1
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Katyal G, Ebanks B, Lucassen M, Papetti C, Chakrabarti L. Sequence and structure comparison of ATP synthase F0 subunits 6 and 8 in notothenioid fish. PLoS One 2021; 16:e0245822. [PMID: 34613983 PMCID: PMC8494342 DOI: 10.1371/journal.pone.0245822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 09/09/2021] [Indexed: 11/20/2022] Open
Abstract
Mitochondrial changes such as tight coupling of the mitochondria have facilitated sustained oxygen and respiratory activity in haemoglobin-less icefish of the Channichthyidae family. We aimed to characterise features in the sequence and structure of the proteins directly involved in proton transport, which have potential physiological implications. ATP synthase subunit a (ATP6) and subunit 8 (ATP8) are proteins that function as part of the F0 component (proton pump) of the F0F1complex. Both proteins are encoded by the mitochondrial genome and involved in oxidative phosphorylation. To explore mitochondrial sequence variation for ATP6 and ATP8 we analysed sequences from C. gunnari and C. rastrospinosus and compared them with their closely related red-blooded species and eight other vertebrate species. Our comparison of the amino acid sequence of these proteins reveals important differences that could underlie aspects of the unique physiology of the icefish. In this study we find that changes in the sequence of subunit a of the icefish C. gunnari at position 35 where there is a hydrophobic alanine which is not seen in the other notothenioids we analysed. An amino acid change of this type is significant since it may have a structural impact. The biology of the haemoglobin-less icefish is necessarily unique and any insights about these animals will help to generate a better overall understanding of important physiological pathways.
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Affiliation(s)
- Gunjan Katyal
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Brad Ebanks
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | | | | | - Lisa Chakrabarti
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Nottingham, United Kingdom
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2
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Wu Z, Zhao D, Li S, Wang J, Bi C, Zhang X. Combinatorial modulation of initial codons for improved zeaxanthin synthetic pathway efficiency in Escherichia coli. Microbiologyopen 2019; 8:e930. [PMID: 31532062 PMCID: PMC6925171 DOI: 10.1002/mbo3.930] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 08/13/2019] [Accepted: 08/16/2019] [Indexed: 11/09/2022] Open
Abstract
A balanced and optimized metabolic pathway is the basis for efficient production of a target metabolite. Traditional strategies mostly involve the manipulation of promoters or ribosome-binding sites, which can encompass long sequences and can be complex to operate. In this work, we found that by changing only the three nucleotides of the initiation codons, expression libraries of reporter proteins RFP, GFP, and lacZ with a large dynamic range and evenly distributed expression levels could be established in Escherichia coli (E. coli). Thus, a novel strategy that uses combinatorial modulation of initial codons (CMIC) was developed for metabolic pathway optimization and applied to the three genes crtZ, crtY, and crtI of the zeaxanthin synthesis pathway in E. coli. The initial codons of these genes were changed to random nucleotides NNN, and the gene cassettes were assembled into vectors via an optimized strategy based on type II restriction enzymes. With minimal labor time, a combinatorial library was obtained containing strains with various zeaxanthin production levels, including a strain with a titer of 6.33 mg/L and specific production value of 1.24 mg/g DCW-a striking 10-fold improvement over the starting strain. The results demonstrated that CMIC was a feasible technique for conveniently optimizing metabolic pathways. To our best knowledge, this is the first metabolic engineering strategy that relies on manipulating the initiation codons for pathway optimization in E. coli.
