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Can cell exist without Ribosomes?

Can cell exist without Ribosomes?


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Last night I came across a question that goes as follows:-

Cells cannot exist without a) cell wall b) cell membrane c) mitochondria d) ribosomes

I am getting confused with option B and option D


If RBC is lacking ribosomes then where the antigen proteins on RBC are coming from ?


The most essential thing for a cell to survive is a membrane. Without a membrane there is no boundary between cell and its surroundings. A selectively permeable membrane is needed for cells (from single celled organisms to elephants and giraffes and whales) to survive. Cells will die quickly on removal of cell membrane.

The RBCs are good example of cells without mitochondria or ribosomes which survive for 120 days.


Please read the article on Erythropoiesis for detailed information on how RBCs form and how they have proteins in their surface.

In short, the RBCs acquire the surface proteins during their formation period in the bone marrow. Inside the bone marrow the premature RBCs have nucleus, ribosomes, mitochondria, etc… and produce all the required structural and functional proteins. On maturing they loose the nucleus and cell organelles and contain only hemoglobin in their cytoplasm.


Cells can survive without ribosomes, but they would accumulate damage and be unable to restore worn out or exhausted supplies of any proteins they may require. The ribosome is necessary to be able to perform protein translation from RNA. Thus, if the cell can survive without protein, then it would be able to survive without ribosomes. No known organism that exists today meets that definition, if I am not mistaken. However, at some point, it is theorized that the earliest cells were able to perform replication and metabolism without the use of protein. So, it is likely, but not something that is seen in life today.

Nicholas H. Barton Derek E.G. Briggs Jonathan A. Eisen , David B. Goldstein and Nipam H. Patel.(2010). Evolution. Cold Stone Harbor Laboratory Press.


Ribosome

Ribosomes ( / ˈ r aɪ b ə ˌ s oʊ m , - b oʊ -/ [1] ) are macromolecular machines, found within all living cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to form polypeptide chains. Ribosomes consist of two major components: the small and large ribosomal subunits. Each subunit consists of one or more ribosomal RNA (rRNA) molecules and many ribosomal proteins (RPs or r-proteins). [2] [3] [4] The ribosomes and associated molecules are also known as the translational apparatus.


Can cell exist without Ribosomes? - Biology

All living cells contain ribosomes, tiny organelles composed of approximately 60 percent ribosomal RNA ( rRNA ) and 40 percent protein. However, though they are generally described as organelles, it is important to note that ribosomes are not bound by a membrane and are much smaller than other organelles. Some cell types may hold a few million ribosomes, but several thousand is more typical. The organelles require the use of an electron microscope to be visually detected.

Ribosomes are mainly found bound to the endoplasmic reticulum and the nuclear envelope, as well as freely scattered throughout the cytoplasm, depending upon whether the cell is plant, animal, or bacteria. The organelles serve as the protein production machinery for the cell and are consequently most abundant in cells that are active in protein synthesis, such as pancreas and brain cells. Some of the proteins synthesized by ribosomes are for the cell's own internal use, especially those that are produced by free ribosomes. Many of the proteins produced by bound ribosomes, however, are transported outside of the cell.

In eukaryotes, the rRNA in ribosomes is organized into four strands, and in prokaryotes, three strands. Eukaryote ribosomes are produced and assembled in the nucleolus. Ribosomal proteins enter the nucleolus and combine with the four rRNA strands to create the two ribosomal subunits (one small and one large) that will make up the completed ribosome (see Figure 1). The ribosome units leave the nucleus through the nuclear pores and unite once in the cytoplasm for the purpose of protein synthesis. When protein production is not being carried out, the two subunits of a ribosome are separated.

In 2000, the complete three-dimensional structure of the large and small subunits of a ribosome was established. Evidence based on this structure suggests, as had long been assumed, that it is the rRNA that provides the ribosome with its basic formation and functionality, not proteins. Apparently the proteins in a ribosome help fill in structural gaps and enhance protein synthesis, although the process can take place in their absence, albeit at a much slower rate.

The units of a ribosome are often described by their Svedberg ( s ) values, which are based upon their rate of sedimentation in a centrifuge. The ribosomes in a eukaryotic cell generally have a Svedberg value of 80S and are comprised of 40s and 60s subunits. Prokaryotic cells, on the other hand, contain 70S ribosomes, each of which consists of a 30s and a 50s subunit. As demonstrated by these values, Svedberg units are not additive, so the values of the two subunits of a ribosome do not add up to the Svedberg value of the entire organelle. This is because the rate of sedimentation of a molecule depends upon its size and shape, rather than simply its molecular weight.

