ElShamah Ministries: Defending the Christian Worldview and Creationism
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ElShamah Ministries: Defending the Christian Worldview and Creationism

Otangelo Grasso: This is my personal virtual library, where i collect information, which leads in my view to the Christian faith, creationism, and Intelligent Design as the best explanation of the origin of the physical Universe, life, and biodiversity

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Carboxysomes - Nanotechnology reveals hidden depths of bacterial 'machines'

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Carboxysomes - Nanotechnology reveals hidden depths of bacterial 'machines'


The ability to use light energy for the accumulation and fixation of CO2 has given cyanobacteria the ability to thrive in diverse and extreme environments. Cyanobacteria play a central role in the global carbon cycle and have changed the earth’s atmosphere by generating oxygen and depleting CO2. The CO2 concentrating mechanism (CCM) consists of active transport systems for inorganic carbon acquisition and a distinctive protein-based organelle, the carboxysome. Recent advances in structural and systems biology and biological imaging have built upon decades of biochemical and genetic research to advance our understanding of the carboxysome. 8

The shell exhibits two important properties. First, the shell creates a physical barrier between the encapsulated proteins and the cytoplasm, resulting in a cellular environment that is distinct from the cytoplasmic space. Second, the shell provides selectivity for the passage of substrate and products between the cytoplasm and the interior of the compartment.

The CO2 concentrating mechanism (CCM)  enables photosynthetic microorganisms to raise the CO2 level at the carboxylating sites, carboxysomes in prokaryotes and pyrenoids in eukaryotes, and thereby overcome the large difference (approximately 5–20-fold, in green algae and cyanobacteria, respectively) between the Km(CO2) of their carboxylating enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) and the concentration of dissolved CO2 at equilibrium with air. 9
Light energy is being used to fuel the accumulation of inorganic carbon (Ci) within the cells and to maintain the cytoplasmic CO2 concentration much lower than expected at chemical equilibrium; thereby, providing the gradient for inward diffusion of CO2 and minimizes its leak from the cells. In addition to compensating for the relatively low affinity of RubisCO for CO2, the elevation of CO2 concentration at the carboxylating site activates the enzyme.

This is an amazing find. That means, no carboxysome, no sufficient CO2 concentration, and Rubisco would not work !! That means interdependence at its best !! But it means as well, that the carboxysome is as essential and indispensable for advanced life as Rubisco, the most abundant and essential enzyme on the planet !!  How did evolution manage to get the two together to work interdependently ? 

The Carboxysome consists of a protein shell that houses the enzymes involved in carbon fixation reactions. 3 The carboxysome sequesters these enzymes from the rest of the cell. Carbon fixation reactions are sensitive to the environment and could not proceed unprotected in the cytoplasm. Carboxysomes even have pores that allow influx of the raw materials needed to carry out the carbon fixation reactions and the outgo of reaction products.
When initially detected in bacterial cytoplasm, microbiologists thought carboxysomes were viral particles that had invaded the cell. The paradigm that prokaryotes lacked internal compartmentalization was so pervasive that no
one could envision these inclusions actually being organelles. It was only after carbon fixation enzymes were found associated with carboxysomes that this deeply entrenched paradigm was abandoned. Organelles, like carboxysomes, are widespread among bacteria.  The last decade of research has overturned the traditional view of bacteria. These little "bags of molecules" actually display an incredible degree of internal organization. They also possess exquisite composition of biochemical activity in spatial and temporal terms. As microbiologists continue to probe, more examples of structural and functional organization are sure to be discovered.
Bacterial internal organization seems to be universal among microorganisms and seems to be a property necessary for life. It adds another dimension to life's minimal complexity. In other words, minimal life not only requires the simultaneous occurrence of a relatively large number of gene products but also their spatial and temporal organization.

Bacterial microcompartments, such as carboxysomes,  sequester certain enzymatic reactions that would be either inhibited by or toxic to cytoplasmic conditions. 4

That raises the question: Since the enzymatic reactions protected by carboxysomes are toxic to the cell, had they not have to be fully setup and present in the first cells ?

Carboxysomes - Nanotechnology reveals hidden depths of bacterial 'machines' Carbox10

Figure 1: Schematic view of the carboxysome. The RuBisCO and the carbonic anhydrase are surrounded by different carboxysomal shell proteins, which form a defined structure. The carbon fixation takes places inside the carboxysome.