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Affiliation(s)
- Zaiqiang Wu
- Center for Molecular Metabolism, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Siwei Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Junsong Wang
- Center for Molecular Metabolism, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
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3
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López Tobón A, Suresh M, Jin J, Vitriolo A, Pietralla T, Tedford K, Bossenz M, Mahnken K, Kiefer F, Testa G, Fischer KD, Püschel AW. The guanine nucleotide exchange factor Arhgef7/βPix promotes axon formation upstream of TC10. Sci Rep 2018; 8:8811. [PMID: 29891904 PMCID: PMC5995858 DOI: 10.1038/s41598-018-27081-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/29/2018] [Indexed: 11/10/2022] Open
Abstract
The characteristic six layers of the mammalian neocortex develop sequentially as neurons are generated by neural progenitors and subsequently migrate past older neurons to their final position in the cortical plate. One of the earliest steps of neuronal differentiation is the formation of an axon. Small GTPases play essential roles during this process by regulating cytoskeletal dynamics and intracellular trafficking. While the function of GTPases has been studied extensively in cultured neurons and in vivo much less is known about their upstream regulators. Here we show that Arhgef7 (also called βPix or Cool1) is essential for axon formation during cortical development. The loss of Arhgef7 results in an extensive loss of axons in cultured neurons and in the developing cortex. Arhgef7 is a guanine-nucleotide exchange factor (GEF) for Cdc42, a GTPase that has a central role in directing the formation of axons during brain development. However, active Cdc42 was not able to rescue the knockdown of Arhgef7. We show that Arhgef7 interacts with the GTPase TC10 that is closely related to Cdc42. Expression of active TC10 can restore the ability to extend axons in Arhgef7-deficient neurons. Our results identify an essential role of Arhgef7 during neuronal development that promotes axon formation upstream of TC10.
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Affiliation(s)
- Alejandro López Tobón
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität, Schloßplatz 5, D-48149, Münster, Germany.,Cells-in-Motion Cluster of Excellence, University of Münster, D-48149, Münster, Germany.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, 20122, Italy.,European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Megalakshmi Suresh
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität, Schloßplatz 5, D-48149, Münster, Germany.,Cells-in-Motion Cluster of Excellence, University of Münster, D-48149, Münster, Germany
| | - Jing Jin
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität, Schloßplatz 5, D-48149, Münster, Germany.,Cells-in-Motion Cluster of Excellence, University of Münster, D-48149, Münster, Germany
| | - Alessandro Vitriolo
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, 20122, Italy.,European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Thorben Pietralla
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität, Schloßplatz 5, D-48149, Münster, Germany
| | - Kerry Tedford
- Institut für Biochemie und Zellbiologie, Otto-von-Guericke-University, Medical Faculty, Leipziger Str. 44, 39120, Magdeburg, 39120, Germany
| | - Michael Bossenz
- Institut für Biochemie und Zellbiologie, Otto-von-Guericke-University, Medical Faculty, Leipziger Str. 44, 39120, Magdeburg, 39120, Germany
| | - Kristina Mahnken
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität, Schloßplatz 5, D-48149, Münster, Germany
| | - Friedemann Kiefer
- Cells-in-Motion Cluster of Excellence, University of Münster, D-48149, Münster, Germany.,Max-Planck-Institute for Molecular Biomedicine, Mammalian cell signaling laboratory, Röntgenstr. 20, D-48149, Münster, Germany.,European Institute for Molecular Imaging, Westfälische Wilhelms-Universität, Waldeyerstr. 15, D-48149, Münster, Germany
| | - Giuseppe Testa
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, 20122, Italy.,European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Klaus-Dieter Fischer
- Institut für Biochemie und Zellbiologie, Otto-von-Guericke-University, Medical Faculty, Leipziger Str. 44, 39120, Magdeburg, 39120, Germany
| | - Andreas W Püschel
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität, Schloßplatz 5, D-48149, Münster, Germany. .,Cells-in-Motion Cluster of Excellence, University of Münster, D-48149, Münster, Germany.