Protein synthesis requires the assistance of two other kinds of RNA molecules in addition to rRNA. Messenger RNA ( mRNA ) provides the template of instructions from the cellular DNA for building a specific protein. Transfer RNA ( tRNA ) brings the protein building blocks, amino acids, to the ribosome. There are three adjacent tRNA binding sites on a ribosome: the aminoacyl binding site for a tRNA molecule attached to the next amino acid in the protein (as illustrated in Figure 1), the peptidyl binding site for the central tRNA molecule containing the growing peptide chain, and an exit binding site to discharge used tRNA molecules from the ribosome.

Once the protein backbone amino acids are polymerized, the ribosome releases the protein and it is transported to the cytoplasm in prokaryotes or to the Golgi apparatus in eukaryotes. There, the proteins are completed and released inside or outside the cell. Ribosomes are very efficient organelles. A single ribosome in a eukaryotic cell can add 2 amino acids to a protein chain every second. In prokaryotes, ribosomes can work even faster, adding about 20 amino acids to a polypeptide every second.

In addition to the most familiar cellular locations of ribosomes, the organelles can also be found inside mitochondria and the chloroplasts of plants. These ribosomes notably differ in size and makeup than other ribosomes found in eukaryotic cells, and are more akin to those present in bacteria and blue-green algae cells. The similarity of mitochondrial and chloroplast ribosomes to prokaryotic ribosomes is generally considered strong supportive evidence that mitochondria and chloroplasts evolved from ancestral prokaryotes.


MOTHER OF ALL MOLECULES

While contemplating his post-graduate life, Badran found himself once again pondering the central dogma. As a student researcher, he’d seen the emergence of new tools to manipulate two of its components — DNA and RNA — but not many to modify proteins. “That’s in part because the ribosome is unwieldy and not well understood,” he said.

The ribosome has earned the nickname “mother of all molecules” for good reason. Three RNA molecules and more than 50 proteins come together to make this biological machine, one of the largest complexes in the cell. The ribosome is so essential to cellular life that probing it without killing the cell is incredibly difficult. In fact, a colleague once advised Badran that he would never get tenure by studying the ribosome. Unfazed by this warning, and with the fields of directed evolution and synthetic biology coming into their own, Badran felt the time was ripe to tinker with the cell’s protein factory.

So Badran looked beyond the usual next step of postdoctoral research. The chance to start his own lab, without the teaching responsibilities of academic research and with more time at the bench, appealed to him. As a Broad Fellow for the past few years, Badran has been free to focus on high-risk research aimed at understanding the ribosome well enough to give it new capabilities, such as building proteins that don’t exist in nature.

To do this, Badran will need to get the ribosome to learn a new language. RNA, ribosomes, and proteins communicate using three-letter “words” called codons, which tell the ribosome which amino acids to string together to form a protein. With four letters of the DNA alphabet – A, T, C, and G – there are 64 possible 3-letter codons that collectively encode for the 20 standard amino acids. While 20 building blocks are plenty for naturally occurring proteins, Badran wants to build novel proteins that incorporate non-standard or engineered amino acids that have been generated by other researchers. To do so, he’ll need a ribosome that can read more than just 64 codons.

Badran and members of his lab are using directed evolution to engineer new ribosomal parts and convince the complex to read four-letter words, which would increase the number of possible codons from 64 to 256. Some of these “quadruplet codons” would encode the 20 natural amino acids, but the rest would each alert the ribosomal complex to add one of dozens of synthetic amino acids, resulting in novel proteins with potentially useful properties. Techniques already exist to incorporate a few additional non-standard amino acids into a protein by altering one of the 64 triplet codons, but Badran’s quadruplet approach could add many different kinds of non-standard amino acids into a single protein.


Can cell exist without Ribosomes? - Biology

In short the answer to your question is "no".

A cell's cytoplasm is a complex mix of water, sugars, ions, proteins, and other molecules. Because of all these additives the cytoplasm is a very viscose liquid, probably better compared with Jell-O, than with water.

For a thing to be considered "alive", certain criteria must be fulfilled. Among these criteria are the existence of a metabolism, the capability of reproduction and reaction to external stimuli. There are others, but these three will do for the following explanation. All of them require the transport of material (chemical residues) and receptors or machines (enzymes) in form of proteins.

Without water the transport of molecules inside of a cell would break down. The cell would be left unable to react to internal or external stimuli, because no part of the cell would know what is happening in any other part. The metabolites (sugars, amino acids, etc.) necessary for life would never reach their destination. Without internal signaling the cell wouldn't know, when to start reproduction. Further, without water, the ion-concentration gradient over the membranes couldn't exist and cells would lose this helper in energy maintenance.

