Tag Archives: cell biology

Where did your cells come from?

If you look at your cells under a microscope, you’ll see nearly all of them have a nucleus, mitochondria and other equipment inside them. Eukaryotic cells, cells with a nucleus, are the basis of all complex life fungi, plants and us. The change from prokaryotic cell to complex cell is profoundly important to evolution of life, but how did it happen?

The favoured explanation has been that an archaeon swallowed a bacterium. The two developed a symbiotic relationship and evolved into eukaryotes. This explanation bothers me slightly because it needs the pair to do a lot of work fast, but I suppose if archaea are eating bacteria millions upon millions of times each day, then they’re making a lot of attempts.

David Baum, a University of Wisconsin-Madison professor of botany and evolutionary biologist, has proposed a new model for eukaryote evolution. His model is inside out and, to a non-biologist like me, it looks plausible.

Baum and his cousin Buzz Baum at UCL, argue that archaea developed protrusions called blebs, little arms if you like. These enabled the cells to interact with their environment better. Along the way they encountered bacteria and started to develop ways to exploit the energy of bacteria, while the bacteria were still outside the cell. The cells that did this better survived more often and reproduced until they had engulfed the bacterium.

Inside-out model for the evolution of eukaryotic cell organization. Model showing the stepwise evolution of eukaryotic cell organization from (A) an eocyte ancestor with a single bounding membrane and a glycoprotein rich cell wall (S-layer) interacting with epibiotic α-proteobacteria (proto-mitochondria). (B) We envision the eocyte cell forming protrusions, aided by protein-membrane interactions at the protrusion neck. These protrusions facilitated material exchange with proto-mitochondria. (C) Selection for a greater area of contact between the symbionts would have led to bleb enlargement and the eventual loss of the S-layer from the protrusions. (D) Blebs would have then been further stabilized by the development of a symmetric nuclear pore outer ring complex (Figure 2) and through the establishment of LINC complexes that, following the gradual loss of the S-layer, physically connected the original cell body (the nascent nuclear compartment) to the inner bleb membranes. (E) With the expansion of blebs to enclose the proto-mitochondria, a process that would have facilitated the acquisition of bacterial lipid biosynthesis machinery by the host, the site of cell growth would have progressively shifted to the cytoplasm, facilitated by the development of regulated traffic through the nuclear pore. At the same time, the spaces between blebs would have enabled the gradual maturation of proteins secreted into the environment via the perinuclear space through glycosylation and proteolytic cleavage. (F) Finally, bleb fusion would have connected cytoplasmic compartments and driven the formation of an intact plasma membrane, perhaps through a process akin to phagocytosis whereby one bleb enveloped the whole. This simple topological transition would have isolated the endoplasmic reticulum from the outside world, driven the full development of a system of vesicular trafficking, and established strict vertical transmission of mitochondria, leading to a cell with modern eukaryotic cell organization. Baum and Baum BMC Biology 2014 12:76   doi:10.1186/s12915-014-0076-2

Inside-out model for the evolution of eukaryotic cell organization. Model showing the stepwise evolution of eukaryotic cell organization from
(A) an eocyte ancestor with a single bounding membrane and a glycoprotein rich cell wall (S-layer) interacting with epibiotic α-proteobacteria (proto-mitochondria).
(B) We envision the eocyte cell forming protrusions, aided by protein-membrane interactions at the protrusion neck. These protrusions facilitated material exchange with proto-mitochondria.
(C) Selection for a greater area of contact between the symbionts would have led to bleb enlargement and the eventual loss of the S-layer from the protrusions.
(D) Blebs would have then been further stabilized by the development of a symmetric nuclear pore outer ring complex (Figure 2) and through the establishment of LINC complexes that, following the gradual loss of the S-layer, physically connected the original cell body (the nascent nuclear compartment) to the inner bleb membranes.
(E) With the expansion of blebs to enclose the proto-mitochondria, a process that would have facilitated the acquisition of bacterial lipid biosynthesis machinery by the host, the site of cell growth would have progressively shifted to the cytoplasm, facilitated by the development of regulated traffic through the nuclear pore. At the same time, the spaces between blebs would have enabled the gradual maturation of proteins secreted into the environment via the perinuclear space through glycosylation and proteolytic cleavage.
(F) Finally, bleb fusion would have connected cytoplasmic compartments and driven the formation of an intact plasma membrane, perhaps through a process akin to phagocytosis whereby one bleb enveloped the whole. This simple topological transition would have isolated the endoplasmic reticulum from the outside world, driven the full development of a system of vesicular trafficking, and established strict vertical transmission of mitochondria, leading to a cell with modern eukaryotic cell organization.
Baum and Baum BMC Biology 2014 12:76 doi:10.1186/s12915-014-0076-2

What I like is that there are steps to bringing the bacterium inside the cell, instead of Pow! it’s there and everything has to develop now. That’s probably an unfair over-simplication of the standard model, but the inside-out model makes sense as each step along the way seems to either use material it already has, or confer a small advantage for survival by itself.

