of HOX transcription factors recognizes similar DNA-binding sequences. Indeed, the lack of DNA-binding specificity is a problem for all transcription factors (TFs), as the DNA-binding domains generally recognize small targets of five to six bases in length. Although not the initial intent of the study, I found extensive non-specificity of TF function. Multiple TFs including HOX and HD-containing and non-HD-containing TFs induced both wingless and eyeless phenotypes. The TFs Labial (LAB), Deformed (DFD), Fushi tarazu (FTZ), and Squeeze (SQZ) induced ectopic larval thoracic (T) 1 beard formation in T2 and T3. The TF Doublesex male (DSXM) rescued the reduced maxillary palp pb phenotype. These examples of non-specificity of TF function across classes of TFs, combined with previous observations, compromise the implicit, initial assumption often made that an intrinsic mechanism of TF specificity is important for function. Interestingly, the functional complementation of the pb phenotype may suggest a larger role for regulation of expression of TFs in restriction of function as opposed to an intrinsic specificity of TF function. These observations have major ramifications for analysis of functional conservation in evolution and development.
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7
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Field A, Xiang J, Anderson WR, Graham P, Pick L. Activation of Ftz-F1-Responsive Genes through Ftz/Ftz-F1 Dependent Enhancers. PLoS One 2016; 11:e0163128. [PMID: 27723822 PMCID: PMC5056698 DOI: 10.1371/journal.pone.0163128] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/03/2016] [Indexed: 12/11/2022] Open
Abstract
The orphan nuclear receptor Ftz-F1 is expressed in all somatic nuclei in Drosophila embryos, but mutations result in a pair-rule phenotype. This was explained by the interaction of Ftz-F1 with the homeodomain protein Ftz that is expressed in stripes in the primordia of segments missing in either ftz-f1 or ftz mutants. Ftz-F1 and Ftz were shown to physically interact and coordinately activate the expression of ftz itself and engrailed by synergistic binding to composite Ftz-F1/Ftz binding sites. However, attempts to identify additional target genes on the basis of Ftz-F1/ Ftz binding alone has met with only limited success. To discern rules for Ftz-F1 target site selection in vivo and to identify additional target genes, a microarray analysis was performed comparing wildtype and ftz-f1 mutant embryos. Ftz-F1-responsive genes most highly regulated included engrailed and nine additional genes expressed in patterns dependent on both ftz and ftz-f1. Candidate enhancers for these genes were identified by combining BDTNP Ftz ChIP-chip data with a computational search for Ftz-F1 binding sites. Of eight enhancer reporter genes tested in transgenic embryos, six generated expression patterns similar to the corresponding endogenous gene and expression was lost in ftz mutants. These studies identified a new set of Ftz-F1 targets, all of which are co-regulated by Ftz. Comparative analysis of enhancers containing Ftz/Ftz-F1 binding sites that were or were not bona fide targets in vivo suggested that GAF negatively regulates enhancers that contain Ftz/Ftz-F1 binding sites but are not actually utilized. These targets include other regulatory factors as well as genes involved directly in morphogenesis, providing insight into how pair-rule genes establish the body pattern.
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Affiliation(s)
- Amanda Field
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, Maryland, 20742, United States of America
| | - Jie Xiang
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, Maryland, 20742, United States of America
| | - W. Ray Anderson
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, Maryland, 20742, United States of America
| | - Patricia Graham
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, Maryland, 20742, United States of America
| | - Leslie Pick
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, Maryland, 20742, United States of America
- * E-mail:
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8
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Short S, Peterkin T, Guille M, Patient R, Sharpe C. Short linear motif acquisition, exon formation and alternative splicing determine a pathway to diversity for NCoR-family co-repressors. Open Biol 2016; 5:rsob.150063. [PMID: 26289800 PMCID: PMC4554918 DOI: 10.1098/rsob.150063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Vertebrate NCoR-family co-repressors play central roles in the timing of embryo and stem cell differentiation by repressing the activity of a range of transcription factors. They interact with nuclear receptors using short linear motifs (SLiMs) termed co-repressor for nuclear receptor (CoRNR) boxes. Here, we identify the pathway leading to increasing co-repressor diversity across the deuterostomes. The final complement of CoRNR boxes arose in an ancestral cephalochordate, and was encoded in one large exon; the urochordates and vertebrates then split this region between 10 and 12 exons. In Xenopus, alternative splicing is prevalent in NCoR2, but absent in NCoR1. We show for one NCoR1 exon that alternative splicing can be recovered by a single point mutation, suggesting NCoR1 lost the capacity for alternative splicing. Analyses in Xenopus and zebrafish identify that cellular context, rather than gene sequence, predominantly determines species differences in alternative splicing. We identify a pathway to diversity for the NCoR family beginning with the addition of a SLiM, followed by gene duplication, the generation of alternatively spliced isoforms and their differential deployment.
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Affiliation(s)
- Stephen Short
- Institute of Marine Sciences, School of Biological Science, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Tessa Peterkin
- The Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Matthew Guille
- Institute of Biomolecular and Biomedical Science, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK European Xenopus Resource Centre, University of Portsmouth, St Michael's Building, Portsmouth PO1 2DT, UK
| | - Roger Patient
- The Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Colin Sharpe
- Institute of Biomolecular and Biomedical Science, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK European Xenopus Resource Centre, University of Portsmouth, St Michael's Building, Portsmouth PO1 2DT, UK
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9
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Bartlett M, Thompson B, Brabazon H, Del Gizzi R, Zhang T, Whipple C. Evolutionary Dynamics of Floral Homeotic Transcription Factor Protein-Protein Interactions. Mol Biol Evol 2016; 33:1486-501. [PMID: 26908583 PMCID: PMC4868119 DOI: 10.1093/molbev/msw031] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Protein–protein interactions (PPIs) have widely acknowledged roles in the regulation of development, but few studies have addressed the timing and mechanism of shifting PPIs over evolutionary history. The B-class MADS-box transcription factors, PISTILLATA (PI) and APETALA3 (AP3) are key regulators of floral development. PI-like (PIL) and AP3-like (AP3L) proteins from a number of plants, including Arabidopsis thaliana (Arabidopsis) and the grass Zea mays (maize), bind DNA as obligate heterodimers. However, a PIL protein from the grass relative Joinvillea can bind DNA as a homodimer. To ascertain whether Joinvillea PIL homodimerization is an anomaly or indicative of broader trends, we characterized PIL dimerization across the Poales and uncovered unexpected evolutionary lability. Both obligate B-class heterodimerization and PIL homodimerization have evolved multiple times in the order, by distinct molecular mechanisms. For example, obligate B-class heterodimerization in maize evolved very recently from PIL homodimerization. A single amino acid change, fixed during domestication, is sufficient to toggle one maize PIL protein between homodimerization and obligate heterodimerization. We detected a signature of positive selection acting on residues preferentially clustered in predicted sites of contact between MADS-box monomers and dimers, and in motifs that mediate MADS PPI specificity in Arabidopsis. Changing one positively selected residue can alter PIL dimerization activity. Furthermore, ectopic expression of a Joinvillea PIL homodimer in Arabidopsis can homeotically transform sepals into petals. Our results provide a window into the evolutionary remodeling of PPIs, and show that novel interactions have the potential to alter plant form in a context-dependent manner.
