scholarly journals Oxygen-sensing mechanisms across eukaryotic kingdoms and their roles in complex multicellularity

Science ◽  
2020 ◽  
Vol 370 (6515) ◽  
pp. eaba3512 ◽  
Author(s):  
Emma U. Hammarlund ◽  
Emily Flashman ◽  
Sofie Mohlin ◽  
Francesco Licausi

Oxygen-sensing mechanisms of eukaryotic multicellular organisms coordinate hypoxic cellular responses in a spatiotemporal manner. Although this capacity partly allows animals and plants to acutely adapt to oxygen deprivation, its functional and historical roots in hypoxia emphasize a broader evolutionary role. For multicellular life-forms that persist in settings with variable oxygen concentrations, the capacity to perceive and modulate responses in and between cells is pivotal. Animals and higher plants represent the most complex life-forms that ever diversified on Earth, and their oxygen-sensing mechanisms demonstrate convergent evolution from a functional perspective. Exploring oxygen-sensing mechanisms across eukaryotic kingdoms can inform us on biological innovations to harness ever-changing oxygen availability at the dawn of complex life and its utilization for their organismal development.

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Somya Mani ◽  
Tsvi Tlusty

Abstract Background Multicellular organisms are characterized by a wide diversity of forms and complexity despite a restricted set of key molecules and mechanisms at the base of organismal development. Development combines three basic processes—asymmetric cell division, signaling, and gene regulation—in a multitude of ways to create this overwhelming diversity of multicellular life forms. Here, we use a generative model to test the limits to which such processes can be combined to generate multiple differentiation paths during development, and attempt to chart the diversity of multicellular organisms generated. Results We sample millions of biologically feasible developmental schemes, allowing us to comment on the statistical properties of cell differentiation trajectories they produce. We characterize model-generated “organisms” using the graph topology of their cell type lineage maps. Remarkably, tree-type lineage differentiation maps are the rarest in our data. Additionally, a majority of the “organisms” generated by our model appear to be endowed with the ability to regenerate using pluripotent cells. Conclusions Our results indicate that, in contrast to common views, cell type lineage graphs are unlikely to be tree-like. Instead, they are more likely to be directed acyclic graphs, with multiple lineages converging on the same terminal cell type. Furthermore, the high incidence of pluripotent cells in model-generated organisms stands in line with the long-standing hypothesis that whole body regeneration is an epiphenomenon of development. We discuss experimentally testable predictions of our model and some ways to adapt the generative framework to test additional hypotheses about general features of development.


Author(s):  
Andrew Clarke

Freezing is a widespread ecological challenge, affecting organisms in over half the terrestrial environment as well as both polar seas. With very few exceptions, if a cell freezes internally, it dies. Polar teleost fish in shallow waters avoid freezing by synthesising a range of protein or glycoprotein antifreezes. Terrestrial organisms are faced with a far greater thermal challenge, and exhibit a more complex array of responses. Unicellular organisms survive freezing temperatures by preventing ice nucleating within the cytosol, and tolerating the cellular dehydration and membrane disruption that follows from ice forming in the external environment. Multicellular organisms survive freezing temperatures by manipulating the composition of the extracellular body fluids. Terrestrial organisms may freeze at high subzero temperatures, often promoted by ice nucleating proteins, and small molecular mass cryoprotectants (often sugars and polyols) moderate the osmotic stress on cells. A range of chaperone proteins (dehydrins, LEA proteins) help maintain the integrity of membranes and macromolecules. Thermal hysteresis (antifreeze) proteins prevent damaging recrystallisation of ice. In some cases arthropods and higher plants prevent freezing in their extracellular fluids and survive by supercooling. Vitrification of extracellular water, or of the cell cytosol, may be a more widespread response to very cold temperatures than recognised to date.


Author(s):  
John Maynard Smith ◽  
Eors Szathmary

Complex multicellular organisms, whose bodies consist of differentiated cells of many kinds, have evolved independently on three occasions—animals, higher plants and fungi. In addition, multicellular organisms with a lesser degree of cellular differentiation have evolved on a number of occasions. For example, the algae have given rise to ‘seaweeds’ several times. In this and the next three chapters, we discuss the origin and subsequent evolution of such organisms. Some 540 million years ago, at the beginning of the Cambrian, there appeared an array of multicellular marine animals, including the major phyla that exist today—coelenterates, platyhelminths, annelids, arthropods, molluscs, echinoderms and others. Chordates are also present in the Cambrian: they are not known from the earliest deposits, in which only hard parts are preserved, but are present in the slightly later Burgess Shale, in which soft-bodied forms are preserved. Forty years ago, this sudden appearance of metazoan fossils was not only a puzzle but something of an embarassment: the absence of any known fossils from earlier rocks was a weapon widely used by creationists. Today, the fossil evidence for prokaryotes goes back 3000 million years, and for protists some 1000 million years. The Cambrian explosion remains a puzzle, however, which has been only fitfully illuminated by the discovery of the enigmatic soft-bodied Ediacaran fauna, which had a worldwide distribution between 580 and 560 million years ago. There are still doubts about how these fossils should be interpreted (Conway Morris, 1993). The orthodox, and more plausible, view is that the fauna is dominated by coelenterates, with some specimens identified as echinoderms and annelids. An alternative interpretation (Seilacher, 1992) is that they belong to an extinct clade of multicellular eukaryotes, the ventobionts, probably lacking an alimentary canal, muscles and nervous system. Although such organisms may have existed, at least some of the Ediacaran fauna have been successfully compared to recent metazoans. If the interpretation of most of these fossils as coelenterates proves to be correct, it would fit in well with the morphological and molecular evidence. The molecular data suggest that coelenterates arose early, but probably not independently of other metazoans. Morphologically they are simple in being diploblastic (formed from two cell layers), in contrast to the triploblastic animals that predominate in the Cambrian.