A carboxysome is a bacterial microcompartment (BMC) surrounded by a protein shell. 1  Naturally, they occur in CO2 fixing bacteria like cyanobacteria. Therefore they are the enzyme-containing organelles for these metabolic pathways.  Carboxysomes are formed by different shell proteins, surrounding an enzyme-containing lumen, which is rigorously separated from the cytoplasm. Thus, the possibility is given to enable reaction pathways strictly with the conditions in the cytoplasm. A schematic image of the carboxysome is given in figure 1. The protein shell consists of two different types of proteins. Pentamers are used for the vertices of the icosaeder and hexamers for the facets. The main constituent of the shell is the CsoS1A protein, which contributes around 13 % of the total protein mass. Carboxysomes are between 80 and 120 nm in diameter. In the interior, there are two different types of enzymes. On the one hand, there is RuBisCO which catalyzes the carboxylation or oxygenation of ribulose-1,5-bisphosphate. This reaction is one essential step in the Calvin cycle, the pathway for carbon fixation in autotrophic bacteria. On the other hand, there is the carbonic anhydrase which converts hydrogen carbonate (HCO3-) to carbon dioxide. The resulting carbon dioxide is the substrate for RuBisCO.

The advantage of the microcompartment is the concentration of carbon dioxide in its lumen. Carboxysomes play a central role in carbon concentrating mechanisms (CCM) The reactions inside the carboxysome are illustrated in figure 2. This mechanism is used for the accumulation of CO2 in autotrophic prokaryotes. The first reaction of the CCM is the transport of atmospheric carbon dioxide or hydrogencarbonate (HCO3-) into the cells. Accumulation of inorganic carbon is achieved by transmembrane pumps and transporters localized in the cell membrane. At physiological pH values of around 7, the equilibrium is clearly on the side of hydrogencarbonate. Hydrogencarbonate is able to diffuse across the shell of the carboxysome. The carbonic anhydrase (CA), located inside the carboxysome, catalyzes the conversion of hydrogencarbonate to gaseous carbon dioxide serving as substrate for RuBisCO. The CA is associated with the shell and presents only a small number of the carboxysome proteins. CA, also called CSOS3, acts to saturate the lumen with carbon dioxide and enables high effective concentrations of CO2, due to this RuBisCO is able to work near its maximal reaction rate with high specificity. The product of RuBisCO, 3-phosphoglycerate, is used in the metabolism of the cells.  Diffusive loss of carbon dioxide is probably provided by the outer shell as it acts as a barrier.

Carboxysomes - Nanotechnology reveals hidden depths of bacterial 'machines' Carbox11

Figure 2: Reaction mechanism of the carboxysome inside the bacterial cell. CA catalyzed the conversion of hydrogencarbonate to CO2. During fixation of CO2 via ribulose-1,5-bisphosphate by RuBisCO two molecules of 3-phosphoglycerate are generated.

The protein shell, structurally resembling virus capsids, is made of multiple protein paralogs forming hexagons and pentagons, and acts as a physical barrier that controls the passage of substrates and products of enzymatic reactions. 2

Carboxysomes - Nanotechnology reveals hidden depths of bacterial 'machines' Carbox10
Another ‘unexpected’ example of convergent evolution. Carboxysomes of bacteria that are strikingly similar to the protein coats of viruses, but are independently evolved. Upper, transmission electron micrographs of carboxysomes in a cyanobacterium (Synechocystis). (a) Entire cell in the process of dividing, five polyhedral carboxysomes are visible. Scale bar, 200 nm; (b) individual carboxysome. Scale bar, 50 nm. Reproduced from fig. 1a,b  Protein structures forming the shell of primitive bacterial organelles. Science 309, 936–938; with the permission of AAAS and the authors. (c) and (d) show the alternative models for the carboxysome shell. Each is based on a shell constructed of 740 hexameral units and 12 pentamers, and the two models (c,d) differ in terms of the orientation of the hexamers. Atomic-level models of the bacterial carboxysome shell. 

Carboxysomes and viruses

Consider first the viruses. While the notion that they may be the most primitive forms of life has been largely abandoned, they do provide a useful proxy for the minimum desiderata for an organism. One of the defining characteristics of a virus is, of course, the highly organized protein coat. When we turn to the micro-compartments of a number of eubacteria, and especially the carboxysomes (figure 2), they too build a polyhedral protein coat in a strikingly similar fashion (Cannon et al. 2001Kerfeld et al. 2005Bobik 2006). To be sure the carboxysomes are not icosahedral and the coat itself is thinner (perhaps because of its organelle-like status; see Tsai et al. 2007), but the tightly packed hexameral arrangement evidently forms by self-assembly (Yeates et al. 2007), and the striking similarity between carboxysomes and viral coats has been repeatedly stressed. And with respect to viruses themselves, we see striking examples of convergence (e.g. Bull et al. 1997Cuevas et al. 2002), no small matter given their role in disease (e.g. De Lamballerie et al. 2008Kryazhimskiy et al. 2008). However, in terms of viral convergence arguably the most fascinating examples involve the giant DNA viruses, best known in the form of the mimivirus (e.g. Suhre 2005). These viruses are effectively re-inventing themselves as true organisms, with genomes substantially larger than some bacteria, and driven by both gene duplication and lateral transfer from their hosts. Significantly, however, the two principal groups (T4 and NCLDVs) are strikingly convergent in not only the methods of genome increase, but also the locations of the laterally transferred material in the viral genome (Fileé & Chandler 2008).

