1
|
Lima MA, Rudd TR, Fernig DG, Yates EA. Phosphorylation and sulfation share a common biosynthetic pathway, but extend biochemical and evolutionary diversity of biological macromolecules in distinct ways. JOURNAL OF THE ROYAL SOCIETY, INTERFACE 2022; 19:20220391. [PMID: 35919982 PMCID: PMC9346353 DOI: 10.1098/rsif.2022.0391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phosphate and sulfate groups are integral to energy metabolism and introduce negative charges into biological macromolecules. One purpose of such modifications is to elicit precise binding/activation of protein partners. The physico-chemical properties of the two groups, while superficially similar, differ in one important respect—the valency of the central (phosphorus or sulfur) atom. This dictates the distinct properties of their respective esters, di-esters and hence their charges, interactions with metal ions and their solubility. These, in turn, determine the contrasting roles for which each group has evolved in biological systems. Biosynthetic links exist between the two modifications; the sulfate donor 3′-phosphoadenosine-5′-phosphosulfate being formed from adenosine triphosphate (ATP) and adenosine phosphosulfate, while the latter is generated from sulfate anions and ATP. Furthermore, phosphorylation, by a xylosyl kinase (Fam20B, glycosaminoglycan xylosylkinase) of the xylose residue of the tetrasaccharide linker region that connects nascent glycosaminoglycan (GAG) chains to their parent proteoglycans, substantially accelerates their biosynthesis. Following observations that GAG chains can enter the cell nucleus, it is hypothesized that sulfated GAGs could influence events in the nucleus, which would complete a feedback loop uniting the complementary anionic modifications of phosphorylation and sulfation through complex, inter-connected signalling networks and warrants further exploration.
Collapse
Affiliation(s)
- M A Lima
- Centre for Glycosciences, Keele University, Keele ST5 5BG, UK.,School of Life Sciences, Keele University, Keele ST5 5BG, UK
| | - T R Rudd
- Analytical and Biological Science Department, National Institute of Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar EN6 3QG, UK.,Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
| | - D G Fernig
- Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
| | - E A Yates
- School of Life Sciences, Keele University, Keele ST5 5BG, UK.,Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
| |
Collapse
|
2
|
Timsit Y, Grégoire SP. Towards the Idea of Molecular Brains. Int J Mol Sci 2021; 22:ijms222111868. [PMID: 34769300 PMCID: PMC8584932 DOI: 10.3390/ijms222111868] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 02/06/2023] Open
Abstract
How can single cells without nervous systems perform complex behaviours such as habituation, associative learning and decision making, which are considered the hallmark of animals with a brain? Are there molecular systems that underlie cognitive properties equivalent to those of the brain? This review follows the development of the idea of molecular brains from Darwin’s “root brain hypothesis”, through bacterial chemotaxis, to the recent discovery of neuron-like r-protein networks in the ribosome. By combining a structural biology view with a Bayesian brain approach, this review explores the evolutionary labyrinth of information processing systems across scales. Ribosomal protein networks open a window into what were probably the earliest signalling systems to emerge before the radiation of the three kingdoms. While ribosomal networks are characterised by long-lasting interactions between their protein nodes, cell signalling networks are essentially based on transient interactions. As a corollary, while signals propagated in persistent networks may be ephemeral, networks whose interactions are transient constrain signals diffusing into the cytoplasm to be durable in time, such as post-translational modifications of proteins or second messenger synthesis. The duration and nature of the signals, in turn, implies different mechanisms for the integration of multiple signals and decision making. Evolution then reinvented networks with persistent interactions with the development of nervous systems in metazoans. Ribosomal protein networks and simple nervous systems display architectural and functional analogies whose comparison could suggest scale invariance in information processing. At the molecular level, the significant complexification of eukaryotic ribosomal protein networks is associated with a burst in the acquisition of new conserved aromatic amino acids. Knowing that aromatic residues play a critical role in allosteric receptors and channels, this observation suggests a general role of π systems and their interactions with charged amino acids in multiple signal integration and information processing. We think that these findings may provide the molecular basis for designing future computers with organic processors.