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Affiliation(s)
- Madelaine Bartlett
- Department of Biology, University of Massachusetts Amherst Department of Biology, Brigham Young University
| | | | | | | | - Thompson Zhang
- Department of Biology, University of Massachusetts Amherst
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10
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Pick L. Hox genes, evo-devo, and the case of the ftz gene. Chromosoma 2015; 125:535-51. [PMID: 26596987 DOI: 10.1007/s00412-015-0553-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/11/2015] [Accepted: 10/15/2015] [Indexed: 12/29/2022]
Abstract
The discovery of the broad conservation of embryonic regulatory genes across animal phyla, launched by the cloning of homeotic genes in the 1980s, was a founding event in the field of evolutionary developmental biology (evo-devo). While it had long been known that fundamental cellular processes, commonly referred to as housekeeping functions, are shared by animals and plants across the planet-processes such as the storage of information in genomic DNA, transcription, translation and the machinery for these processes, universal codon usage, and metabolic enzymes-Hox genes were different: mutations in these genes caused "bizarre" homeotic transformations of insect body parts that were certainly interesting but were expected to be idiosyncratic. The isolation of the genes responsible for these bizarre phenotypes turned out to be highly conserved Hox genes that play roles in embryonic patterning throughout Metazoa. How Hox genes have changed to promote the development of diverse body plans remains a central issue of the field of evo-devo today. For this Memorial article series, I review events around the discovery of the broad evolutionary conservation of Hox genes and the impact of this discovery on the field of developmental biology. I highlight studies carried out in Walter Gehring's lab and by former lab members that have continued to push the field forward, raising new questions and forging new approaches to understand the evolution of developmental mechanisms.
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Affiliation(s)
- Leslie Pick
- Department of Entomology and Program in Molecular and Cell Biology, University of Maryland, College Park, MD, 20742, USA.
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11
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Newman SA. The Developmental Genetic Toolkit and the Molecular Homology—Analogy Paradox. ACTA ACUST UNITED AC 2015. [DOI: 10.1162/biot.2006.1.1.12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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12
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Cheatle Jarvela AM, Hinman VF. Evolution of transcription factor function as a mechanism for changing metazoan developmental gene regulatory networks. EvoDevo 2015; 6:3. [PMID: 25685316 PMCID: PMC4327956 DOI: 10.1186/2041-9139-6-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 12/18/2014] [Indexed: 11/10/2022] Open
Abstract
The form that an animal takes during development is directed by gene regulatory networks (GRNs). Developmental GRNs interpret maternally deposited molecules and externally supplied signals to direct cell-fate decisions, which ultimately leads to the arrangements of organs and tissues in the organism. Genetically encoded modifications to these networks have generated the wide range of metazoan diversity that exists today. Most studies of GRN evolution focus on changes to cis-regulatory DNA, and it was historically theorized that changes to the transcription factors that bind to these cis-regulatory modules (CRMs) contribute to this process only rarely. A growing body of evidence suggests that changes to the coding regions of transcription factors play a much larger role in the evolution of developmental gene regulatory networks than originally imagined. Just as cis-regulatory changes make use of modular binding site composition and tissue-specific modules to avoid pleiotropy, transcription factor coding regions also predominantly evolve in ways that limit the context of functional effects. Here, we review the recent works that have led to this unexpected change in the field of Evolution and Development (Evo-Devo) and consider the implications these studies have had on our understanding of the evolution of developmental processes.
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Affiliation(s)
- Alys M Cheatle Jarvela
- Department of Biological Sciences, Carnegie Mellon University, 4400 5th Ave, Pittsburgh, PA 15213 USA
| | - Veronica F Hinman
- Department of Biological Sciences, Carnegie Mellon University, 4400 5th Ave, Pittsburgh, PA 15213 USA
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13
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Sivanantharajah L, Percival-Smith A. Differential pleiotropy and HOX functional organization. Dev Biol 2014; 398:1-10. [PMID: 25448696 DOI: 10.1016/j.ydbio.2014.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 10/31/2014] [Accepted: 11/01/2014] [Indexed: 12/14/2022]
Abstract
Key studies led to the idea that transcription factors are composed of defined modular protein motifs or domains, each with separable, unique function. During evolution, the recombination of these modular domains could give rise to transcription factors with new properties, as has been shown using recombinant molecules. This archetypic, modular view of transcription factor organization is based on the analyses of a few transcription factors such as GAL4, which may represent extreme exemplars rather than an archetype or the norm. Recent work with a set of Homeotic selector (HOX) proteins has revealed differential pleiotropy: the observation that highly-conserved HOX protein motifs and domains make small, additive, tissue specific contributions to HOX activity. Many of these differentially pleiotropic HOX motifs may represent plastic sequence elements called short linear motifs (SLiMs). The coupling of differential pleiotropy with SLiMs, suggests that protein sequence changes in HOX transcription factors may have had a greater impact on morphological diversity during evolution than previously believed. Furthermore, differential pleiotropy may be the genetic consequence of an ensemble nature of HOX transcription factor allostery, where HOX proteins exist as an ensemble of states with the capacity to integrate an extensive array of developmental information. Given a new structural model for HOX functional domain organization, the properties of the archetypic TF may require reassessment.
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Affiliation(s)
- Lovesha Sivanantharajah
- Department of Biology, The University of Western Ontario, BGS231, London, Ontario, Canada N6A 5B7.
| | - Anthony Percival-Smith
- Department of Biology, The University of Western Ontario, BGS231, London, Ontario, Canada N6A 5B7
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14
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Hsiao HC, Gonzalez KL, Catanese DJ, Jordy KE, Matthews KS, Bondos SE. The intrinsically disordered regions of the Drosophila melanogaster Hox protein ultrabithorax select interacting proteins based on partner topology. PLoS One 2014; 9:e108217. [PMID: 25286318 PMCID: PMC4186791 DOI: 10.1371/journal.pone.0108217] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 08/27/2014] [Indexed: 02/05/2023] Open
Abstract
Interactions between structured proteins require a complementary topology and surface chemistry to form sufficient contacts for stable binding. However, approximately one third of protein interactions are estimated to involve intrinsically disordered regions of proteins. The dynamic nature of disordered regions before and, in some cases, after binding calls into question the role of partner topology in forming protein interactions. To understand how intrinsically disordered proteins identify the correct interacting partner proteins, we evaluated interactions formed by the Drosophila melanogaster Hox transcription factor Ultrabithorax (Ubx), which contains both structured and disordered regions. Ubx binding proteins are enriched in specific folds: 23 of its 39 partners include one of 7 folds, out of the 1195 folds recognized by SCOP. For the proteins harboring the two most populated folds, DNA-RNA binding 3-helical bundles and α-α superhelices, the regions of the partner proteins that exhibit these preferred folds are sufficient for Ubx binding. Three disorder-containing regions in Ubx are required to bind these partners. These regions are either alternatively spliced or multiply phosphorylated, providing a mechanism for cellular processes to regulate Ubx-partner interactions. Indeed, partner topology correlates with the ability of individual partner proteins to bind Ubx spliceoforms. Partners bind different disordered regions within Ubx to varying extents, creating the potential for competition between partners and cooperative binding by partners. The ability of partners to bind regions of Ubx that activate transcription and regulate DNA binding provides a mechanism for partners to modulate transcription regulation by Ubx, and suggests that one role of disorder in Ubx is to coordinate multiple molecular functions in response to tissue-specific cues.