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4
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Omelchenko T, Rabadan MA, Hernández-Martínez R, Grego-Bessa J, Anderson KV, Hall A. β-Pix directs collective migration of anterior visceral endoderm cells in the early mouse embryo. Genes Dev 2015; 28:2764-77. [PMID: 25512563 PMCID: PMC4265679 DOI: 10.1101/gad.251371.114] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Rac1 is essential for generating the protrusive activity that drives the collective migration of anterior visceral endoderm (AVE) cells in the early mouse embryo. Omelchenko et al. identified β-Pix as a potential regulator of Rac1. Genetic deletion of β-Pix in mice disrupts collective AVE migration. Collective epithelial migration is important throughout embryonic development. The underlying mechanisms are poorly understood but likely involve spatially localized activation of Rho GTPases. We previously reported that Rac1 is essential for generating the protrusive activity that drives the collective migration of anterior visceral endoderm (AVE) cells in the early mouse embryo. To identify potential regulators of Rac1, we first performed an RNAi screen of Rho family exchange factors (guanine nucleotide exchange factor [GEF]) in an in vitro collective epithelial migration assay and identified β-Pix. Genetic deletion of β-Pix in mice disrupts collective AVE migration, while high-resolution live imaging revealed that this is associated with randomly directed protrusive activity. We conclude that β-Pix controls the spatial localization of Rac1 activity to drive collective AVE migration at a critical stage in mouse development.
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Affiliation(s)
| | | | - Rocío Hernández-Martínez
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Joaquim Grego-Bessa
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Kathryn V Anderson
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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5
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Park J, Kim Y, Park ZY, Park D, Chang S. Neuronal specific βPix-b stimulates actin-dependent processes via the interaction between its PRD and WH1 domain of N-WASP. J Cell Physiol 2012; 227:1476-84. [PMID: 21618538 DOI: 10.1002/jcp.22863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
βPix, a Pak-interacting nucleotide exchange factor (Cool-1/p85SPR), is a Cdc42/Rac1-specific guanine nucleotide exchange factor (GEF) involved in various actin-related processes. Many previous studies have focused on ubiquitously expressed βPix-a, while the role of the neuronal-specific isoform βPix-b is still unknown, especially whether its role is distinct from or similar to βPix-a. Here we show that unlike βPix-a, overexpression of βPix-b stimulates actin-dependent comet formation in BHK21 cells. This effect is attributed to the interaction between its proline-rich domain (PRD) and the WH1 domain of N-WASP. In addition, we show that overexpression of βPix-b stimulates actin-dependent dendritic spine formation in rat hippocampal neurons in culture, a formation that is blocked by co-expression of the WH1 domain of N-WASP or the PRD of βPix-b. Knocking-down endogenous expression of βPix-b by shRNA reduced the number of dendritic spines, which were rescued only by PRD-containing βPix-b mutants. GEF activity of βPix-b is also required for these effects. The results show that neuronal-specific βPix-b stimulates actin-dependent processes in cells via the interaction between its PRD and the WH1 domain of N-WASP. Our results identify N-WASP as the first protein shown to interact with the PRD of βPix-b, raising the possibility that, as an N-WASP WH1-binding protein, βPix-b may regulate N-WASP's activity in cells.
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Affiliation(s)
- Joohyun Park
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
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6
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Interaction of microtubules and actin with the N-terminus of βPix-b(L) directs cellular pinocytosis. Mol Cell Biochem 2011; 351:207-15. [PMID: 21249427 DOI: 10.1007/s11010-011-0728-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 01/10/2011] [Indexed: 12/30/2022]
Abstract
βPix is a Rac/Cdc42 guanine nucleotide exchange factor (GEF) that is known to be a regulator of actin cytoskeleton remodeling. Recently, a novel splicing isoform, βPix-b(L), was identified as an alternative translational product of the βPix-b mRNA with an extended N-terminus comprising a partial calponin homology (CH) domain and a serine-rich (SR) domain. However, the cellular function of βPix-b(L) is largely unknown. In the current study, we analyzed the genomic DNA structure and cellular functions of βPix-b(L). The results of this study demonstrate that βPix is composed of 24 exons and 21 introns spanning around 100 kb. RT-PCR experiments revealed that there are two forms of βPix mRNA with distinct 5' UTRs that are the result of alternative splicing of exon 1 and 2 from βPix genomic DNA. In addition, affinity chromatography analysis and a pull-down assay with the N-terminal region of βPix-b(L) revealed that βPix-b(L) interacts with tubulin and actin via its N-terminal CH and SR domains, respectively. Interaction with tubulin enabled βPix-b(L) to bundle the microtubule and form membrane protrusions. Furthermore, the N-terminus of βPix-b(L) was also critical for its localization to cellular vesicles. Functionally, βPix-b(L) induced pinocytosis through cooperative action of the CH and Dbl homology (DH) domains, demonstrating the role of βPix-b(L) in the regulation of membrane dynamics.