Collapse
Affiliation(s)
- Youri Timsit
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
- Correspondence:
| | - Sergeant-Perthuis Grégoire
- Institut de Mathématiques de Jussieu—Paris Rive Gauche (IMJ-PRG), UMR 7586, CNRS-Université Paris Diderot, 75013 Paris, France;
| |
Collapse
|
3
|
Kritzer JA, Freyzon Y, Lindquist S. Yeast can accommodate phosphotyrosine: v-Src toxicity in yeast arises from a single disrupted pathway. FEMS Yeast Res 2018; 18:4931722. [PMID: 29546391 PMCID: PMC6454501 DOI: 10.1093/femsyr/foy027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/08/2018] [Indexed: 12/29/2022] Open
Abstract
Tyrosine phosphorylation is a key biochemical signal that controls growth and differentiation in multicellular organisms. Saccharomyces cerevisiae and nearly all other unicellular eukaryotes lack intact phosphotyrosine signaling pathways. However, many of these organisms have primitive phosphotyrosine-binding proteins and tyrosine phosphatases, leading to the assumption that the major barrier for emergence of phosphotyrosine signaling was the negative consequences of promiscuous tyrosine kinase activity. In this work, we reveal that the classic oncogene v-Src, which phosphorylates many dozens of proteins in yeast, is toxic because it disrupts a specific spore wall remodeling pathway. Using genetic selections, we find that expression of a specific cyclic peptide, or overexpression of SMK1, a MAP kinase that controls spore wall assembly, both lead to robust growth despite a continuous high level of phosphotyrosine in the yeast proteome. Thus, minimal genetic manipulations allow yeast to tolerate high levels of phosphotyrosine. These results indicate that the introduction of tyrosine kinases within single-celled organisms may not have been a major obstacle to the evolution of phosphotyrosine signaling.
Collapse
Affiliation(s)
- Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford MA 02155, USA
| | - Yelena Freyzon
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge MA 02139, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge MA 02139, USA
| |
Collapse
|
4
|
Plattner H. Evolutionary Cell Biology of Proteins from Protists to Humans and Plants. J Eukaryot Microbiol 2017; 65:255-289. [PMID: 28719054 DOI: 10.1111/jeu.12449] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/04/2017] [Accepted: 07/07/2017] [Indexed: 01/10/2023]
Abstract
During evolution, the cell as a fine-tuned machine had to undergo permanent adjustments to match changes in its environment, while "closed for repair work" was not possible. Evolution from protists (protozoa and unicellular algae) to multicellular organisms may have occurred in basically two lineages, Unikonta and Bikonta, culminating in mammals and angiosperms (flowering plants), respectively. Unicellular models for unikont evolution are myxamoebae (Dictyostelium) and increasingly also choanoflagellates, whereas for bikonts, ciliates are preferred models. Information accumulating from combined molecular database search and experimental verification allows new insights into evolutionary diversification and maintenance of genes/proteins from protozoa on, eventually with orthologs in bacteria. However, proteins have rarely been followed up systematically for maintenance or change of function or intracellular localization, acquirement of new domains, partial deletion (e.g. of subunits), and refunctionalization, etc. These aspects are discussed in this review, envisaging "evolutionary cell biology." Protozoan heritage is found for most important cellular structures and functions up to humans and flowering plants. Examples discussed include refunctionalization of voltage-dependent Ca2+ channels in cilia and replacement by other types during evolution. Altogether components serving Ca2+ signaling are very flexible throughout evolution, calmodulin being a most conservative example, in contrast to calcineurin whose catalytic subunit is lost in plants, whereas both subunits are maintained up to mammals for complex functions (immune defense and learning). Domain structure of R-type SNAREs differs in mono- and bikonta, as do Ca2+ -dependent protein kinases. Unprecedented selective expansion of the subunit a which connects multimeric base piece and head parts (V0, V1) of H+ -ATPase/pump may well reflect the intriguing vesicle trafficking system in ciliates, specifically in Paramecium. One of the most flexible proteins is centrin when its intracellular localization and function throughout evolution is traced. There are many more examples documenting evolutionary flexibility of translation products depending on requirements and potential for implantation within the actual cellular context at different levels of evolution. From estimates of gene and protein numbers per organism, it appears that much of the basic inventory of protozoan precursors could be transmitted to highest eukaryotic levels, with some losses and also with important additional "inventions."