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Affiliation(s)
- Hao-Ching Hsiao
- Reynolds Medical Building, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas, United States of America
| | - Kim L. Gonzalez
- Reynolds Medical Building, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas, United States of America
| | - Daniel J. Catanese
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Kristopher E. Jordy
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Kathleen S. Matthews
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Sarah E. Bondos
- Reynolds Medical Building, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas, United States of America
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
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15
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Cheatle Jarvela AM, Brubaker L, Vedenko A, Gupta A, Armitage BA, Bulyk ML, Hinman VF. Modular evolution of DNA-binding preference of a Tbrain transcription factor provides a mechanism for modifying gene regulatory networks. Mol Biol Evol 2014; 31:2672-88. [PMID: 25016582 PMCID: PMC4166925 DOI: 10.1093/molbev/msu213] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Gene regulatory networks (GRNs) describe the progression of transcriptional states that take a single-celled zygote to a multicellular organism. It is well documented that GRNs can evolve extensively through mutations to cis-regulatory modules (CRMs). Transcription factor proteins that bind these CRMs may also evolve to produce novelty. Coding changes are considered to be rarer, however, because transcription factors are multifunctional and hence are more constrained to evolve in ways that will not produce widespread detrimental effects. Recent technological advances have unearthed a surprising variation in DNA-binding abilities, such that individual transcription factors may recognize both a preferred primary motif and an additional secondary motif. This provides a source of modularity in function. Here, we demonstrate that orthologous transcription factors can also evolve a changed preference for a secondary binding motif, thereby offering an unexplored mechanism for GRN evolution. Using protein-binding microarray, surface plasmon resonance, and in vivo reporter assays, we demonstrate an important difference in DNA-binding preference between Tbrain protein orthologs in two species of echinoderms, the sea star, Patiria miniata, and the sea urchin, Strongylocentrotus purpuratus. Although both orthologs recognize the same primary motif, only the sea star Tbr also has a secondary binding motif. Our in vivo assays demonstrate that this difference may allow for greater evolutionary change in timing of regulatory control. This uncovers a layer of transcription factor binding divergence that could exist for many pairs of orthologs. We hypothesize that this divergence provides modularity that allows orthologous transcription factors to evolve novel roles in GRNs through modification of binding to secondary sites.
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Affiliation(s)
| | - Lisa Brubaker
- Department of Biological Sciences, Carnegie Mellon University
| | - Anastasia Vedenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Anisha Gupta
- Department of Chemistry, Carnegie Mellon University
| | | | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
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16
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Percival-Smith A, Sivanantharajah L, Pelling JJH, Teft WA. Developmental competence and the induction of ectopic proboscises in Drosophila melanogaster. Dev Genes Evol 2013; 223:375-387. [DOI: 10.1007/s00427-013-0454-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/02/2013] [Indexed: 10/26/2022]
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Abstract
Despite enormous body plan variation, genes regulating embryonic development are highly conserved. Here, we probe the mechanisms that predispose ancient regulatory genes to reutilization and diversification rather than evolutionary loss. The Hox gene fushi tarazu (ftz) arose as a homeotic gene but functions as a pair-rule segmentation gene in Drosophila. ftz shows extensive variation in expression and protein coding regions but has managed to elude loss from arthropod genomes. We asked what properties prevent this loss by testing the importance of different protein motifs and partners in the developing CNS, where ftz expression is conserved. Drosophila Ftz proteins with mutated protein motifs were expressed under the control of a neurogenic-specific ftz cis-regulatory element (CRE) in a ftz mutant background rescued for segmentation defects. Ftz CNS function did not require the variable motifs that mediate differential cofactor interactions involved in homeosis or segmentation, which vary in arthropods. Rather, CNS function did require the shared DNA-binding homeodomain, which plays less of a role in Ftz segmentation activity. The Antennapedia homeodomain substituted for Ftz homeodomain function in the Drosophila CNS, but full-length Antennapedia did not rescue CNS defects. These results suggest that a core CNS function retains ftz in arthropod genomes. Acquisition of a neurogenic CRE led to ftz expression in unique CNS cells, differentiating its role from neighboring Hox genes, rendering it nonredundant. The inherent flexibility of modular CREs and protein domains allows for stepwise acquisition of new functions, explaining broad retention of regulatory genes during animal evolution.
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Affiliation(s)
- Alison Heffer
- Department of Entomology and Program in Molecular and Cell Biology, University of Maryland, College Park, MD 20742
| | - Jie Xiang
- Department of Entomology and Program in Molecular and Cell Biology, University of Maryland, College Park, MD 20742
| | - Leslie Pick
- Department of Entomology and Program in Molecular and Cell Biology, University of Maryland, College Park, MD 20742
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18
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Heffer A, Pick L. Conservation and variation in Hox genes: how insect models pioneered the evo-devo field. ANNUAL REVIEW OF ENTOMOLOGY 2013; 58:161-179. [PMID: 23317041 DOI: 10.1146/annurev-ento-120811-153601] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Evolutionary developmental biology, or evo-devo, broadly investigates how body plan diversity and morphological novelties have arisen and persisted in nature. The discovery of Hox genes in Drosophila, and their subsequent identification in most other metazoans, led biologists to try to understand how embryonic genes crucial for proper development have changed to promote the vast morphological variation seen in nature. Insects are ideal model systems for studying this diversity and the mechanisms underlying it because phylogenetic relationships are well established, powerful genetic tools have been developed, and there are many examples of evolutionary specializations that have arisen in nature in different insect lineages, such as the jumping leg of orthopterans and the helmet structures of treehoppers. Here, we briefly introduce the field of evo-devo and Hox genes, discuss functional tools available to study early developmental genes in insects, and provide examples in which changes in Hox genes have contributed to changes in body plan or morphology.
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Affiliation(s)
- Alison Heffer
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, Maryland 20742, USA
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19
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Wilson MJ, Dearden PK. Pair-rule gene orthologues have unexpected maternal roles in the honeybee (Apis mellifera). PLoS One 2012; 7:e46490. [PMID: 23029534 PMCID: PMC3460886 DOI: 10.1371/journal.pone.0046490] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 09/04/2012] [Indexed: 02/04/2023] Open
Abstract
Pair-rule genes are a class of segmentation genes first identified in Drosophila melanogaster. In Drosophila, these genes act to translate non-periodic information produced by the overlapping patterns of gap gene expression into patterns of gene expression in every other segment. While pair-rule genes are, for the most part, conserved in metazoans, their function in pair-rule patterning is not. Many of these genes do, however, regulate segmentation in arthropods and do so with dual-segment periodicity. Here we examine the expression and function of honeybee orthologues of Drosophila pair-rule genes. Knockdown of the expression of these genes leads to extensive patterning defects, implying that they act in early patterning, as well as segmentation in honeybee embryos. We show that these pair-rule gene orthologues indeed regulate the expression of honeybee maternal and gap genes implying roles in maternal patterning of the honeybee embryo.
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Affiliation(s)
- Megan J. Wilson
- Laboratory for Evolution and Development, National Research Centre for Growth and Development and Genetics Otago, Biochemistry Department, University of Otago, Dunedin, New Zealand-Aotearoa
| | - Peter K. Dearden
- Laboratory for Evolution and Development, National Research Centre for Growth and Development and Genetics Otago, Biochemistry Department, University of Otago, Dunedin, New Zealand-Aotearoa
- * E-mail:
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20
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Pick L, Heffer A. Hoxgene evolution: multiple mechanisms contributing to evolutionary novelties. Ann N Y Acad Sci 2012; 1256:15-32. [DOI: 10.1111/j.1749-6632.2011.06385.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Andrioli LP. Toward new Drosophila paradigms. Genesis 2012; 50:585-98. [DOI: 10.1002/dvg.22019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 02/07/2012] [Accepted: 02/08/2012] [Indexed: 11/07/2022]
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22
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Heffer A, Löhr U, Pick L. ftz Evolution: Findings, hypotheses and speculations (response to DOI 10.1002/bies.201100019). Bioessays 2011; 33:910-8. [DOI: 10.1002/bies.201100112] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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23
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Merabet S, Litim-Mecheri I, Karlsson D, Dixit R, Saadaoui M, Monier B, Brun C, Thor S, Vijayraghavan K, Perrin L, Pradel J, Graba Y. Insights into Hox protein function from a large scale combinatorial analysis of protein domains. PLoS Genet 2011; 7:e1002302. [PMID: 22046139 PMCID: PMC3203194 DOI: 10.1371/journal.pgen.1002302] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 07/24/2011] [Indexed: 11/19/2022] Open
Abstract
Protein function is encoded within protein sequence and protein domains. However, how protein domains cooperate within a protein to modulate overall activity and how this impacts functional diversification at the molecular and organism levels remains largely unaddressed. Focusing on three domains of the central class Drosophila Hox transcription factor AbdominalA (AbdA), we used combinatorial domain mutations and most known AbdA developmental functions as biological readouts to investigate how protein domains collectively shape protein activity. The results uncover redundancy, interactivity, and multifunctionality of protein domains as salient features underlying overall AbdA protein activity, providing means to apprehend functional diversity and accounting for the robustness of Hox-controlled developmental programs. Importantly, the results highlight context-dependency in protein domain usage and interaction, allowing major modifications in domains to be tolerated without general functional loss. The non-pleoitropic effect of domain mutation suggests that protein modification may contribute more broadly to molecular changes underlying morphological diversification during evolution, so far thought to rely largely on modification in gene cis-regulatory sequences.