While the event happened unseen billions of years ago, Baum and Baum have some ideas of how they can test the idea. Genetic data could help indicate that an inside out model is more likely than the standard model. Their model predicts that some parts of the cell developed in the opposite order to the standard model, though I’ll admit I don’t understand the details of how “COPII-like coatomers are derived from structural components of the nuclear pore, rather than the reverse”. However, I can see a list of clear predictions that Baum and Baum are making that someone can test, even if it’s clearly not me.

Fossil data would be nice, but highly unlikely, but there is another prediction. If prokaryotes can gain an advantage by developing blebs to interact with bacteria, then it should be possible to see some prokaryotes in the wild that look like the first eukaryote before it engulfed its partner.

Best of all, it’s a very positive paper. Baum and Baum aren’t simply saying everyone else is wrong, they’re proposing new topics to research and new things to study, new ways to look at problems. Even if it turns out they’re wrong, they could be wrong in a really interesting and helpful way.

You can pick up the paper through Open Access from BMC Biology.

Baum D.A. & Baum B. (2014). An inside-out origin for the eukaryotic cell, BMC Biology, 12 (1) 76. DOI: http://dx.doi.org/10.1186/s12915-014-0076-2

Tann-fastic, a new plant organelle(!!)

The cell is the fundamental unit of construction from which all living things are built, whether it is a microscopic unicellular amoeba or an enormous multicellular giant redwood. Internally, each cell is furnished with a range of smaller bodies – termed organelles – that perform various essential functions; e.g. chloroplasts in plant cells that are involved in photosynthesis, mitochondria in both animal and plant cells that engage in respiration, and ribosomes that facilitate protein synthesis. Given the importance of cells and cell structure you might be forgiven for thinking that we know all there is to know – well, at least are aware of all of the organelles that exist. Not so, as work by Jean-Marc Brillouet and colleagues demonstrate. The team, based in Montpellier, Le Mans (both in France) and Budapest (Hungary), have identified a new organelle in plant cells. They have called it the tannosome because it is involved in the formation of condensed tannins (compounds present in most land plants and which are thought to provide defence against herbivores and pathogens). Although tannins have been recognised as present within the vacuoles in plant cells, their site of synthesis has hitherto not been determined. Using a wide range of techniques – including light and electron microscopy, antibody-localisation, chemical analysis and cell fractionation – the team concludes that the tannins are formed within a new type of plastid (a group of plant organelles that includes the chloroplast and the amyloplast), the aforementioned tannosome. These are derived from the thylakoids within the chloroplast and once formed, small protrusions develop from the latter’s surface and the tannin-packed tannosomes are transported as tiny membrane-bound spheres to the vacuole, in which organelle they accumulate. Examining a range of plants from the groups in the plant kingdom, including cycads, ginkgo, horse-tails, ferns, conifers and flowering plants, they conclude that tannosomes are likely to be universal amongst those so-called vascular plants. Aside from their protective roles in plants, tannins are also important in making tea and red wine taste the way they do. It isn’t every day that a new organelle is identified, but this goes to show that something as commonplace and seemingly familiar as the cell still has secrets to be discovered. I wonder how long it will take for tannosome to be rechristened tannoplast (or will that cause too much confusion with tonoplast…)?

[And if you’re wondering when the previous new plant organelle was identified, my suggestion is plastid stromules (in 1997…). And for more on plant tannin research, check out this work by Dr Irene Müller-Harvey at the University of Reading (UK) – Ed.]

Homage to a nanotubule…

Image: Frank Boumphrey/Wikimedia Commons.

Image: Frank Boumphrey/Wikimedia Commons.

Frequently, journals will devote a whole issue to a particular theme, maybe even to a single species (even whole journals are seemingly devoted to Arabidopsis thaliana…). But rarely will they be devoted to a single journal article. Well, such is the power of ‘Ledbetter and Porter (1963)’ that the July 2013 issue of the Plant Journal pays due homage to that seminal publication.