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7
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Mayhew MW, Jeffery ED, Sherman NE, Nelson K, Polefrone JM, Pratt SJ, Shabanowitz J, Parsons JT, Fox JW, Hunt DF, Horwitz AF. Identification of phosphorylation sites in betaPIX and PAK1. J Cell Sci 2008; 120:3911-8. [PMID: 17989089 DOI: 10.1242/jcs.008177] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Mark W Mayhew
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
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8
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Seligmann H. Cost minimization of ribosomal frameshifts. J Theor Biol 2007; 249:162-7. [PMID: 17706680 DOI: 10.1016/j.jtbi.2007.07.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Revised: 07/08/2007] [Accepted: 07/09/2007] [Indexed: 11/24/2022]
Abstract
Properties of mRNA leading regions that modulate protein synthesis are little known (besides effects of their secondary structure). Here I explore how coding properties of leading regions may account for their disparate efficiencies. Trinucleotides that form off frame stop codons decrease costs of ribosomal slippages during protein synthesis: protein activity (as a proxy of gene expression, and as measured in experiments using artificial variants of 5' leading sequences of beta galactosidase in Escherichia coli) increases proportionally to the number of stop motifs in any frame in the 5' leading region. This suggests that stop codons in the 5' leading region, upstream of the recognized coding sequence, terminate eventual translations that sometimes start before ribosomes reach the mRNA's recognized start codon, increasing efficiency. This hypothesis is confirmed by further analyses: mRNAs with 5' leading regions containing in the same frame a start preceding a stop codon (in any frame) produce less enzymatic activity than those with the stop preceding the start. Hence coding properties, in addition to other properties, such as the secondary structure of the 5' leading region, regulate translation. This experimentally (a) confirms that within coding regions, off frame stops increase protein synthesis efficiency by early stopping frameshifted translation; (b) suggests that this occurs for all frames also in 5' leading regions and that (c) several alternative start codons that function at different probabilities should routinely be considered for all genes in the region of the recognized initiation codon. An unknown number of short peptides might be translated from coding and non-coding regions of RNAs.
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Affiliation(s)
- Hervé Seligmann
- Department of Evolution, Systematics and Ecology, The Hebrew University of Jerusalem, Jerusalem 91404, Israel.
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9
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Liu J, Fraser SD, Faloon PW, Rollins EL, Vom Berg J, Starovic-Subota O, Laliberte AL, Chen JN, Serluca FC, Childs SJ. A betaPix Pak2a signaling pathway regulates cerebral vascular stability in zebrafish. Proc Natl Acad Sci U S A 2007; 104:13990-5. [PMID: 17573532 PMCID: PMC1955796 DOI: 10.1073/pnas.0700825104] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2007] [Indexed: 11/18/2022] Open
Abstract
The vasculature tailors to the needs of different tissues and organs. Molecular, structural, and functional specializations are observed in different vascular beds, but few genetic models give insight into how these differences arise. We identify a unique cerebrovascular mutation in the zebrafish affecting the integrity of blood vessels supplying the brain. The zebrafish bubblehead (bbh) mutant exhibits hydrocephalus and severe cranial hemorrhage during early embryogenesis, whereas blood vessels in other regions of the embryo appear intact. Here we show that hemorrhages are associated with poor cerebral endothelial-mesenchymal contacts and an immature vascular pattern in the head. Positional cloning of bbh reveals a hypomorphic mutation in betaPix, a binding partner for the p21-activated kinase (Pak) and a guanine nucleotide exchange factor for Rac and Cdc42. betaPix is broadly expressed during embryonic development and is enriched in the brain and in large blood vessels. By knockdown of specific betaPix splice variants, we show that they play unique roles in embryonic vascular stabilization or hydrocephalus. Finally, we show that Pak2a signaling is downstream of betaPix. These data identify an essential in vivo role for betaPix and Pak2a during embryonic development and illuminate a previously unrecognized pathway specifically involved in cerebrovascular stabilization.