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Affiliation(s)
- Samir Merabet
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR6216 CNRS, Parc Scientifique de Luminy, Case 907, Marseille, France
- Université de la Méditerranée, Parc Scientifique de Luminy, Marseille, France
| | - Isma Litim-Mecheri
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR6216 CNRS, Parc Scientifique de Luminy, Case 907, Marseille, France
- Université de la Méditerranée, Parc Scientifique de Luminy, Marseille, France
| | - Daniel Karlsson
- Department of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden
| | - Richa Dixit
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Mehdi Saadaoui
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR6216 CNRS, Parc Scientifique de Luminy, Case 907, Marseille, France
- Université de la Méditerranée, Parc Scientifique de Luminy, Marseille, France
| | - Bruno Monier
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR6216 CNRS, Parc Scientifique de Luminy, Case 907, Marseille, France
- Université de la Méditerranée, Parc Scientifique de Luminy, Marseille, France
| | - Christine Brun
- Université de la Méditerranée, Parc Scientifique de Luminy, Marseille, France
- TAGC, U928 Inserm, Parc Scientifique de Luminy, Case 928, Marseille, France
- CNRS, Marseille, France
| | - Stefan Thor
- Department of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden
| | - K. Vijayraghavan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Laurent Perrin
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR6216 CNRS, Parc Scientifique de Luminy, Case 907, Marseille, France
- Université de la Méditerranée, Parc Scientifique de Luminy, Marseille, France
| | - Jacques Pradel
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR6216 CNRS, Parc Scientifique de Luminy, Case 907, Marseille, France
- Université de la Méditerranée, Parc Scientifique de Luminy, Marseille, France
| | - Yacine Graba
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR6216 CNRS, Parc Scientifique de Luminy, Case 907, Marseille, France
- Université de la Méditerranée, Parc Scientifique de Luminy, Marseille, France
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Functional synthetic Antennapedia genes and the dual roles of YPWM motif and linker size in transcriptional activation and repression. Proc Natl Acad Sci U S A 2011; 108:11959-64. [PMID: 21712439 DOI: 10.1073/pnas.1108686108] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Segmental identity along the anteroposterior axis of bilateral animals is specified by Hox genes. These genes encode transcription factors, harboring the conserved homeodomain and, generally, a YPWM motif, which binds Hox cofactors and increases Hox transcriptional specificity in vivo. Here we derive synthetic Drosophila Antennapedia genes, consisting only of the YPWM motif and homeodomain, and investigate their functional role throughout development. Synthetic peptides and full-length Antennapedia proteins cause head-to-thorax transformations in the embryo, as well as antenna-to-tarsus and eye-to-wing transformations in the adult, thus converting the entire head to a mesothorax. This conversion is achieved by repression of genes required for head and antennal development and ectopic activation of genes promoting thoracic and tarsal fates, respectively. Synthetic Antennapedia peptides bind DNA specifically and interact with Extradenticle and Bric-à-brac interacting protein 2 cofactors in vitro and ex vivo. Substitution of the YPWM motif by alanines abolishes Antennapedia homeotic function, whereas substitution of YPWM by the WRPW repressor motif, which binds the transcriptional corepressor Groucho, allows all proteins to act as repressors only. Finally, naturally occurring variations in the size of the linker between the homeodomain and YPWM motif enhance Antennapedia repressive or activating efficiency, emphasizing the importance of linker size, rather than sequence, for specificity. Our results clearly show that synthetic Antennapedia genes are functional in vivo and therefore provide powerful tools for synthetic biology. Moreover, the YPWM motif is necessary--whereas the entire N terminus of the protein is dispensable--for Antennapedia homeotic function, indicating its dual role in transcriptional activation and repression by recruiting either coactivators or corepressors.
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25
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Merabet S, Hudry B. On the border of the homeotic function: Re-evaluating the controversial role of cofactor-recruiting motifs. Bioessays 2011; 33:499-507. [DOI: 10.1002/bies.201100019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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26
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Heffer A, Pick L. Rapid isolation of gene homologs across taxa: Efficient identification and isolation of gene orthologs from non-model organism genomes, a technical report. EvoDevo 2011; 2:7. [PMID: 21362165 PMCID: PMC3055837 DOI: 10.1186/2041-9139-2-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 03/01/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tremendous progress has been made in the field of evo-devo through comparisons of related genes from diverse taxa. While the vast number of species in nature precludes a complete analysis of the molecular evolution of even one single gene family, this would not be necessary to understand fundamental mechanisms underlying gene evolution if experiments could be designed to systematically sample representative points along the path of established phylogenies to trace changes in regulatory and coding gene sequence. This isolation of homologous genes from phylogenetically diverse, representative species can be challenging, especially if the gene is under weak selective pressure and evolving rapidly. RESULTS Here we present an approach - Rapid Isolation of Gene Homologs across Taxa (RIGHT) - to efficiently isolate specific members of gene families. RIGHT is based upon modification and a combination of degenerate polymerase chain reaction (PCR) and gene-specific amplified fragment length polymorphism (AFLP). It allows targeted isolation of specific gene family members from any organism, only requiring genomic DNA. We describe this approach and how we used it to isolate members of several different gene families from diverse arthropods spanning millions of years of evolution. CONCLUSIONS RIGHT facilitates systematic isolation of one gene from large gene families. It allows for efficient gene isolation without whole genome sequencing, RNA extraction, or culturing of non-model organisms. RIGHT will be a generally useful method for isolation of orthologs from both distant and closely related species, increasing sample size and facilitating the tracking of molecular evolution of gene families and regulatory networks across the tree of life.
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Affiliation(s)
- Alison Heffer
- Program in Molecular & Cell Biology and Department of Entomology, University of Maryland, 4112 Plant Sciences Building, College Park, MD 20742, USA.
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27
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Selection of distinct Hox-Extradenticle interaction modes fine-tunes Hox protein activity. Proc Natl Acad Sci U S A 2011; 108:2276-81. [PMID: 21262810 DOI: 10.1073/pnas.1006964108] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hox genes encode transcription factors widely used for diversifying animal body plans in development and evolution. To achieve functional specificity, Hox proteins associate with PBC class proteins, Pre-B cell leukemia homeobox (Pbx) in vertebrates, and Extradenticle (Exd) in Drosophila, and were thought to use a unique hexapeptide-dependent generic mode of interaction. Recent findings, however, revealed the existence of an alternative, UbdA-dependent paralog-specific interaction mode providing diversity in Hox-PBC interactions. In this study, we investigated the basis for the selection of one of these two Hox-PBC interaction modes. Using naturally occurring variations and mutations in the Drosophila Ultrabithorax protein, we found that the linker region, a short domain separating the hexapeptide from the homeodomain, promotes an interaction mediated by the UbdA domain in a context-dependent manner. While using a UbdA-dependent interaction for the repression of the limb-promoting gene Distalless, interaction with Exd during segment-identity specification still relies on the hexapeptide motif. We further show that distinctly assembled Hox-PBC complexes display subtle but distinct repressive activities. These findings identify Hox-PBC interaction as a template for subtle regulation of Hox protein activity that may have played a major role in the diversification of Hox protein function in development and evolution.