Bacteria: re-running the tape 5
it is not suggested that bacteria are derived from viruses (or viral coats from carboxysomes), but these examples are indicative that the evolution of viruses may be more constrained than might be imagined. So too among the prokaryotes, we find many striking convergences not only within the archaea and eubacteria, but also more significantly between these two groups. One of the most interesting, and especially important because of its misappropriation by the proponents of the scientific fiction referred to as ‘intelligent design’, is the independent evolution of the flagellar motor in either bacterial group. Among the other convergences that occur between the archaea and the ubacteria, particularly striking examples can be found among the extremophiles, notably the halophiles  and thermophiles. Given such extremophiles are a major focus of attention for what may be typical extraterrestrial environments, and recalling that thermophiles can flourish at 122°C  and in supersaturated brines, then these convergences may confer an unexpected predictability in terms of remote microbial biospheres.

This is indeed striking. The authors prefer an extremely unlikely scenario of convergent evolution, where viruses and bacterias got the same carboxysome mantle, rather than infer common design. And on top of that, calling the design inference fiction. How does that make sense ? 

Carboxysomes - Nanotechnology reveals hidden depths of bacterial 'machines' Microc11

The majority of the observed hexamers contain a central pore (coincident with the cyclic symmetry axis) that is assumed to be constitutively open. 6

Carboxysomes - Nanotechnology reveals hidden depths of bacterial 'machines' Carbox12

The structure of carboxysomes and the Rubisco octamers occupying them as determined using cryo electron microscopy. The sizes of individual carboxysomes in this organism (Synechococcus strain WH8102) varied from 114 nm to 137 nm, and were approximately icosahedral. There are on average ≈250 Rubisco octamers per carboxysome, organized into three to four concentric layers. Synechococcus cells usually contain about 5-10 carboxysomes. 7

1. http://2014.igem.org/Team:Bielefeld-CeBiTec/Project/CO2-fixation/Carboxysome
2. http://pubs.rsc.org.sci-hub.cc/en/content/articlelanding/2017/nr/c7nr02524f#!divAbstract
3. Cells design, Fazale Rana
4. https://www.alcf.anl.gov/events/carboxysome-case-study-structure-and-function-prokaryotic-organelles
5. http://rstb.royalsocietypublishing.org/content/365/1537/133
6. http://www.sciencedirect.com.sci-hub.cc/science/article/pii/S0966842X14002121
7. http://book.bionumbers.org/how-many-photons-does-it-take-to-make-a-cyanobacterium/
8. The Cell Biology of Cyanobacteria ,page 171
9. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390856/




Tiny factories
Some researchers are taking a closer look at elegant bacterial protein containers called microcompartments. First seen about 50 years ago, these polyhedron-shaped protein capsules resemble the outer shell of a virus10. But unlike viruses, which package genetic material, microcompartments contain enzymes that carry out important reactions, such as converting carbon dioxide into a form of carbon that is usable by the cell. Scientists suspect that the shells make reactions more efficient, keep toxic intermediate products away from the rest of the cell and protect enzymes from molecules that could hinder their performance.

In 2005, protein crystallographers helped to reveal the capsules' finer details. Microcompartments “simply hadn't attracted the attention yet of structural biologists”, says Todd Yeates, a structural biologist himself at the University of California, Los Angeles. He and his colleagues found that some shell proteins assemble into six-sided tiles that come together to form the sides of a microcompartment11. Each tile has a hole in the centre that could allow molecules to pass through.

In addition to having an orderly structure, microcompartments can also line up in neat rows. Pamela Silver, a synthetic biologist at Harvard Medical School in Boston, Massachusetts, and her colleagues reported12 last year that in cyanobacteria, certain microcompartments called carboxysomes “more or less stayed in a line down the centre of the cell”, says Silver. This tidy arrangement allows cells to allot carboxysomes evenly to daughter cells when dividing.

Biologists are now eager to exploit these capsules for industrial uses by loading them with different enzymes. For instance, Yeates and his team are planning to try engineering microcompartments to produce biofuel. Some researchers have managed to package fluorescent proteins or enzymes from other species into the shells, suggesting that it is possible to modify the capsules' contents.

Microcompartments still offer plenty of unexplored territory. Scientists aren't sure, for instance, exactly how enzymes are organized inside the capsules, says Cheryl Kerfeld, a structural biologist at Lawrence Berkeley National Laboratory in Berkeley, California. “We don't really know what it looks like in there.”



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