Worst of all, without water and ions, proteins would denaturate and cease to be functional. This happens, because the polar water coating and the loaded ions help bring a protein into it's functional form. Since proteins and nucleic acids (which would also drasticly change there conformation in lack of water) are the backbone of life as we know it, life could not exist without water as medium.

Of course, it is possible to imagine and "construct" a form of life, which is not dependent on water. I think, that a liquid as medium would be necessary in any of these constructs. Probably, that would then also qualify as cytoplasm, when it is combined with the molecules of that life-form.

Try the links in the MadSci Library for more information on Cell Biology.


Ribosomes: Structure, Composition, and Assembly (With Diagram)

We will be concerned with the organi­zation, composition, and assembly of the cytoplasmic ribosomes of prokaryotic and eukaryotic cells.

The ribosomes present in cytoplasmic organelles (e.g., chloroplast and mitochondrial ribosomes). Although func­tionally analogous, many differences exist between the ribosomes of prokaryotic and eukaryotic cells (Ta­ble 22-2).

Considerably more is known about the structure and composition of bacterial ribosomes than ribosomes of eukaryotic cells, as will become evident during the discussion that follows. Most of the work on prokaryotic ribosomes has been carried out using Escherichia coli. Although some variations are ob­served among the prokaryotes, findings using E. coli are generally representative.

Ribosomes in the cytoplasm of eukaryotic cells have a sedimentation coefficient of about 80 S (MW about 4.5 x 10 6 ) and are composed of 40 S and 60 S subunits. In prokaryotic cells, ribosomes are typically about 70 S (MW about 2.7 x 10 6 ) and are formed from 30 S and 50 S subunits.

The complete ribosome formed by combination of the subunits is also referred to as a monomer. Although ribosomes from both prokaryotic and eukaryotic sources are about 30 to 45% protein (by weight), with the remainder being ribonucleic acid, the specific protein and RNA components of these two major classes of ribosomes differ (Table 22- 2 and Fig. 22-1) carbohydrate and lipid are virtually absent.

Magnesium ions (and perhaps other cations) play an important role in maintaining the structure of the ribosome. Dissociation into subunits occurs when Mg 2+ is removed. The precise role (or roles) of Mg 2+ remains uncertain, although interaction with ionized phosphate of subunit RNA is presumed.

Prokaryotic Ribosomes:

RNA Content The small subunit of prokaryote riboso­mes contains one molecule of an RNA called 16 S RNA (MW 0.6 x 10 6 ), and the large subunit contains two RNA molecules, a 23 S RNA (MW 1.1 x 106) and a 5 S RNA (MW 3.2 x 10 4 ) (see Table 22-2). All three rRNAs are products of closely linked genes tran­scribed by RNA polymerase in the sequence 16 S 23 S 5 S. This assures an equal proportion of each RNA.

The rRNA operon also contains genes for some tRNAs (Fig. 22-2). The transcription product of the rRNA operon consists of a 30 S RNA this transcript is successively cleaved and trimmed to produce the fi­nal 16 S, 23 S, and 5 S RNAs that are incorporated into the small and large ribosomal subunits. Figure 22-2 presents the scheme of maturation of the pro­karyotic rRNAs.

For clarity, the incorporation of the ribosomal proteins is not shown. Ribosomal proteins combine with the rRNAs at various stages of subunit assembly: some are incorporated during transcrip­tion, others following release of the primary tran­script and during processing, and still others once the mature rRNA products are formed. Certain proteins bind to the rRNAs only transiently and are not found in the fully assembled subunits.

Multiple copies of the rRNA genes occur in the genomes of prokaryotic (and eukaryotic) cells (Table 22-3) this is known as reiteration. In E. coli the num­ber of rRNA genes is estimated to be between 5 and 10 and accounts for about 0.4% of the cell’s total DNA. The primary structures of the three prokaryotic rRNAs have been extensively studied. 5 S RNA was identified in 1963 and, being the smallest of the three rRNAs (about 120 nucleotides), was sequenced first (in 1967).

Analyses of the nucleotide sequence of the E. coli 16 S RNA (1542 nucleotides) and 23 S RNA (2904 nu­cleotides) have recently been completed and the sec­ondary structure of the 16 S RNA is shown in Figure 22-3. Methylation of certain bases in the sequence of 16 S RNA (and also in the sequence of 23 S RNA) oc­curs while transcription is taking place. No methyla­tion of 5 S RNA nucleotides occurs.

Unlike 5 S RNA in which duplication of certain sequences occurs, no repeated sequences are found in 16 S and 23 S RNA. The rRNAs contain a number of double-helical regions that are stabilized by conventional, complementary base pairing. In E. coli 16 S rRNA, about half of all nucleotides present are involved in base pairing. Several palindromes (base sequences reading the same from either the 5′ or 3′ ends) exist in 16 S RNA, and these may play a role in restricting the for­mation of the double-helical regions.