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28
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Surprising flexibility in a conserved Hox transcription factor over 550 million years of evolution. Proc Natl Acad Sci U S A 2010; 107:18040-5. [PMID: 20921393 DOI: 10.1073/pnas.1010746107] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Although metazoan body plans are remarkably diverse, the structure and function of many embryonic regulatory genes are conserved because large changes would be detrimental to development. However, the fushi tarazu (ftz) gene has changed dramatically during arthropod evolution from Hox-like to a pair-rule segmentation gene in Drosophila. Changes in both expression and protein sequence contributed to this new function: ftz expression switched from Hox-like to stripes and changes in Ftz cofactor interaction motifs led to loss of homeotic and gain of segmentation potential. Here, we reconstructed ftz changes in a rigorous phylogenetic context. We found that ftz did not simply switch from Hox-like to segmentation function; rather, ftz is remarkably labile, having undergone multiple changes in sequence and expression. The segmentation LXXLL motif was stably acquired in holometabolous insects after the appearance of striped expression in early insect lineages. The homeotic YPWM motif independently degenerated multiple times. These "degen-YPWMs" showed varying degrees of homeotic potential when expressed in Drosophila, suggesting variable loss of Hox function in different arthropods. Finally, the intensity of ftz Hox-like expression decreased to marginal levels in some crustaceans. We propose that decreased expression levels permitted ftz variants to arise and persist in populations without disadvantaging organismal development. This process, in turn, allowed evolutionary transitions in protein function, as weakly expressed "hopeful gene variants" were coopted into alternative developmental pathways. Our findings show that variation of a pleiotropic transcription factor is more extensive than previously imagined, suggesting that evolutionary plasticity may be widespread among regulatory genes.
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29
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Hsia CC, Paré AC, Hannon M, Ronshaugen M, McGinnis W. Silencing of an abdominal Hox gene during early development is correlated with limb development in a crustacean trunk. Evol Dev 2010; 12:131-43. [PMID: 20433454 DOI: 10.1111/j.1525-142x.2010.00399.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We tested whether Artemia abd-A could repress limbs in Drosophila embryos, and found that although abd-A transcripts were produced, ABD-A protein was not. Similarly, developing Artemia epidermal cells showed expression of abd-A transcripts without accumulation of ABD-A protein. This finding in Artemia reveals a new variation in Hox gene function that is associated with morphological evolution. In this case, a HOX protein expression pattern is completely absent during early development, although the HOX protein is expressed at later stages in the central nervous system in a "homeotic-like" pattern. The combination of an absence of ABD-A protein expression in the Artemia limb primordia and the weak repressive function of Artemia UBX protein on the limb-promoting gene Dll are likely to be two reasons why homonomous limbs develop throughout the entire Artemia trunk.
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Affiliation(s)
- Cheryl C Hsia
- Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
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30
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Walrad PB, Hang S, Joseph GS, Salas J, Gergen JP. Distinct contributions of conserved modules to Runt transcription factor activity. Mol Biol Cell 2010; 21:2315-26. [PMID: 20462957 PMCID: PMC2893994 DOI: 10.1091/mbc.e09-11-0953] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
An investigation of the in vivo roles of conserved regions of the Drosophila Runt protein outside of the DNA-binding Runt domain reveals distinct requirements in different regulatory activities. The conserved VWRPY-containing C-terminus required for repression of only a subset of targets is also found to participate in activation of other targets. Runx proteins play vital roles in regulating transcription in numerous developmental pathways throughout the animal kingdom. Two Runx protein hallmarks are the DNA-binding Runt domain and a C-terminal VWRPY motif that mediates interaction with TLE/Gro corepressor proteins. A phylogenetic analysis of Runt, the founding Runx family member, identifies four distinct regions C-terminal to the Runt domain that are conserved in Drosophila and other insects. We used a series of previously described ectopic expression assays to investigate the functions of these different conserved regions in regulating gene expression during embryogenesis and in controlling axonal projections in the developing eye. The results indicate each conserved region is required for a different subset of activities and identify distinct regions that participate in the transcriptional activation and repression of the segmentation gene sloppy-paired-1 (slp1). Interestingly, the C-terminal VWRPY-containing region is not required for repression but instead plays a role in slp1 activation. Genetic experiments indicating that Groucho (Gro) does not participate in slp1 regulation further suggest that Runt's conserved C-terminus interacts with other factors to promote transcriptional activation. These results provide a foundation for further studies on the molecular interactions that contribute to the context-dependent properties of Runx proteins as developmental regulators.
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Affiliation(s)
- Pegine B Walrad
- Department of Biochemistry and Cell Biology and the Center for Developmental Genetics, Graduate Programs in Molecular and Cellular Biology and Biochemistry and Structural Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
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31
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Prazak L, Fujioka M, Gergen JP. Non-additive interactions involving two distinct elements mediate sloppy-paired regulation by pair-rule transcription factors. Dev Biol 2010; 344:1048-59. [PMID: 20435028 DOI: 10.1016/j.ydbio.2010.04.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 04/08/2010] [Accepted: 04/23/2010] [Indexed: 11/18/2022]
Abstract
The relatively simple combinatorial rules responsible for establishing the initial metameric expression of sloppy-paired-1 (slp1) in the Drosophila blastoderm embryo make this system an attractive model for investigating the mechanism of regulation by pair-rule transcription factors. This investigation of slp1 cis-regulatory architecture identifies two distinct elements, a proximal early stripe element (PESE) and a distal early stripe element (DESE) located from -3.1kb to -2.5kb and from -8.1kb to -7.1kb upstream of the slp1 promoter, respectively, that mediate this early regulation. The proximal element expresses only even-numbered stripes and mediates repression by Even-skipped (Eve) as well as by the combination of Runt and Fushi-tarazu (Ftz). A 272 basepair sub-element of PESE retains an Eve-dependent repression, but is expressed throughout the even-numbered parasegments due to the loss of repression by Runt and Ftz. In contrast, the distal element expresses both odd and even-numbered stripes and also drives inappropriate expression in the anterior half of the odd-numbered parasegments due to an inability to respond to repression by Eve. Importantly, a composite reporter gene containing both early stripe elements recapitulates pair-rule gene-dependent regulation in a manner beyond what is expected from combining their individual patterns. These results indicate that interactions involving distinct cis-elements contribute to the proper integration of pair-rule regulatory information. A model fully accounting for these results proposes that metameric slp1 expression is achieved through the Runt-dependent regulation of interactions between these two pair-rule response elements and the slp1 promoter.
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Affiliation(s)
- Lisa Prazak
- Department of Biochemistry and Cell Biology and the Center for Developmental Genetics, Stony Brook University, Stony Brook, NY 11794-5215, USA
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32
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Merabet S, Sambrani N, Pradel J, Graba Y. Regulation of Hox activity: insights from protein motifs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 689:3-16. [PMID: 20795319 DOI: 10.1007/978-1-4419-6673-5_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Deciphering the molecular bases of animal body plan construction is a central question in developmental and evolutionary biology. Genome analyses of a number of metazoans indicate that widely conserved regulatory molecules underlie the amazing diversity of animal body plans, suggesting that these molecules are reiteratively used for multiple purposes. Hox proteins constitute a good example of such molecules and provide the framework to address the mechanisms underlying transcriptional specificity and diversity in development and evolution. Here we examine the current knowledge of the molecular bases of Hox-mediated transcriptional control, focusing on how this control is encoded within protein sequences and structures. The survey suggests that the homeodomain is part of an extended multifunctional unit coordinating DNA binding and activity regulation and highlights the need for further advances in our understanding of Hox protein activity.
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Affiliation(s)
- Samir Merabet
- Institute of Developmental Biology of Marseille Luminy, University of the Mediterranean, Marseille, France.