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Affiliation(s)
- Jing Liu
- *Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, Canada T2N 4N1
| | - Sherri D. Fraser
- *Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, Canada T2N 4N1
| | - Patrick W. Faloon
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139
| | - Evvi Lynn Rollins
- *Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, Canada T2N 4N1
| | - Johannes Vom Berg
- *Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, Canada T2N 4N1
| | - Olivera Starovic-Subota
- *Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, Canada T2N 4N1
| | - Angie L. Laliberte
- *Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, Canada T2N 4N1
| | - Jau-Nian Chen
- Department of Molecular, Cellular, and Developmental Biology, University of California, Los Angeles, CA 90095; and
| | - Fabrizio C. Serluca
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139
| | - Sarah J. Childs
- *Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, Canada T2N 4N1
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Osmani N, Vitale N, Borg JP, Etienne-Manneville S. Scrib controls Cdc42 localization and activity to promote cell polarization during astrocyte migration. Curr Biol 2006; 16:2395-405. [PMID: 17081755 DOI: 10.1016/j.cub.2006.10.026] [Citation(s) in RCA: 176] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Revised: 09/26/2006] [Accepted: 10/12/2006] [Indexed: 12/30/2022]
Abstract
BACKGROUND Mammalian Scribble (Scrib) plays a conserved role in polarization of epithelial and neuronal cells. Polarization is essential for migration of a variety of cell types; however, the function of Scrib in this context remains unclear. Scrib has been shown to interact with betaPIX, a guanine nucleotide exchange factor for the small GTPases Rac and Cdc42. Cdc42 controls cell polarity from yeast to mammals during asymmetric cell division and epithelial cell polarization, as well as during cell migration. Cdc42 is, in particular, required for polarization and orientation of astrocytes in a scratch-induced polarized migration assay. Using this assay, we characterized Scrib function during polarized cell migration. RESULTS Depletion of Scrib by siRNA or expression of dominant-negative constructs inhibits astrocyte polarization. Like Cdc42, Scrib controls protrusion formation, cytoskeleton polarization, and centrosome and Golgi reorientation. Scrib interacts and colocalizes with betaPIX at the front edge of polarizing astrocytes. Perturbation of Scrib localization or of Scrib-betaPIX interaction inhibits betaPIX polarized recruitment. We further show that betaPIX is required for astrocyte polarization and that both the Scrib-binding motif and the GEF activity of betaPIX are essential for its function. Scrib and betaPIX control Cdc42 activation and localization during astrocyte polarization. Thereby, Scrib regulates Cdc42-dependent APC and Dlg1 recruitment to the leading edge to promote cell orientation. CONCLUSION We conclude that Scrib plays a key role in the establishment of cell polarity during migration. By interacting with betaPIX, Scrib controls localization and activation of the small GTPase Cdc42 and regulates Cdc42-dependent polarization pathways.
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Affiliation(s)
- Naël Osmani
- Cell Polarity and Migration Group, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris cedex 15, France
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11
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Abstract
The cell has many ways to regulate the production of proteins. One mechanism is through the changes to the machinery of translation initiation. These alterations favor the translation of one subset of mRNAs over another. It was first shown that internal ribosome entry sites (IRESes) within viral RNA genomes allowed the production of viral proteins more efficiently than most of the host proteins. The RNA secondary structure of viral IRESes has sometimes been conserved between viral species even though the primary sequences differ. These structures are important for IRES function, but no similar structure conservation has yet to be shown in cellular IRES. With the advances in mathematical modeling and computational approaches to complex biological problems, is there a way to predict an IRES in a data set of unknown sequences? This review examines what is known about cellular IRES structures, as well as the data sets and tools available to examine this question. We find that the lengths, number of upstream AUGs, and %GC content of 5'-UTRs of the human transcriptome have a similar distribution to those of published IRES-containing UTRs. Although the UTRs containing IRESes are on the average longer, almost half of all 5'-UTRs are long enough to contain an IRES. Examination of the available RNA structure prediction software and RNA motif searching programs indicates that while these programs are useful tools to fine tune the empirically determined RNA secondary structure, the accuracy of de novo secondary structure prediction of large RNA molecules and subsequent identification of new IRES elements by computational approaches, is still not possible.