In 16 S RNA, a seven-nucleotide segment of the chain at the 3′ end is believed to interact with mRNA, leading to its binding during the initiation of translation. The 5 S and 23 S RNAs interact with one another in the large subunit, and both appear to be involved in aminoacyl-tRNA and peptidyl-tRNA binding during polypeptide chain elongation. Because the 16 S RNA as well as several proteins of the small subunit interact with 23 S RNA, the latter RNA may also have a role in subunit associ­ation.

Ribosomal RNA transcripts are not translated into proteins (i.e., rRNAs cannot serve as messengers), however, ribosomal proteins are the products of a typi­cal transcription-translation process. Protein Content Nomura, Kurland, and others have established that the small prokaryotic ribosomal subu­nit contains 21 different protein molecules these are identified as S1, S2, S3 . . . S21. The large subunit contains 34 proteins (L1, L2, L3 . . . L34) but only 31 are different, that is, four copies of one of the proteins are present.

The genes for the 52 different ribosomal proteins together with those for the three RNAs con­stitute about 5% of the genome of the bacterial cell. All the ribosomal proteins have been isolated and characterized, and nearly all have been fully se­quenced. The small subunit proteins range in molecu­lar weight from 10,900 to 65,000 and the large subunit proteins vary in molecular weight from 9600 to 31,500 (Table 22-4). Most of the ribosomal proteins are basic in nature, being rich in basic amino acids and having isoelectric points around pH 10 or higher.

An exhaus­tive analysis of the primary structures of prokaryotic ribosomal proteins done in order to evaluate their de­gree of homology indicates that these proteins did not have a common evolutionary ancestor. Homologies among them do not occur more often than would be expected on a random basis.

tRNA-Protein Interaction:

Lake, Nomura, Wittmann, Traut, Stoffler, Kurland, and others have studied the relationships between the three rRNAs and the ribo­somal proteins and have shown that about 30 proteins bind specifically and directly to the rRNAs these are the primary binding proteins.

Those proteins that do not bind directly to rRNA (i.e., the secondary binding proteins) interact with the primary binding proteins in the assembled ribosome. Figure 22-4 shows that ap­proximate regions of 16 S RNA with which the small subunit proteins associate. It is believed that the back­bone of the 16 S RNA polynucleotide winds its way among the proteins, with interactions occurring be­tween hairpin turns of the RNA and surface residues of the protein molecules.

Assembly of Prokaryotic Ribosomes:

Because all of the proteins and RNAs of the prokary­otic ribosome subunits may be isolated, it is possible through recombination studies to examine the assem­bly process. Nomura and others have shown that the assembly of individual subunits and their association to form functional ribosomes (i.e., ribosomes capable of translating mRNA into protein) occur spontane­ously in vitro when all the individual rRNAs and pro­tein components are available.

Thus the ribosome is capable of self-assembly, and this is believed to be the mechanism in situ. The assembly is promoted by the unique and complementary structures of the riboso­mal protein and RNA molecules and proceeds through the formation of hydrogen bonds and hydrophobic in­teractions. There is order to the assembly in that cer­tain proteins combine with the rRNAs prior to the ad­dition of others. Cooperativity also exists, because addition of certain proteins to the growing subunit facilitates addition and binding of others.

No self-assembly takes place when L proteins are added to 16 S RNA or when S proteins are added to 5 S and 23 S RNA. However, it is interesting to note that RNA from the 30 S subunit of one prokaryotic species will combine with the S proteins of another prokaryote to form functional subunits. The same is true for 50 S subunit proteins and RNAs from differ­ent prokaryotes.

Assembly of hybrid subunits and for­mation of functional monomers from these occur in spite of the fact that ribosomal proteins and RNAs from different prokaryotes have different primary structures. It is clear that their secondary and ter­tiary structures, which are very similar, are more im­portant in guiding rRNA-protein interactions. Al­though some proteins from yeast, reticulocyte, and rat liver cell ribosomes can be replaced by E. coli ribo- somal proteins, hybrid monomers formed from these prokaryotic-eukaryotic subunits will not function in protein synthesis.

Model of the Prokaryotic Ribosome:

Based on the available electron-microscopic data, results of small-angle X-ray analysis, and, of course, chemical studies, and several proposals can be made about the structure of the ribosome monomer and its sub- units. The 30 S subunit approximates a prolate ellip­soid of revolution (Fig. 22-5a).