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33
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Hofmann CM, O'Quin KE, Marshall NJ, Cronin TW, Seehausen O, Carleton KL. The eyes have it: regulatory and structural changes both underlie cichlid visual pigment diversity. PLoS Biol 2009; 7:e1000266. [PMID: 20027211 PMCID: PMC2790343 DOI: 10.1371/journal.pbio.1000266] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Accepted: 11/12/2009] [Indexed: 11/18/2022] Open
Abstract
A major goal of evolutionary biology is to unravel the molecular genetic mechanisms that underlie functional diversification and adaptation. We investigated how changes in gene regulation and coding sequence contribute to sensory diversification in two replicate radiations of cichlid fishes. In the clear waters of Lake Malawi, differential opsin expression generates diverse visual systems, with sensitivities extending from the ultraviolet to the red regions of the spectrum. These sensitivities fall into three distinct clusters and are correlated with foraging habits. In the turbid waters of Lake Victoria, visual sensitivity is constrained to longer wavelengths, and opsin expression is correlated with ambient light. In addition to regulatory changes, we found that the opsins coding for the shortest- and longest-wavelength visual pigments have elevated numbers of potentially functional substitutions. Thus, we present a model of sensory evolution in which both molecular genetic mechanisms work in concert. Changes in gene expression generate large shifts in visual pigment sensitivity across the collective opsin spectral range, but changes in coding sequence appear to fine-tune visual pigment sensitivity at the short- and long-wavelength ends of this range, where differential opsin expression can no longer extend visual pigment sensitivity.
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Affiliation(s)
- Christopher M Hofmann
- Department of Biology, University of Maryland, College Park, Maryland, United States of America.
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Hou HY, Heffer A, Anderson WR, Liu J, Bowler T, Pick L. Stripy Ftz target genes are coordinately regulated by Ftz-F1. Dev Biol 2009; 335:442-53. [PMID: 19679121 DOI: 10.1016/j.ydbio.2009.08.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 07/26/2009] [Accepted: 08/03/2009] [Indexed: 01/12/2023]
Abstract
During development, cascades of regulatory genes act in a hierarchical fashion to subdivide the embryo into increasingly specified body regions. This has been best characterized in Drosophila, where genes encoding regulatory transcription factors form a network to direct the development of the basic segmented body plan. The pair-rule genes are pivotal in this process as they are responsible for the first subdivision of the embryo into repeated metameric units. The Drosophila pair-rule gene fushi tarazu (ftz) is a derived Hox gene expressed in and required for the development of alternate parasegments. Previous studies suggested that Ftz achieves its distinct regulatory specificity as a segmentation protein by interacting with a ubiquitously expressed cofactor, the nuclear receptor Ftz-F1. However, the downstream target genes regulated by Ftz and other pair-rule genes to direct segment formation are not known. In this study, we selected candidate Ftz targets by virtue of their early expression in Ftz-like stripes. This identified two new Ftz target genes, drumstick (drm) and no ocelli (noc), and confirmed that Ftz regulates a serotonin receptor (5-HT2). These are the earliest Ftz targets identified to date and all are coordinately regulated by Ftz-F1. Engrailed (En), the best-characterized Ftz/Ftz-F1 downstream target, is not an intermediate in regulation. The drm genomic region harbors two separate seven-stripe enhancers, identified by virtue of predicted Ftz-F1 binding sites, and these sites are necessary for stripe expression in vivo. We propose that pair-rule genes, exemplified by Ftz/Ftz-F1, promote segmentation by acting at different hierarchical levels, regulating first, other segmentation genes; second, other regulatory genes that in turn control specific cellular processes such as tissue differentiation; and, third, 'segmentation realizator genes' that are directly involved in morphogenesis.
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Affiliation(s)
- Hui Ying Hou
- Department of Entomology, University of Maryland, College Park, 20742, USA
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Merabet S, Hudry B, Saadaoui M, Graba Y. Classification of sequence signatures: a guide to Hox protein function. Bioessays 2009; 31:500-11. [PMID: 19334006 DOI: 10.1002/bies.200800229] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Hox proteins are part of the conserved superfamily of homeodomain-containing transcription factors and play fundamental roles in shaping animal body plans in development and evolution. However, molecular mechanisms underlying their diverse and specific biological functions remain largely enigmatic. Here, we have analyzed Hox sequences from the main evolutionary branches of the Bilateria group. We have found that four classes of Hox protein signatures exist, which together provide sufficient support to explain how different Hox proteins differ in their control and function. The homeodomain and its surrounding sequences accumulate nearly all signatures, constituting an extended module where most of the information distinguishing Hox proteins is concentrated. Only a small fraction of these signatures has been investigated at the functional level, but these show that approaches relying on Hox protein alterations still have a large potential for deciphering molecular mechanisms of Hox differential control.
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Affiliation(s)
- Samir Merabet
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR 6216, CNRS, Université de la Méditerranée, Parc Scientifique de Luminy, Case 907, Marseille Cedex 09, France.
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36
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Nardmann J, Reisewitz P, Werr W. Discrete shoot and root stem cell-promoting WUS/WOX5 functions are an evolutionary innovation of angiosperms. Mol Biol Evol 2009; 26:1745-55. [PMID: 19387013 DOI: 10.1093/molbev/msp084] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The morphologically diverse bodies of seed plants comprising gymnosperms and angiosperms, which separated some 350 Ma, grow by the activity of meristems containing stem cell niches. In the dicot model Arabidopsis thaliana, these are maintained by the stem cell-promoting functions of WUS and WUSCHEL-related homeobox 5 (WOX5) in the shoot and the root, respectively. Both genes are members of the WOX gene family, which has a monophyletic origin in green algae. The establishment of the WOX gene phylogeny from basal land plants through gymnosperms to basal and higher angiosperms reveals three major branches: a basal clade consisting of WOX13-related genes present in some green algae and throughout all land plant genomes, a second clade containing WOX8/9/11/12 homologues, and a modern clade restricted to seed plants. The analysis of the origin of the modern branch in two basal angiosperms (Amborella trichopoda and Nymphaea jamesoniana) and three gymnosperms (Pinus sylvestris, Ginkgo biloba, and Gnetum gnemon) shows that all members of the modern clade consistently found in monocots and dicots exist at the base of the angiosperm lineage, including WUS and WOX5 orthologues. In contrast, our analyses identify a single WUS/WOX5 homologue in all three gymnosperm genomes, consistent with a monophyletic origin in the last common ancestor of gymnosperms and angiosperms. Phylogenetic data, WUS- and WOX5-specific evolutionary signatures, as well as the expression pattern and stem cell-promoting function of the single gymnosperm WUS/WOX5 pro-orthologue in Arabidopsis indicate a gene duplication event followed by subfunctionalization at the base of angiosperms.
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Affiliation(s)
- Judith Nardmann
- Institut für Entwicklungsbiologie, Universität zu Köln, Köln, Germany
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Hittinger CT, Carroll SB. Evolution of an insect-specific GROUCHO-interaction motif in the ENGRAILED selector protein. Evol Dev 2008; 10:537-45. [PMID: 18803772 PMCID: PMC2597661 DOI: 10.1111/j.1525-142x.2008.00269.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Animal morphology evolves through alterations in the genetic regulatory networks that control development. Regulatory connections are commonly added, subtracted, or modified via mutations in cis-regulatory elements, but several cases are also known where transcription factors have gained or lost activity-modulating peptide motifs. In order to better assess the role of novel transcription factor peptide motifs in evolution, we searched for synapomorphic motifs in the homeotic selectors of Drosophila melanogaster and related insects. Here, we describe an evolutionarily novel GROUCHO (GRO)-interaction motif in the ENGRAILED (EN) selector protein. This "ehIFRPF" motif is not homologous to the previously characterized "engrailed homology 1" (eh1) GRO-interaction motif of EN. This second motif is an insect-specific "WRPW"-type motif that has been maintained by purifying selection in at least the dipteran/lepidopteran lineage. We demonstrate that this motif contributes to in vivo repression of the wingless (wg) target gene and to interaction with GRO in vitro. The acquisition and conservation of this auxiliary peptide motif shows how the number and activity of short peptide motifs can evolve in transcription factors while existing regulatory functions are maintained.