Why does L&B ’63 deserve this honour? Simply stated, that rather modest paper, entitled ‘A “microtubule” in plant cell fine structure’, virtually single-handedly initiated a whole new area of plant cell biology research – the role of the cytoskeleton, particularly in connection with cell wall formation. Its trend-setting and iconic status can largely be traced back to some of the most influential ‘throw-away’ comments ever penned, such as, ‘It is noted that the cortical tubules are in a favored position to… exert an influence over the disposition of cell wall materials. In this regard it may be of some significance that the tubules just beneath the surface of the protoplast mirror the orientation of the cellulose microfibrils of the adjacent cell walls’ (from the article’s abstract).

Nowadays, after a further half-century of study, elements of the plant cytoskeletonespecially tubulin-constructed microtubles, actin-based microfilaments, and cytoskeleton-associated proteins – have been implicated in many aspects of plant cell biology and continue to provide fruitful areas of investigation. Many dimensions of those new and emerging microtubule-rooted areas of study are covered in the issue’s 12 review articles. And with titles such as ‘The role of the cytoskeleton and associated proteins in determination of the plant cell division plane’, ‘Microtubules and biotic interactions’, ‘Microtubules in viral replication and transport’, ‘Microtubules, signalling and abiotic stress’ and ‘Cytoskeleton-dependent endomembrane organization in plant cells: an emerging role for microtubules’, you begin to appreciate the true nature of the debt owed to that original Ledbetter and Porter article. But the best bit of all this? Each of the dozen review articles and the Editorial by Peter Hepler, Jeremy Pickett-Heaps and Brian Gunning are all… FREE(!). What a great teaching resource! Thank you, Plant Journal.

[A question for those who know more about such things than I: why are microtubules still permitted to be called microtubules, whilst microfilaments are almost overwhelmingly termed actin filaments in modern scientific literature…? Is it because the corresponding term ‘tubulin tubules’ would seem slightly silly? If so – and for consistency (surely, an admirable scientific principle?) – why don’t we go back to those simpler times of microtubules and microfilaments? – Ed.]

 

Focus on transfer cells

Image: Kelvin Song/Wikimedia Commons.

Image: Kelvin Song/Wikimedia Commons.

I love transfer cells. They are plant cells (which is great), but with a difference; they are ‘specialized parenchyma cells that have an increased surface area, due to infoldings of the plasma membrane. They facilitate the transport of sugars from a sugar source, mainly leaves, to a sugar sink, often developing fruits. They are found in nectaries of flowers and some carnivorous plants’. Those plasma membrane infoldings are the result of cell wall ingrowths and transfer cells (TCs) appear to have been present in angiosperms for over 50 million years.

The term ‘transfer cell’ was coined in recognition of proposed general functions in transferring solutes between interconnected protoplasts (symplast) and non-living spaces (apoplast) in or surrounding the plant. TCs are found in many widely dispersed plant types and their importance probably lies in their role in nutrient distribution, as they facilitate high rates of transport at sites that might otherwise present ‘bottlenecks’ for apo-/symplasmic solute exchange; e.g. crop yield in many species may ultimately depend as much upon proper functioning of internal TCs as it does on externally applied fertiliser(!). So, the more that is known about development, etc, of TCs the better for all of us. Well, good news then that Kiruba Chinnappa et al. have developed phloem parenchyma TCs in Arabidopsis as an experimental system to identify transcriptional regulators of wall ingrowth formation. Exploiting this system, they’ve so far identified ‘master switches’ that respond to various inductive signals to co-ordinate wall ingrowth deposition in TCs. Ultimately, the hope is that manipulation of this process may provide new opportunities for improving crop yield. I’m sure we can all wish them well in that noble endeavour.

[Ed. – And, if your appetite for TCs has now been whetted, these curious cells will feature in a future Research Topic in Frontiers of Plant Physiology to be edited by David McCurdy and Gregorio Hueros. But, if you can’t wait until then, Felicity Andriunas et al.’s article “Intersection of transfer cells with phloem biology—broad evolutionary trends, function, and induction” is available now…]

Waste not, want not…

Image: Mariana Ruiz/Wikimedia Commons.

Image: Mariana Ruiz/Wikimedia Commons.

A little while ago we looked at auxotrophic algae getting a helping hand from bacteria; now we’ll take a look at ‘proper plants’ that get a little help from animals (in a sort of mixotrophy). But it’s not exactly willing on the animal’s part! We talk of those amazing angiosperms known as carnivorous plants (‘the most wonderful plants in the world’) who supplement their nitrogen requirements by digesting animals that they often trap.