A transverse partition or groove encircles the long axis of the subunit, divid­ing it into segments of one-third (i.e., the head) and two-thirds (i.e., the base). A small protuberance called a platform extends from the base. The 50 S subunit is somewhat more spherical and possesses a flattened region on one surface (Fig. 22-5a). Extending from the main body of the large subunit are a stalk and central protuberance. Association of the subunits to form the 70 S monomer is depicted in Figure 22-5b.

There is considerable morphological and biochemical evidence supporting the idea that the small tunnel formed between the two subunits upon their associa­tion (Fig. 22-5b) is the site of mRNA and aminoacyl- tRNA binding during protein synthesis (Fig. 22-5c).

(1) In many electron photomicVographs of polyribosomes, the thin mRNA’ strand seems to “disappear” into the ribosomes

(2) In vitro experi­ments have shown that when the synthetic messenger polyU is associated with the 70 S monomer, the poly­nucleotide is protected from ribonuclease attack over a length of about 70 to 120 nucleotides and

(3) Trans­fer RNA is protected from cleavage by nuclease when associated with the ribosome. The observation that small nascent (i.e., growing) polypeptides are pro­tected from proteolysis suggests that a stretch of the polypeptide chain may be enclosed within a second tunnel formed in the large subunit (Fig. 22-5c).

Genes for Ribosomal RNA and Protein:

The genome of E. coli and other prokaryotes consists of a single, long, circular DNA molecule supercoiled and packed into the “nuclear” region of the cell. The E. coli chromosome is about 1100 nm long and ap­pears to contain at least three separate regions coding for rRNA. Each region contains closely linked 5 S, 23 S, and 16 S rDNA genes.

Because some 5 to 10 cop­ies of each gene occur in the genome, more than one copy of each gene is likely present in each rDNA re­gion. Genes coding for ribosomal proteins are present in at least two separate regions of the E. coli chromo­some. The same regions also appear to contain genes for RNA polymerase, some transfer RNAs, and the elongation factors required for protein biosynthesis.

Lake, Nomura, and others have employed the tech­niques of immune electron microscopy and neutron diffraction to map the surface of the ribosomal sub- units and identify the positions of the ribosomal pro­teins (Fig. 22-6).

Eukaryotic Ribosomes:

The cytoplasmic ribosomes of eukaryotic cells differ from those of prokaryotes in both size and chemical composition (Table 22-2, Fig. 22-1). The monomer has a sedimentation coefficient of 80 S and is formed from 40 S and 60 S subunits. In addition, ribosomes occur in two states in the cytoplasm.

They may be as­sociated with cellular membranes such as those of the endoplasmic reticulum (i.e., “attached” ribosomes) and engaged in the synthesis of secretory, lysosomal, or membrane proteins or they may be freely distrib­uted in the cytosol. The functional differences be­tween attached and free ribosomes will be pursued later, but let us turn first to a consideration of the chemical and morphological characteristics of eukary­otic ribosomes.

The small subunit of the eukaryotic ribosome contains one molecule of 18 S RNA (MW 0.7 x 10 6 ) and large subunit contains 28 S (MW 1.7 x 10 6 ), 5 S (MW 3.2吆 4 ), and 5.8 S (MW 5 x 1(H) RNAs. Hence, in addition to molecular weight or size differences, a major distinction between the RNA complements of prokaryotic and eukaryotic ribosomes is the presence of an additional molecule of RNA (i.e., 5.8 S RNA) in the large subunit of eukaryotes.

18 S, 5.8 S, and 28 S rRNAs are the transcription products of closely linked genes in the chromosomes of the nucleolar organizing region (NOR) of the cell nucleus. Considerable redundancy exists as hundreds, perhaps even thousands, of copies of these rRNA genes are believed to be present (see Table 22-3). The genes for 5 S RNA are not present in the NOR but oc­cur elsewhere in the nucleus. Consequently, unlike prokaryotes in which the 5 S RNA genes are linked to the genes for other rRNAs, the 5 S RNA genes of eukaryotes occur separately in the nucleus.

Figure 22-7 depicts the transcription and post- transcriptional processing of eukaryotic rRNAs. As in prokaryotes, transcription of DNA is mediated by the enzyme RNA polymerase however, in eukaryotes there are three forms of this enzyme, each producing different transcription products.

The RNA poly­merases of, prokaryotes and eukaryotes are compared in Table 22-5. The high-molecular-weight primary transcript, 45 S RNA, contains the precursors of 18 S, 5.8 S, and 28 S rRNAs. About half of the 45 S RNA molecule is represented by spacer sequences at the 5′ end of the transcript and between the presumptive rRNAs. The spacers are removed during processing.

As shown in Figure 22-7, the 5.8 S RNA produced during processing becomes hydrogen bonded to the 28 S RNA and the complex is incorporated into the 60 S subunit. Not shown in Figure 22-7 but discussed later is the incorporation of the ribosomal proteins. It should be noted that 5 S RNA is a primary transcrip­tion product and is not the product of posttranscriptional trimming.