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Affiliation(s)
- Chris Todd Hittinger
- Laboratory of Genetics, Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI 53706-1534, USA
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38
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Copley RR. The animal in the genome: comparative genomics and evolution. Philos Trans R Soc Lond B Biol Sci 2008; 363:1453-61. [PMID: 18192189 PMCID: PMC2614226 DOI: 10.1098/rstb.2007.2235] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Comparisons between completely sequenced metazoan genomes have generally emphasized how similar their encoded protein content is, even when the comparison is between phyla. Given the manifest differences between phyla and, in particular, intuitive notions that some animals are more complex than others, this creates something of a paradox. Simplistic explanations have included arguments such as increased numbers of genes; greater numbers of protein products produced through alternative splicing; increased numbers of regulatory non-coding RNAs and increased complexity of the cis-regulatory code. An obvious value of complete genome sequences lies in their ability to provide us with inventories of such components. I examine progress being made in linking genome content to the pattern of animal evolution, and argue that the gap between genomic and phenotypic complexity can only be understood through the totality of interacting components.
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Abstract
The use of phylogenetic analysis to predict positive selection specific to human genes is complicated by the very close evolutionary relationship with our nearest extant primate relatives, chimpanzees. To assess the power and limitations inherent in use of maximum-likelihood (ML) analysis of codon substitution patterns in such recently diverged species, a series of simulations was performed to assess the impact of several parameters of the evolutionary model on prediction of human-specific positive selection, including branch length and d(N)/d(S) ratio. Parameters were varied across a range of values observed in alignments of 175 transcription factor (TF) genes that were sequenced in 12 primate species. The ML method largely lacks the power to detect positive selection that has occurred since the most recent common ancestor between humans and chimpanzees. An alternative null model was developed on the basis of gene-specific evaluation of the empirical distribution of ML results, using simulated neutrally evolving sequences. This empirical test provides greater sensitivity to detect lineage-specific positive selection in the context of recent evolutionary divergence.
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Carroll SB. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 2008; 134:25-36. [PMID: 18614008 DOI: 10.1016/j.cell.2008.06.030] [Citation(s) in RCA: 1253] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Biologists have long sought to understand which genes and what kinds of changes in their sequences are responsible for the evolution of morphological diversity. Here, I outline eight principles derived from molecular and evolutionary developmental biology and review recent studies of species divergence that have led to a genetic theory of morphological evolution, which states that (1) form evolves largely by altering the expression of functionally conserved proteins, and (2) such changes largely occur through mutations in the cis-regulatory sequences of pleiotropic developmental regulatory loci and of the target genes within the vast networks they control.
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Affiliation(s)
- Sean B Carroll
- Howard Hughes Medical Institute, Laboratory of Molecular Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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41
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The gene regulatory logic of transcription factor evolution. Trends Ecol Evol 2008; 23:377-85. [DOI: 10.1016/j.tree.2008.03.006] [Citation(s) in RCA: 151] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 03/10/2008] [Accepted: 03/28/2008] [Indexed: 11/22/2022]
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Taghli-Lamallem O, Hsia C, Ronshaugen M, McGinnis W. Context-dependent regulation of Hox protein functions by CK2 phosphorylation sites. Dev Genes Evol 2008; 218:321-32. [PMID: 18504607 PMCID: PMC2443945 DOI: 10.1007/s00427-008-0224-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Accepted: 04/21/2008] [Indexed: 10/22/2022]
Abstract
Variations in Hox protein sequences and functions have been proposed to contribute to evolutionary changes in appendage shape and number in crustaceans and insects. One model is that insect Hox proteins of the Ultrabithorax (UBX) ortholog class evolved increased abilities to repress Distal-less (Dll) transcription and appendage development in part through the loss of serine and threonine residues in casein kinase 2 (CK2) phosphorylation sites. To explore this possibility, we constructed and tested the appendage repression function of chimeric proteins with insertions of different CK2 consensus sites or phosphomimetics of CK2 sites in C-terminal regions of Drosophila melanogaster UBX. Our results indicate that CK2 sites C-terminal to the homeodomain can inhibit the appendage repression functions of UBX proteins, but only in the context of specific amino acid sequences. Our results, combined with previous findings on evolutionary changes in Hox protein, suggest how intra-protein regulatory changes can diversify Hox protein function, and thus animal morphology.
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Affiliation(s)
- Ouarda Taghli-Lamallem
- Neuroscience & Aging Research Center, The Burnham Institute for Medical Research, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Cheryl Hsia
- Section in Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA, e-mail:
| | - Matthew Ronshaugen
- The Healing Foundation Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - William McGinnis
- Section in Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA, e-mail:
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Prince F, Katsuyama T, Oshima Y, Plaza S, Resendez-Perez D, Berry M, Kurata S, Gehring WJ. The YPWM motif links Antennapedia to the basal transcriptional machinery. Development 2008; 135:1669-79. [DOI: 10.1242/dev.018028] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
HOX genes specify segment identity along the anteroposterior axis of the embryo. They code for transcription factors harbouring the highly conserved homeodomain and a YPWM motif, situated amino terminally to it. Despite their highly diverse functions in vivo, HOX proteins display similar biochemical properties in vitro, raising the question of how this specificity is achieved. In our study, we investigated the importance of the Antennapedia(Antp) YPWM motif for homeotic transformations in adult Drosophila. By ectopic overexpression, the head structures of the fly can be transformed into structures of the second thoracic segment, such as antenna into second leg, head capsule into thorax (notum) and eye into wing. We found that the YPWM motif is absolutely required for the eye-to-wing transformation. Using the yeast two-hybrid system, we were able to identify a novel ANTP-interacting protein, Bric-à-brac interacting protein 2(BIP2), that specifically interacts with the YPWM motif of ANTP in vitro, as well as in vivo, transforming eye to wing tissue. BIP2 is a TATA-binding protein associated factor (also known as dTAFII3) that links ANTP to the basal transcriptional machinery.
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Affiliation(s)
- Frédéric Prince
- Biozentrum, University of Basel, Klingelberstrasse 70, CH-4056 Basel,Switzerland
| | | | - Yoshiteru Oshima
- ETH Zurich, Department of Biosystems, CH-4058 Basel, Switzerland
| | - Serge Plaza
- CNS-Centre de Biologie du Developpement, 118 route de NARBONNE, Bat 4R3, 31062 Toulouse, France
| | | | - Meera Berry
- Micromet AG, Am Klopferspitz 19, 82152 Martinsried/Munich, Germany
| | - Shoichiro Kurata
- ETH Zurich, Department of Biosystems, CH-4058 Basel, Switzerland
| | - Walter J. Gehring
- Biozentrum, University of Basel, Klingelberstrasse 70, CH-4056 Basel,Switzerland
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Divergent and conserved roles of extradenticle in body segmentation and appendage formation, respectively, in the cricket Gryllus bimaculatus. Dev Biol 2008; 313:67-79. [DOI: 10.1016/j.ydbio.2007.09.060] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 09/19/2007] [Accepted: 09/26/2007] [Indexed: 11/19/2022]
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45
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Abstract
An important tenet of evolutionary developmental biology ("evo devo") is that adaptive mutations affecting morphology are more likely to occur in the cis-regulatory regions than in the protein-coding regions of genes. This argument rests on two claims: (1) the modular nature of cis-regulatory elements largely frees them from deleterious pleiotropic effects, and (2) a growing body of empirical evidence appears to support the predominant role of gene regulatory change in adaptation, especially morphological adaptation. Here we discuss and critique these assertions. We first show that there is no theoretical or empirical basis for the evo devo contention that adaptations involving morphology evolve by genetic mechanisms different from those involving physiology and other traits. In addition, some forms of protein evolution can avoid the negative consequences of pleiotropy, most notably via gene duplication. In light of evo devo claims, we then examine the substantial data on the genetic basis of adaptation from both genome-wide surveys and single-locus studies. Genomic studies lend little support to the cis-regulatory theory: many of these have detected adaptation in protein-coding regions, including transcription factors, whereas few have examined regulatory regions. Turning to single-locus studies, we note that the most widely cited examples of adaptive cis-regulatory mutations focus on trait loss rather than gain, and none have yet pinpointed an evolved regulatory site. In contrast, there are many studies that have both identified structural mutations and functionally verified their contribution to adaptation and speciation. Neither the theoretical arguments nor the data from nature, then, support the claim for a predominance of cis-regulatory mutations in evolution. Although this claim may be true, it is at best premature. Adaptation and speciation probably proceed through a combination of cis-regulatory and structural mutations, with a substantial contribution of the latter.