mBio ◽  
2019 ◽  
Vol 10 (2) ◽  
Author(s):  
Celia Florimond ◽  
Charlotte Cordonnier ◽  
Rahil Taujale ◽  
Hanke van der Wel ◽  
Natarajan Kannan ◽  
...  

ABSTRACTAs the protozoan parasiteToxoplasma gondiidisseminates through its host, it responds to environmental changes by altering its gene expression, metabolism, and other processes. Oxygen is one variable environmental factor, and properly adapting to changes in oxygen levels is critical to prevent the accumulation of reactive oxygen species and other cytotoxic factors. Thus, oxygen-sensing proteins are important, and among these, 2-oxoglutarate-dependent prolyl hydroxylases are highly conserved throughout evolution.Toxoplasmaexpresses two such enzymes, TgPHYa, which regulates the SCF-ubiquitin ligase complex, and TgPHYb. To characterize TgPHYb, we created aToxoplasmastrain that conditionally expresses TgPHYb and report that TgPHYb is required for optimal parasite growth under normal growth conditions. However, exposing TgPHYb-depleted parasites to extracellular stress leads to severe decreases in parasite invasion, which is likely due to decreased abundance of parasite adhesins. Adhesin protein abundance is reduced in TgPHYb-depleted parasites as a result of inactivation of the protein synthesis elongation factor eEF2 that is accompanied by decreased rates of translational elongation. In contrast to most other oxygen-sensing proteins that mediate cellular responses to low O2, TgPHYb is specifically required for parasite growth and protein synthesis at high, but not low, O2tensions as well as resistance to reactive oxygen species.In vivo, reduced TgPHYb expression leads to lower parasite burdens in oxygen-rich tissues. Taken together, these data identify TgPHYb as a sensor of high O2levels, in contrast to TgPHYa, which supports the parasite at low O2.IMPORTANCEBecause oxygen plays a key role in the growth of many organisms, cells must know how much oxygen is available. O2-sensing proteins are therefore critical cellular factors, and prolyl hydroxylases are the best-studied type of O2-sensing proteins. In general, prolyl hydroxylases trigger cellular responses to decreased oxygen availability. But, how does a cell react to high levels of oxygen? Using the protozoan parasiteToxoplasma gondii, we discovered a prolyl hydroxylase that allows the parasite to grow at elevated oxygen levels and does so by regulating protein synthesis. Loss of this enzyme also reduces parasite burden in oxygen-rich tissues, indicating that sensing both high and low levels of oxygen impacts the growth and physiology ofToxoplasma.


2019 ◽  
Vol 71 (11) ◽  
pp. 3247-3253 ◽  
Author(s):  
Karl J Niklas ◽  
Stuart A Newman

Abstract The multiple origins of multicellularity had far-reaching consequences ranging from the appearance of phenotypically complex life-forms to their effects on Earth’s aquatic and terrestrial ecosystems. Yet, many important questions remain. For example, do all lineages and clades share an ancestral developmental predisposition for multicellularity emerging from genomic and biophysical motifs shared from a last common ancestor, or are the multiple origins of multicellularity truly independent evolutionary events? In this review, we highlight recent developments and pitfalls in understanding the evolution of multicellularity with an emphasis on plants (here defined broadly to include the polyphyletic algae), but also draw upon insights from animals and their holozoan relatives, fungi and amoebozoans. Based on our review, we conclude that the evolution of multicellular organisms requires three phases (origination by disparate cell–cell attachment modalities, followed by integration by lineage-specific physiological mechanisms, and autonomization by natural selection) that have been achieved differently in different lineages.


Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 909
Author(s):  
Shotaro Okamoto ◽  
Kohei Negishi ◽  
Yuko Toyama ◽  
Takeo Ushijima ◽  
Kengo Morohashi

Gene expression varies stochastically even in both heterogenous and homogeneous cell populations. This variation is not simply useless noise; rather, it is important for many biological processes. Unicellular organisms or cultured cell lines are useful for analyzing the variation in gene expression between cells; however, owing to technical challenges, the biological relevance of this variation in multicellular organisms such as higher plants remain unclear. Here, we addressed the biological relevance of this variation between cells by examining the genetic basis of trichome distribution patterns in Arabidopsis thaliana. The distribution pattern of a trichome on a leaf is stochastic and can be mathematically represented using Turing’s reaction-diffusion (RD) model. We analyzed simulations based on the RD model and found that the variability in the trichome distribution pattern increased with the increase in stochastic variation in a particular gene expression. Moreover, differences in heat-dependent variability of the trichome distribution pattern between the accessions showed a strong correlation with environmental factors to which each accession was adapted. Taken together, we successfully visualized variations in gene expression by quantifying the variability in the Arabidopsis trichome distribution pattern. Thus, our data provide evidence for the biological importance of variations in gene expression for environmental adaptation.