Various studies have established that the small subunits of eukaryotic ribosomes con­tain about 33 proteins (S1, S2, S3, etc.) and the large subunits 45 proteins (L1, L2, L3, etc.). The proteins of eukaryotic ribosomes are not only more numerous but also have greater average molecular weights than those of prokaryotic ribosomes (Table 22-4). From a chemical standpoint, eukaryotic ribosomal proteins have similar general properties as those in prokary­otes (e.g., rich in basic amino acids, high isoelectric point, etc.). Certain eukaryotic and prokaryotic ribo­somal proteins reveal homologous regions, and these homologous proteins appear also to be functionally similar.

Nucleolar Organizing Region:

Eukaryotic cells con­tain several hundred copies of the genes encoding rRNA. These genes are arranged in a tandem fashion on one or more chromosomes of the nucleus. The DNA sequences between successive rDNA regions are not transcribed and represent spacer DNA. The rRNA genes and the spacer segments are usually looped off the main axis of the chromosome and are referred to as the nucleolar organizing region. It is here that most of the rRNA is synthesized. The NOR coalesces with nuclear proteins and forms visible bodies known as nucleoli.

Most eukaryotic cells contain one or a few nucleoli, but certain egg cells are a striking exception. The oocytes of amphibians (e.g., the clawed toad, Xenopus laevis) are extremely large cells and are en­gaged in the synthesis of especially large quantities of cellular protein. These cells produce large numbers of ribosomes in order to provide the means to sustain such quantitative protein synthesis.

Accordingly, it is not unusual to find hundreds or thousands of nucleoli (and NORs) in the nuclei of these cells. Such large numbers of nucleoli are the result of gene amplifica­tion—the differential replication of the rRNA genes of the genome. The ribosomes produced in the oocyte serve its needs for protein synthesis from the period prior to fertilization through the first few weeks of embryonic development.

By gently dispersing nuclear fractions isolated from oocytes of the amphibian Triturus viridescens and “spreading” the material on grids, 0. L. Miller and B. R. Beatty in 1969 were able to obtain photomicro­graphs showing transcription in progress. Since then, a number of other investigators have extended the same approach to mammalian oocytes and to spermat­ocytes and embryo cells from various organisms. The visualization of transcriptional activity is achieved most easily with spread nucleoli because of the high degree of rDNA gene amplification (Fig. 22-8).

The tandem rDNA genes are serially transcribed by RNA polymerases to produce 45 S rRNA. The rRNA (ap­parently complexed with protein) appears as a series of fibrils of varying length extending radially from an axial, linear DNA fiber (Fig. 22-9).

This feather- shaped or “Christmas tree” regions are called matrix units. The spaces between successive matrix units are nontranscribed spacer DNA segments. The ribonucleoprotein (RNP) fibrils are seen to be in various stages of completion. The short fibrils near the tip of each feather are RNA molecules whose synthesis has only just begun and the longest fibrils represent RNA molecules whose synthesis is almost complete. Hence, the direction of rDNA transcription is apparent in the photomicrograph. In high magnification views (Fig. 22-9), even the RNA polymerase enzyme molecules carrying out the transcription of the DNA are visible along the axial DNA fiber.

Success in visualizing transcription has not been re­stricted to nucleolar genes. Almost identical results have been obtained with non-nucleolar chromatin. Here, however, the RNA transcripts represent mes­senger RNA.

Dispersed and spread nuclear fractions contain non- transcribing DNA as well as matrix units (Fig. 22-9). The succession of nucleosomes reveals it­self as a series of beadlike structures along the DNA fiber. Regions in which DNA is undergoing replication (called replicons) can also be seen (Fig. 22-10). S. L. McKnight and O. L. Miller have shown that DNA of homologous “daughter” fibers of the replicon also oc­curs as chains of nucleosomes, suggesting that repli­cation may not require dissociation of nucleosomes or that nucleosomes are almost immediately reformed. Transcriptional activity can be iden­tified within a replicon (Fig. 22-11), indicating that the newly synthesized DNA is almost immediately available for transcription. The growing RNA fibrils are seen in homologous regions of both chromatid arms of the replicon.

Assembly of Eukaryotic Ribosomes:

The assembly of eukaryotic ribosomes is more complex than that of prokaryotic ribosomes. The principal stages of the process are outlined in Figure 22-12. Transcribed 45 S RNA combines with proteins in the nucleolus to form ribonucleoprotein complexes.