Collapse
Affiliation(s)
- Helmut Plattner
- Department of Biology, University of Konstanz, P. O. Box M625, Konstanz, 78457, Germany
| |
Collapse
|
5
|
Simon M, Plattner H. Unicellular Eukaryotes as Models in Cell and Molecular Biology. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 309:141-98. [DOI: 10.1016/b978-0-12-800255-1.00003-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
6
|
Miller WT. Tyrosine kinase signaling and the emergence of multicellularity. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:1053-7. [PMID: 22480439 DOI: 10.1016/j.bbamcr.2012.03.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 03/19/2012] [Accepted: 03/20/2012] [Indexed: 11/30/2022]
Abstract
Tyrosine phosphorylation is an essential element of signal transduction in multicellular animals. Although tyrosine kinases were originally regarded as specific to the metazoan lineage, it is now clear that they evolved prior to the split between unicellular and multicellular eukaryotes (≈600million years ago). Genome analyses of choanoflagellates and other protists show an abundance of tyrosine kinases that rivals the most complex animals. Some of these kinases are orthologs of metazoan enzymes (e.g., Src), but others display unique domain compositions not seen in any metazoan. Biochemical experiments have highlighted similarities and differences between the unicellular and multicellular tyrosine kinases. In particular, it appears that the complex systems of kinase autoregulation may have evolved later in the metazoan lineage.
Collapse
Affiliation(s)
- W Todd Miller
- Department of Physiology and Biophysics, School of Medcine, Stony Brook University, Stony Brook, NY 11794-8661, USA.
| |
Collapse
|
7
|
An inside job: hacking into Janus kinase/signal transducer and activator of transcription signaling cascades by the intracellular protozoan Toxoplasma gondii. Infect Immun 2011; 80:476-82. [PMID: 22104110 DOI: 10.1128/iai.05974-11] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The intracellular protozoan Toxoplasma gondii is well known for its skill at invading and living within host cells. New discoveries are now also revealing the astounding ability of the parasite to inject effector proteins into the cytoplasm to seize control of the host cell. This review summarizes recent advances in our understanding of one such secretory protein called ROP16. This molecule is released from rhoptries into the host cell during invasion. The ROP16 molecule acts as a kinase, directly activating both signal transducer and activator of transcription 3 (STAT3) and STAT6 signaling pathways. In macrophages, an important and preferential target cell of parasite infection, the injection of ROP16 has multiple consequences, including downregulation of proinflammatory cytokine signaling and macrophage deviation to an alternatively activated phenotype.
Collapse
|
8
|
Mesquita RD, Woods NT, Seabra-Junior ES, Monteiro ANA. Tandem BRCT Domains: DNA's Praetorian Guard. Genes Cancer 2011; 1:1140-6. [PMID: 21533002 DOI: 10.1177/1947601910392988] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The cell's ability to sense and respond to specific stimuli is a complex system derived from precisely regulated protein-protein interactions. Some of these protein-protein interactions are mediated by the recognition of linear peptide motifs by protein modular domains. BRCT (BRCA1 C-terminal) domains and their linear motif counterparts, which contain phosphoserines, are one such pair-wise interaction system that seems to have evolved to serve as a surveillance system to monitor threats to the cell's genetic integrity. Evidence indicates that BRCT domains found in tandem can cooperate to provide sequence-specific binding of phosphorylated peptides as is the case for the breast and ovarian cancer susceptibility gene BRCA1 and the PAX transcription factor-interacting protein PAXIP1. Particular interest has been paid to tandem BRCT domains as "readers" of signaling events in the form of phosphorylated serine moieties induced by the activation of DNA damage response kinases ATM, ATR, and DNA-PK. However, given the diversity of tandem BRCT-containing proteins, questions remain as to the origin and evolution of this domain. Here, we discuss emerging views of the origin and evolving roles of tandem BRCT domain repeats in the DNA damage response.