2004 ◽  
Vol 359 (1445) ◽  
pp. 759-763 ◽  
Author(s):  
Alejandro Sánchez Alvarado

The problem of regeneration is fundamentally a problem of tissue homeostasis involving the replacement of cells lost to normal ‘wear and tear’ (cell turnover), and/or injury. This attribute is of particular significance to organisms possessing relatively long lifespans, as maintenance of all body parts and their functional integration is essential for their survival. Because tissue replacement is broadly distributed among multicellular life–forms, and the molecules and mechanisms controlling cellular differentiation are considered ancient evolutionary inventions, it should be possible to gain key molecular insights about regenerative processes through the study of simpler animals. We have chosen to study and develop the freshwater planarian Schmidtea mediterranea as a model system because it is one of the simplest metazoans possessing tissue homeostasis and regeneration, and because it has become relatively easy to molecularly manipulate this organism. The developmental plasticity and longevity of S. mediterranea is in marked contrast to its better–characterized invertebrate cohorts: the fruitfly Drosophila melanogaster and the roundworm Caenorhabditis elegans , both of which have short lifespans and are poor at regenerating tissues. Therefore, planarians present us with new, experimentally accessible contexts in which to study the molecular actions guiding cell fate restriction, differentiation and patterning, each of which is crucial not only for regeneration to occur, but also for the survival and perpetuation of all multicellular organisms.


2016 ◽  
Vol 371 (1701) ◽  
pp. 20150442 ◽  
Author(s):  
Eugene V. Koonin

The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of ‘public goods’. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host–parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions. This article is part of the themed issue ‘The major synthetic evolutionary transitions’.


2020 ◽  
Vol 117 (37) ◽  
pp. 23140-23147 ◽  
Author(s):  
Mark D. White ◽  
Laura Dalle Carbonare ◽  
Mikel Lavilla Puerta ◽  
Sergio Iacopino ◽  
Martin Edwards ◽  
...  

In higher plants, molecular responses to exogenous hypoxia are driven by group VII ethylene response factors (ERF-VIIs). These transcriptional regulators accumulate in the nucleus under hypoxia to activate anaerobic genes but are destabilized in normoxic conditions through the action of oxygen-sensing plant cysteine oxidases (PCOs). The PCOs catalyze the reaction of oxygen with the conserved N-terminal cysteine of ERF-VIIs to form cysteine sulfinic acid, triggering degradation via the Cys/Arg branch of the N-degron pathway. The PCOs are therefore a vital component of the plant oxygen signaling system, connecting environmental stimulus with cellular and physiological response. Rational manipulation of PCO activity could regulate ERF-VII levels and improve flood tolerance, but requires detailed structural information. We report crystal structures of the constitutively expressed PCO4 and PCO5 from Arabidopsis thaliana to 1.24 and 1.91 Å resolution, respectively. The structures reveal that the PCOs comprise a cupin-like scaffold, which supports a central metal cofactor coordinated by three histidines. While this overall structure is consistent with other thiol dioxygenases, closer inspection of the active site indicates that other catalytic features are not conserved, suggesting that the PCOs may use divergent mechanisms to oxidize their substrates. Conservative substitution of two active site residues had dramatic effects on PCO4 function both in vitro and in vivo, through yeast and plant complementation assays. Collectively, our data identify key structural elements that are required for PCO activity and provide a platform for engineering crops with improved hypoxia tolerance.


2007 ◽  
Vol 43 ◽  
pp. 1-16 ◽  
Author(s):  
Mathew L. Coleman ◽  
Peter J. Ratcliffe

Low cellular oxygenation (hypoxia) represents a significant threat to the viability of affected tissues. Multicellular organisms have evolved a highly conserved signalling pathway that directs many of the changes in gene expression that underpin physiological oxygen homoeostasis. Oxygen-sensing enzymes in this pathway control the activity of the HIF (hypoxia-inducible factor) transcription factor by the direct incorporation of molecular oxygen into the post-translational hydroxylation of specific residues. This represents the canonical hypoxia signalling pathway which regulates a plethora of genes involved in adaptation to hypoxia. The HIF hydroxylases have been identified in other biological contexts, consistent with the possibility that they have other substrates. Furthermore, several intracellular proteins have been demonstrated, directly or indirectly, to be hydroxylated, although the protein hydroxylases responsible have yet to be identified. This chapter will summarize what is currently known about the canonical HIF hydroxylase signalling pathway and will speculate on the existence of other oxygen-sensing enzymes and the role they may play in signalling hypoxia through other pathways.


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