However, not all the protein molecules of the complex become a part of the completed ribosomal subunit. Instead, certain pro­teins are released as RNA processing ensues these “nucleolar proteins” return to a nucleolar pool and are reutilized. Those proteins that are retained during processing and become part of the completed subunits are, of course, legitimately called “ribosomal pro­teins.”

In the same sense, not all of the RNA of the complex becomes part of the ribsomal subunits, for the spacer is also processed out. (It should be noted that the spacer RNA is produced by transcription of rDNA and not the spacer DNA between genes.) Pro­cessing produces three classes of fragments. One class contains spacer RNA and nucleolar proteins.

The spacer RNA is hydrolyzed and the free nucleolar proteins return to the pool. A second class of RNP fragments contains a complex of 18 S RNA and cer­tain ribosomal proteins that give rise to 40 S subunits. The third class of RNP fragments, which contains 38 S and 5.8 S RNA and ribosomal proteins, combines with 5 S RNA transcribed from extranucleolar rRNA genes and gives rise to 60 S subunits.

Like the genes for 45 S RNA, the extranucleolar 5 S RNA genes oc­cur in multiple tandem copies. Among the various pro­teins synthesized in the cytoplasm using ribosome subunits derived from the nucleus are the ribosomal proteins themselves. These apparently reenter the nu­cleus for incorporation into new RNP complexes.

Model of the Eukaryotic Cytoplasmic Ribosome:

In spite of the differences in overall sizes (as mani­fested in the greater molecular weights, sedimenta­tion constants, sizes, and numbers of RNAs and pro­teins), the cytoplasmic ribosomes of eukaryotes are remarkably similar in morphology to those of prokaryotes. As in 20 S subunits of prokaryote ribosomes, the 40 S eukaryote subunit is divided into head and base segments by a transverse groove (Fig. 22-13).

The 60 S subunit is generally rounder in shape than the small subunit, although one side is flattened this is the side that becomes confluent with the small sub- unit during the formation of the monomer (Fig. 22- 13). The synthesis of proteins that are to be dis­patched into the intracisternal space of the endoplas­mic reticulum (ER) is carried out by ribosomes that attach to the membranes of the ER. As seen in Figure 22-13, attachment occurs via the large subunit.

Free and Attached Ribosomes:

The cytoplasmic ribosomes of eukaryotic cells can be divided into two classes: (1) attached ribosomes and (2) free ribosomes (Fig. 22-14). Attached ribosomes are ribosomes associated with intracellular membranes, primarily the endoplasmic reticulum, whereas free ribosomes are distributed through the hyaloplasm or cytosol. Attached and free ribosomes are chemically the same.

Although all animal and plant cells contain both attached and free ribosomes, the proportion of each varies from one tissue to another and can be caused to shift within a tissue in response to the administration of certain substances, notably hormones and growth factors. Membranes of the endoplasmic reticulum that con­tain attached ribosomes constitute what is called “rough” ER (or RER) and membranes that are devoid of ribosomes are called “smooth” ER (SER).

For many years, there has been considerable contro­versy about the functions of attached and free ribo­somes. The currently accepted view suggests that proteins destined to be secreted from the cell or to be incorporated into such intracellular structures as lysosomes (which may or may not release their contents to the cell exterior) are synthesized on attached riboso­mes.

For example, many of the proteins circulating in the blood plasma are derived via secretion by the liver, and these plasma proteins are known to be synthe­sized exclusively by the attached ribosomes of the liver cells. Most proteins destined to become constituents of the ER membranes or the plasma membranes are also synthesized by attached ribosomes.

Most, but not all, proteins destined for use in the cytosol are synthesized by free ribosomes. Exceptions include certain hormones like thyroglobulin, which is secreted by the thyroid gland and is syn­thesized by free ribosomes. Milk proteins produced by mammary gland cells are also synthesized by free ri­bosomes.


How SARS-CoV-2 disables the human cellular alarm system

A graphic of healthy cellular protein production (left column), compared to how SARS-CoV-2 disrupts these processes (right column). The virus disrupts the processes of splicing, translation, and protein trafficking in order to prevent the cell from calling for help during an infection. Credit: Inna-Marie Strazhnik / Caltech

As the world is more than half a year into the COVID-19 pandemic, doctors and researchers have a fairly good idea of what the main symptoms of the disease look like: cough, fever, shortness of breath, and fatigue, among others. But equally important to treating symptoms is understanding what the coronavirus that causes COVID-19, SARS-CoV-2, is doing inside human cells to make people so sick.

Like all viruses, SARS-CoV-2 breaks into a cell and hijacks its resources and machinery to create more viruses. Evolutionarily speaking, successful viruses are those that can effectively evade a cell's defenses, but refrain from killing the cell outright (after all, the virus needs the cell to remain alive to be able to reproduce).