Collapse
Affiliation(s)
- Rafael D Mesquita
- Instituto Federal de Educação Ciência e Tecnologia, Rio de Janeiro, Brazil
| | | | | | | |
Collapse
|
9
|
Functional Diversity of the Schistosoma mansoni Tyrosine Kinases. JOURNAL OF SIGNAL TRANSDUCTION 2011; 2011:603290. [PMID: 21776387 PMCID: PMC3135232 DOI: 10.1155/2011/603290] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 02/15/2011] [Accepted: 03/15/2011] [Indexed: 01/07/2023]
Abstract
Schistosoma mansoni, one of the causative agents of schistosomiasis, has a complex life cycle infecting over 200 million people worldwide. Such a successful and prolific parasite life cycle has been shown to be dependent on the adaptive interaction between the parasite and hosts. Tyrosine kinases (TKs) play a key role in signaling pathways as demonstrated by a large body of experimental work in eukaryotes. Furthermore, comparative genomics have allowed the identification of TK homologs and provided insights into the functional role of TKs in several biological systems. Finally, TK structural biology has provided a rational basis for obtaining selective inhibitors directed to the treatment of human diseases. This paper covers the important aspects of the phospho-tyrosine signaling network in S. mansoni, Caenorhabditis elegans, and humans, the main process of functional diversification of TKs, that is, protein-domain shuffling, and also discusses TKs as targets for the development of new anti-schistosome drugs.
Collapse
|
10
|
Sebé-Pedrós A, de Mendoza A, Lang BF, Degnan BM, Ruiz-Trillo I. Unexpected repertoire of metazoan transcription factors in the unicellular holozoan Capsaspora owczarzaki. Mol Biol Evol 2010; 28:1241-1254. [PMID: 21087945 DOI: 10.1093/molbev/msq309] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
How animals (metazoans) originated from their single-celled ancestors remains a major question in biology. As transcriptional regulation is crucial to animal development, deciphering the early evolution of associated transcription factors (TFs) is critical to understanding metazoan origins. In this study, we uncovered the repertoire of 17 metazoan TFs in the amoeboid holozoan Capsaspora owczarzaki, a representative of a unicellular lineage that is closely related to choanoflagellates and metazoans. Phylogenetic and comparative genomic analyses with the broadest possible taxonomic sampling allowed us to formulate new hypotheses regarding the origin and evolution of developmental metazoan TFs. We show that the complexity of the TF repertoire in C. owczarzaki is strikingly high, pushing back further the origin of some TFs formerly thought to be metazoan specific, such as T-box or Runx. Nonetheless, TF families whose beginnings antedate the origin of the animal kingdom, such as homeodomain or basic helix-loop-helix, underwent significant expansion and diversification along metazoan and eumetazoan stems.