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Affiliation(s)
- Hopi E Hoekstra
- Department of Organismic and Evolutionary Biology and the Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts 02138, USA.
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46
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Papillon D, Telford MJ. Evolution of Hox3 and ftz in arthropods: insights from the crustacean Daphnia pulex. Dev Genes Evol 2007; 217:315-22. [PMID: 17310351 DOI: 10.1007/s00427-007-0141-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Accepted: 02/01/2007] [Indexed: 11/26/2022]
Abstract
The Drosophila melanogaster genes zerknüllt (zen) and fushi tarazu (ftz) are members of the Hox gene family whose roles have changed significantly in the insect lineage and thus provide an opportunity to study the mechanisms underlying the functional evolution of Hox proteins. We have studied the expression of orthologs of zen (DpuHox3) and ftz (Dpuftz) in the crustacean Daphnia pulex (Branchiopoda), both of which show a dynamic expression pattern. DpuHox3 is expressed in a complex pattern in early embryogenesis, with the most anterior boundary of expression lying at the anterior limit of the second antennal segment as well as a ring of expression around the embryo. In later embryos, DpuHox3 expression is restricted to the mesoderm of mandibular limb buds. Dpuftz is first expressed in a ring around the embryo following the posterior limit of the mandibular segment. Later, Dpuftz is restricted to the posterior part of the mandibular segment. This is the first report of expression of a Hox3 ortholog in a crustacean, and together with Dpuftz data, the results presented here show that Hox3 and ftz have retained a Hox-like expression pattern in crustaceans. This is in accordance with the proposed model of Hox3 and ftz evolution in arthropods and allows a more precise pinpointing of the loss of ftz "Hox-like behaviour": in the lineage between the Branchiopoda and the basal insect Thysanura.
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Affiliation(s)
- Daniel Papillon
- Department of Biology, Darwin building, University College of London, Gower street, London, WC1E 6BT, UK.
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47
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Bowler T, Kosman D, Licht JD, Pick L. Computational Identification of Ftz/Ftz-F1 downstream target genes. Dev Biol 2006; 299:78-90. [PMID: 16996052 DOI: 10.1016/j.ydbio.2006.07.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Revised: 07/04/2006] [Accepted: 07/07/2006] [Indexed: 11/22/2022]
Abstract
Hox genes encode DNA binding transcription factors that regulate the body plans of metazoans by regulating the expression of downstream target 'realizator genes' that direct morphogenesis and growth. Although some Hox target genes have been identified, the code used by Hox proteins to select regulatory targets remains elusive. This failure is due, in part, to the overlapping and promiscuous DNA binding potential of different Hox proteins. The identification of cofactors that modulate Hox DNA binding specificity suggested that target site selection is specified by composite binding sites in the genome for a Hox protein plus its cofactor. Here we have made use of the fact that the DNA binding specificity of the Drosophila Hox protein Fushi Tarazu (Ftz) is modulated by interaction with its partner, the orphan nuclear receptor Ftz-F1, to carry out a computational screen for genomic targets. At least two of the first 30 potential target genes--apontic (apt) and sulfated (Sulf1)--appear to be bona fide targets of Ftz and Ftz-F1. apt is expressed in stripes within the Ftz domain, but posterior to engrailed (en) stripes, suggesting a parasegmental border-independent function of ftz. Ftz/Ftz-F1 activate Sulf1 expression in blastoderm embryos via composite binding sites. Sulf1 encodes a sulfatase thought to be involved in wingless (Wg) signaling. Thus, in addition to regulating en, Ftz and Ftz-F1 coordinately and directly regulate different components of segment polarity pathways in parallel.
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Affiliation(s)
- Timothy Bowler
- Department of Biochemistry, Cellular and Developmental Biology, Mount Sinai Medical School, New York, NY 10029, USA
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48
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Abstract
The family of Hox genes, which number 4 to 48 per genome depending on the animal, control morphologies on the main body axis of nearly all metazoans. The conventional wisdom is that Hox genes are arranged in chromosomal clusters in colinear order with their expression patterns on the body axis. However, recent evidence has shown that Hox gene clusters are fragmented, reduced, or expanded in many animals-findings that correlate with interesting morphological changes in evolution. Hox gene clusters also contain many noncoding RNAs, such as intergenic regulatory transcripts and evolutionarily conserved microRNAs, some of whose developmental functions have recently been explored.
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Affiliation(s)
- Derek Lemons
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
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49
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Aruga J, Kamiya A, Takahashi H, Fujimi TJ, Shimizu Y, Ohkawa K, Yazawa S, Umesono Y, Noguchi H, Shimizu T, Saitou N, Mikoshiba K, Sakaki Y, Agata K, Toyoda A. A wide-range phylogenetic analysis of Zic proteins: Implications for correlations between protein structure conservation and body plan complexity. Genomics 2006; 87:783-92. [PMID: 16574373 DOI: 10.1016/j.ygeno.2006.02.011] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2005] [Revised: 01/19/2006] [Accepted: 02/16/2006] [Indexed: 12/01/2022]
Abstract
We compared Zic homologues from a wide range of animals. Striking conservation was found in the zinc finger domains, in which an exon-intron boundary has been kept in all bilateralians but not cnidarians, suggesting that all of the bilateralian Zic genes are derived from a single gene in a bilateralian ancestor. There were additional conserved amino acid sequences, ZOC and ZF-NC. Combined analysis of the zinc finger, ZOC, and ZF-NC revealed the presence of two classes of Zic, based on the degree of protein structure conservation. The "conserved" class includes Zic proteins from the Arthropoda, Mollusca, Annelida, Echinodermata, and Chordata (vertebrates and cephalochordates), whereas the "diverged" class contains those from the Platyhelminthes, Cnidaria, Nematoda, and Chordata (urochordates). The result indicates that the ancestral bilateralian Zic protein had already acquired an entire set of conserved domains, but that this was lost and diverged in the platyhelminthes, nematodes, and urochordates.
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Affiliation(s)
- Jun Aruga
- Laboratory for Comparative Neurogenesis, RIKEN Brain Science Institute, Wako 351-0198, Japan.
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50
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Pearson JC, Lemons D, McGinnis W. Modulating Hox gene functions during animal body patterning. Nat Rev Genet 2006; 6:893-904. [PMID: 16341070 DOI: 10.1038/nrg1726] [Citation(s) in RCA: 618] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With their power to shape animal morphology, few genes have captured the imagination of biologists as the evolutionarily conserved members of the Hox clusters have done. Recent research has provided new insight into how Hox proteins cause morphological diversity at the organismal and evolutionary levels. Furthermore, an expanding collection of sequences that are directly regulated by Hox proteins provides information on the specificity of target-gene activation, which might allow the successful prediction of novel Hox-response genes. Finally, the recent discovery of microRNA genes within the Hox gene clusters indicates yet another level of control by Hox genes in development and evolution.
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Affiliation(s)
- Joseph C Pearson
- Section in Cell & Developmental Biology, University of California, San Diego, La Jolla, California 92093, USA
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