Impressive as that is,  a danger with this external digestion is that other opportunistic organisms could help themselves to the products of that expensively-produced enzyme catabolism, thereby increasing the costs of this behaviour to the carnivore. Well – and surely providing evidence that either plants are clever or that they’ve been intelligently designed –  Wolfram Adlassnig et al. report that several carnivorous plant species engage in endocytosis of intact proteins in addition to absorption of digested products.

A potential advantage of this endocytosis (a cellular process whereby cells internalise materials by ‘engulfing’ them rather than absorbing them across the cell membrane) is that it reduces the need to release enzymes into the environment (which proteins are themselves expensively-produced, nitrogen-rich molecules that are presumably not resorbed) and so lessens the chances of other organisms appropriating the results of the plant’s extra-corporeal digestive activities. Such endocytotic behaviour was detected in Nepenthes, Drosera, Dionaea, Aldrovanda, Drosophyllum and Cephalotus (but not in Genlisea and Sarracenia).

Yes, I know what you’re thinking. No, not that this is a nice bit of plant cell biology/ecology (which it is!), but what on earth is a non-arabidopsis paper doing in the Plant Journal…? Well, maybe that organ’s own coverage will one day be as broad as the Annals of Botany’s, which would be evidence for plant evolution!

 

Adlassnig, W., Koller‐Peroutka, M., Bauer, S., Koshkin, E., Lendl, T., & Lichtscheidl, I. K. (2012). Endocytotic uptake of nutrients in carnivorous plants. The Plant Journal.

Free paper — Cytogenetic characterization and genome size of the medicinal plant Catharanthus roseus (L.) G. Don

The genome size and organization of the important medicinal plant Catharanthus roseus is shown to correspond to 1C = 0.76 pg (~738 Mbps) and 2n=16 chromosomes. The data  in this recently published paper provide a sound basis for future studies including cytogenetic mapping, genomics and breeding.

The Vacuole: not just an empty hole!

The vacuole is the largest organelle of a plant cell. It accumulates proteins, ions and secondary metabolites while providing turgor for cell growth via water content. It is also a major site for the degradation of macromolecules. A full understanding of the vacuole’s roles in salt and metal ion accumulation and water uptake are hot topics in current research. It is a necessity to understand these processes for potential exploitation in production of future stress tolerant crops. How the vacuole is made and where it comes from remain unanswered questions. What we do know is a plant without vacuoles is a dead plant (Rojo et al 2001)!

The simplest view is of a single vacuole fulfilling all roles. However, to achieve such a diverse set of functions, specialised vacuoles must exist; a single vacuole cannot function as a storage compartment and dustbin at the same time! Lytic Vacuoles (LVs) are hydrolytic, acidic compartments responsible for the breakdown of a variety of macromolecules, while Protein Storage Vacuoles (PSVs) accumulate proteins in storage organs such as seeds. Up until a few years ago it was thought these two vacuole types could coexist. It now appears their coexistence in a single cell is a rare occurrence (Frigerio et al 2008). PSVs are only found in seeds, whilst LVs are prominent in vegetative tissues. Interestingly, the PSV alters it’s identity and function to become an LV during development (Marty 1999 and Zheng et al 2011).

One way researchers identify different vacuoles is by visualising proteins at the vacuolar membrane, such as aquaporins. Aquaporins are membrane channels that transport water and other small molecules; some of which do so at the vacuolar membrane, the tonoplast. These are called Tonoplast Intrinsic Proteins (TIP) and are used as vacuole ‘markers’. In the model plant Arabidopsis thaliana, 10 TIP isoforms exist (Johanson et al 2001). Different isoforms are expressed at different stages of development and in different plant organs. The most recent expression map of these isoforms to date uses translational fluorescent protein fusions to highlight isoforms at different tissues in the root (Gattolin et al 2009). By having an expression map of TIPs, researchers can begin to understand functional differences between isoforms, which could have different roles in water uptake.  The most common markers are TIP3;1 which exclusively labels PSVs in the developing embryo, and TIP1;1 which labels LVs post germination.

Stained plant cells

Left: Arabidopsis leaf epidermal cells, LV tonoplast shown in green using fluorescently tagged TIP1;1. Right: Mature Arabidopsis embryo cotyledon cells, PSV marked using fluorescently tagged TIP3;1 (http://www.illuminatedcell.com/Vacuolarsystem.html)

Confocal microscope images using these markers have most recently been compiled in video form, with a chirpy accompanying song in which the vacuole introduces itself. Created by Dr Anne Osterrieder of Oxford Brookes University in collaboration with Dr Lorenzo Frigerio and PhD student Charlotte Carroll at the University of Warwick; the video and accompanying song are part of a series of organelle teaching aids. Enjoy!