Collapse
Affiliation(s)
- Arnau Sebé-Pedrós
- Departament de Genètica & Institut de Recerca en Biodiversitat (Irbio), Universitat de Barcelona, Barcelona, Spain
| | - Alex de Mendoza
- Departament de Genètica & Institut de Recerca en Biodiversitat (Irbio), Universitat de Barcelona, Barcelona, Spain
| | - B Franz Lang
- Department of Biochemistry, Université de Montréal, H3C 3J7 Montréal, Canada
| | - Bernard M Degnan
- School of Biological Sciences, The University of Queensland, Brisbane Queensland 4072, Australia
| | - Iñaki Ruiz-Trillo
- Departament de Genètica & Institut de Recerca en Biodiversitat (Irbio), Universitat de Barcelona, Barcelona, Spain.,Institució Catalana per a la Recerca i Estudis Avançats (ICREA); Passeig Lluís Companys, 23, 08010 Barcelona, Spain
| |
Collapse
|
11
|
Tumoral prostate shows different expression pattern of somatostatin receptor 2 (SSTR2) and phosphotyrosine phosphatase SHP-1 (PTPN6) according to tumor progression. Adv Urol 2009:723831. [PMID: 19365586 PMCID: PMC2667939 DOI: 10.1155/2009/723831] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2008] [Revised: 02/01/2009] [Accepted: 02/16/2009] [Indexed: 01/24/2023] Open
Abstract
Prostate proliferation is dependent of androgens and many peptide hormones. Recent reports suggest that SSTR2 and SHP-1 were two fundamental components on antiproliferative effect of somatostatin. Many studies on SHP-1 revealed that the expression of this protein was diminished or abolished in several of the cancer cell lines and tissues examined. However, it is necessary to confront the cell lines data with real situation in cancer cases. Our studies have shown that epithelial expressions of both proteins, SHP-1 and SSTR2, in normal and benign hyperplasia are localized in the luminal side of duct and acinar cells. Also, SSTR2 is expressed in stromal cells. In malignant prostate tissue, SHP-1 was diminished in 28/45 cases or absent in 12/45 cases, whereas SSTR2 epithelial was diminished in 38/45 cases or lost in only 2/45 cases. The intensity of immunostained was highly negative correlated with Gleason grade for two proteins.
Collapse
|
12
|
Hunter T. Tyrosine phosphorylation: thirty years and counting. Curr Opin Cell Biol 2009; 21:140-6. [PMID: 19269802 DOI: 10.1016/j.ceb.2009.01.028] [Citation(s) in RCA: 505] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2009] [Accepted: 01/19/2009] [Indexed: 01/04/2023]
Abstract
In the 30 years since its discovery, tyrosine phosphorylation has emerged as a fundamentally important mechanism of signal transduction and regulation in all eukaryotic cells, governing many processes, including cell proliferation, cell cycle progression, metabolic homeostasis, transcriptional activation, neural transmission, differentiation and development, and aging. Perturbations in tyrosine phosphorylation underlie many human diseases, and in particular cancer, and this has prompted the development of inhibitors of tyrosine kinases implicated in disease, a number of which have been approved for clinical use. The following is a brief personal reflection on some of the salient findings over the past 30 years that led to the development of tyrosine kinase inhibitors for disease therapy.
Collapse
Affiliation(s)
- Tony Hunter
- The Salk Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
13
|
Adler EM. 2008: Signaling breakthroughs of the year. Sci Signal 2009; 2:eg1. [PMID: 19126859 DOI: 10.1126/scisignal.252eg1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
This year's signaling breakthroughs extended from protein crystals to cells and subcellular structures to whole genomes. Nominations included research on synapses in brains and in B cells; the evolution and regulation of signaling networks; the identification of a new class of plant hormones; insights into the causes and treatments of disease, such as cancer and schizophrenia; and a possible way to stay in shape while avoiding exercise.
Collapse
|
14
|
Rokas A. The molecular origins of multicellular transitions. Curr Opin Genet Dev 2008; 18:472-8. [PMID: 18926910 DOI: 10.1016/j.gde.2008.09.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 09/16/2008] [Accepted: 09/16/2008] [Indexed: 10/21/2022]
Abstract
Multicellularity has evolved multiple times independently from a variety of ancestral unicellular lineages. Past research on multicellularity was focused more on explaining why it was repeatedly invented and less so on the molecular foundations associated with each transition. Several recent comparative functional analyses of microbial unicellular and multicellular genomes have begun to throw considerable light on the molecular commonalities exhibited by independent multicellular transitions. These have enabled the delineation of the likely functional components of the genetic toolkit required for multicellular existence and to surprising discoveries, such as the presence of several toolkit components in unicellular lineages. The study of these toolkit proteins in a unicellular context has begun yielding insights into their ancestral functions and how they were coopted for multicellular development.
Collapse
Affiliation(s)
- Antonis Rokas
- Vanderbilt University, Department of Biological Sciences, Nashville, TN 37235, USA.
| |
Collapse
|