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Affiliation(s)
- Stephen D Baird
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ontario K1H 8M5, Canada
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12
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Abstract
Alpha and betaPIX belong to the group of guanine nucleotide exchange factors (GEFs) that mediate activation of members of the Rho GTPase family, in particular Rac1 and Cdc42, by stimulating the exchange of GDP for GTP. Rho family proteins are well known as regulators of the actin cytoskeleton and have been implicated in the formation of various types of focal adhesion structures. However, the function of GEF proteins during focal adhesion formation is only beginning to emerge. Here, we highlight the recent findings on alpha and betaPIX and their involvement in integrin-dependent signaling and suggest models for the role of PIX proteins during focal adhesion turnover.
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Affiliation(s)
- Georg Rosenberger
- Institut für Humangenetik, Universitätsklinikum Hamburg-Eppendorf, Butenfeld 42, 22529 Hamburg, Germany
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13
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Kozak M. A second look at cellular mRNA sequences said to function as internal ribosome entry sites. Nucleic Acids Res 2005; 33:6593-602. [PMID: 16314320 PMCID: PMC1298923 DOI: 10.1093/nar/gki958] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2005] [Accepted: 10/26/2005] [Indexed: 01/27/2023] Open
Abstract
This review takes a second look at a set of mRNAs that purportedly employ an alternative mechanism of initiation when cap-dependent translation is reduced during mitosis or stress conditions. A closer look is necessary because evidence cited in support of the internal initiation hypothesis is often flawed. When putative internal ribosome entry sequences (IRESs) are examined more carefully, they often turn out to harbor cryptic promoters or splice sites. This undermines the dicistronic assay, wherein IRES activity is measured by the ability to support translation of the 3' cistron. Most putative IRESs still have not been checked carefully to determine whether the dicistronic vector produces only the intended dicistronic mRNA. The widespread use of the pRF vector is a major problem because this vector, which has Renilla luciferase as the 5' cistron and firefly luciferase as the 3' cistron, has been found to generate spliced transcripts. RNA transfection assays could theoretically circumvent these problems, but most candidate IRESs score very weakly in that test. The practice of calling even very weak results 'positive' is one of the problems discussed herein. The extremely low efficiency of putative IRESs is inconsistent with their postulated biological roles.'
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Affiliation(s)
- Marilyn Kozak
- Department of Biochemistry, Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854, USA.
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14
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Hwang SR, Garza CZ, Wegrzyn JL, Hook VYH. Demonstration of GTG as an alternative initiation codon for the serpin endopin 2B-2. Biochem Biophys Res Commun 2005; 327:837-44. [PMID: 15649421 DOI: 10.1016/j.bbrc.2004.12.053] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2004] [Indexed: 11/19/2022]
Abstract
This study demonstrates GTG as a novel, alternative initiation codon for translation of bovine endopin 2B-2, a serpin protease inhibitor. Molecular cDNA cloning revealed the endopin 2B-1 and endopin 2B-2 isoforms that are predicted to inhibit papain and elastase. Notably, GTG was demonstrated as the initiation codon for endopin 2B-2, whereas endopin 2B-1 possesses ATG as its initiation codon. GTG mediated in vitro translation of 46kDa endopin 2B-2. GTG also mediated translation of EGFP by in vitro translation and by expression in mammalian cells. Notably, mutagenesis of GTG to GTC resulted in the absence of EGFP expression in cells. GTG produced a lower level of protein expression compared to ATG. The use of GTG as an initiation codon to direct translation of endopin 2B, as well as the heterologous protein EGFP, demonstrates the role of GTG in the regulation of mRNA translation in mammalian cells. Significantly, further analyses of mammalian genomes based on GTG as an alternative initiation codon may predict new candidate gene products expressed by mammalian and human genomes.
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Affiliation(s)
- Shin-Rong Hwang
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
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