You can read more about vacuoles at The Illuminated Cell, who kindly provided the image of the tagged plant cells.

References

FRIGERIO L, HINZ G, ROBINSON D.G. (2008). Multiple vacuoles in plant cells: rule or exception? Traffic 9:1564-1570. doi:10.1111/j.1600-0854.2008.00776.x

GATTOLIN S, SORIEUL M, HUNTER P.R, KHONSARI R.H, FRIGERIO L. (2009) In vivo imaging of the tonoplast intrinsic protein family in Arabidopsis roots. BMC Plant Biology 9:133. doi:10.1186/1471-2229-9-133

JOHANSON U., KARLSSON M., JOHANSSON I., GUSTAVSSON S., SJOVALL S., FRAYSSE L., WEIG A.R., KJELLBOM P. (2001) The complete set of genes encoding major intrinsic proteins in Arabidopsis provides a framework for new nomenclature for major intrinsic proteins in plant. Plant Physiology 126:1358-1369. doi:10.1104/pp.126.4.1358

MARTY F. (1999) Plant Vacuoles. Plant Cell 11:587-600. doi:10.1105/tpc.11.4.587

ROJO E, GILLMOR S, KOVALEVA V, SOMERVILLE C.R, RAIKHEL N.V. (2001) VACUOLELESS1 Is an Essential Gene Required for Vacuole Formation and Morphogenesis in Arabidopsis. Developmental Cell 1:303-310. doi:10.1016/S1534-5807(01)00024-7

ZHENG H. and STAEHELIN A.L. (2011) Protein Storage Vacuoles Are Transformed into Lytic Vacuoles in Root Meristematic Cells of Germinating Seedlings by Multiple, Cell Type-Specific Mechanisms. Plant Physiology 155:2023–2035. doi:10.1104/pp.110.170159

Free paper — Dividing without centrioles

Innovative MTOCs organize mitotic spindles in bryophytes, the earliest extant lineages of land.
Triple staining of γ-tubulin, microtubules, and nuclei here reveal that three types of MTOCs initiate spindles in bryophytes. Polar organizers in liverworts and plastid MTOCs in hornworts are unique and nuclear envelope MTOCs in mosses appear like those in seed plants.

  • Roy C. Brown and Betty E. Lemmon

Dividing without centrioles: innovative MTOCs organize mitotic spindles in bryophytes, the earliest extant lineages of land plantsAoB PLANTS  http://dx.doi.org/10.1093/aobpla/plr028

Plant cell biology in the frame!

Image: Andrew Maule, Wikimedia Commons.

Image: Andrew Maule, Wikimedia Commons.

Notwithstanding the centuries we’ve spent peering at, poking, prodding and penetrating the inner workings of plant cells with various types of microscopes and decades undertaking investigations at the sub-cellular level, there are still new discoveries to be made. Here are two, united by the theme of cell–cell transport. First, the recent revelation by Deborah Barton et al. (The Plant Journal 66: 806–817, 2011) that small molecules – up to 10.4 kDa in size – can move between adjacent plant cells via the plasmodesmata. No, that’s not the news, the novelty is the fact that this transport took place within the lumen of the endoplasmic reticulum, which extends between adjacent cells and constitutes the desmotubule, a feature within the plasmodesma itself. Investigating Nicotiana trichomes and Tradescantia epidermides using a fluorescent technique, the group propose that the ER lumen of plant cells is continuous with that of their neighbours, and allows movement of small ER-luminal molecules between cells. All of which adds more intrigue to these curious plant-specific cell–cell portals (http://en.wikipedia.org/wiki/Plasmodesmata). And second, that favourite feature of root anatomists, the Casparian strip, which has just given up some of its secrets. This famous endodermal wall structure acts as a barrier to apoplastic (‘extracellular’) movement of materials within the root and ‘forces’ those solutes across the semi-permeable barrier that is the plasma membrane of the endodermal cells and to follow a symplastic transport pathway. Until now it was unknown why the strip forms where it does, but Daniele Roppolo and co-workers (Nature 473: 380–383, 2011) appear to have solved that puzzle with their identification of CASPs (Casparian strip membrane domain proteins). CASPs specifically mark a membrane domain that predicts the formation of Casparian strips in the endodermal cells and are considered to be the first molecular factors that are shown to establish a plasma membrane and extracellular diffusion barrier in plants. And a timely reminder of the pivotal role that plant cell biology still plays in botanical science is provided by Simon Gilroy’s article entitled ‘Plant cell biology: with grand challenges come great possibilities’ (Frontiers in Plant Science; doi:10.3389/fpls.2011.00003).