Human cells (and, more broadly, mammalian cells) have built-in defense mechanisms to deal with viral infections. The presence of viral genetic material in a cell triggers a cascade of events that lead to the production and secretion of a group of proteins called interferon, which will try to shut down the infection and notify neighboring cells of the threat. Researchers have found that patients with severe COVID-19 symptoms also show low levels of interferon response, suggesting that the interferon response is crucial for combatting the virus. How does the virus suppress these normal defense mechanisms?

A team led by Caltech researchers has now pinpointed the mechanisms through which the SARS-CoV-2 virus incapacitates human cells, essentially disabling the cell's alarm system so that it cannot call for help or warn nearby cells of the infection. Understanding how the virus causes dysfunction at the cellular level gives new insights into how to fight it.

The research was conducted primarily in the laboratory of Mitchell Guttman, professor of biology and Heritage Medical Research Institute investigator. A paper describing the research appears online ahead of publication in the journal Cell.

The SARS-CoV-2 virus produces about 30 viral proteins. In this new research, the Guttman laboratory examined each of these and mapped out how they interact with the molecular components within human cells grown in a lab dish. They found that SARS-CoV-2 proteins attack three critical cellular processes to disrupt human protein production.

"Viruses are amazing," says Emily Bruce, faculty scientist at the University of Vermont and a co-first author on the paper. "Viruses and host cells are continually in an evolutionary arms race to outwit one another. SARS-CoV-2 has evolved intricate and specific ways to disable cells without killing them outright, so that the virus can still use the cell for its own purposes."

Some basic cell biology background first: The cell's nucleus houses its genetic material, written as DNA. This so-called genome can be thought of as a comprehensive instruction manual, with "chapters" that might be titled "How to Send a Signal" or "What to Do in Case of Viral Infection," for example. The rest of the cell contains the machinery that creates the proteins (such as interferon) that carry out these instructions.

The process for turning DNA instructions into useful proteins is called the "central dogma" of biology. The first step is transcription, through which a piece of DNA in the cell's nucleus is read and copied into a form (a molecule called mRNA) that can leave the nucleus and travel to the rest of the cell. Before export out of the nucleus, mRNA is often re-assembled and "matured" in a process called splicing (top row).

After the mRNA is exported out of the nucleus, a piece of cellular machinery called the ribosome attaches to the mature mRNA, reads it, and builds the corresponding protein through a process called translation (middle row).

Some of these proteins are designed to move outside the cell of origin to transmit messages to other cells, for example, to warn about the presence of a viral infection. In this situation, another piece of cellular machinery called the signal recognition particle comes into play it works as a kind of transport system that helps proteins move from inside to outside of a cell. This is known as protein trafficking (bottom row).

A graphic of healthy cellular protein production (left column), compared to how SARS-CoV-2 disrupts these processes (right column). The virus disrupts the processes of splicing, translation, and protein trafficking in order to prevent the cell from calling for help during an infection. Credit: Inna-Marie Strazhnik / Caltech

The Guttman lab discovered that SARS-CoV-2 proteins interfere with this whole process at multiple stages. Some of the virus's proteins prevent mRNA from being fully spliced and properly assembled. Others plug up the ribosome so that it cannot form new proteins. Still other SARS-CoV-2 proteins interfere with the signal recognition particle and block protein transport.

The protein that plugs up the ribosome is called NSP1. Remarkably, the team found, NSP1 blocks human mRNA from entering the ribosome, but allows viral mRNA to pass through just fine. Viral mRNA contains a genetic signature at the beginning of each of its mRNAs that acts like an access code that effectively hijacks the ribosome to make viral proteins but not human proteins. Because viral production depends on this signature, it could represent a potent target for anti-viral therapeutic development.

"Each of the processes that SARS-CoV-2 disrupts— splicing, translation, and protein trafficking—is so important for converting the human genetic material into proteins, and they are essential for human biology," says Guttman. "In fact, discovery of each of these processes has separately led to the awarding of a Nobel Prize. These are machines that are central to life. We cannot exist without them. SARS-CoV-2 has evolved in very specific ways to disable these cellular machines and disrupt their functions."

"Our study illustrates the importance of basic science research, and establishes a pipeline to address newly emerging RNA viruses in the future," says co-first author Abhik Banerjee, a graduate student in the Guttman laboratory. "Additionally, it illustrates the collaborative atmosphere of science at Caltech and elsewhere in the scientific community at its best. Here at Caltech, we have access to leaders in several keystone areas of biology, including professors Rebecca Voorhees (co-author on the published manuscript), Bil Clemons, and Shu-ou Shan in structural biology, all of whom were willing to discuss ramifications of our data and provide expertise in this relatively new area for us."

Mario Blanco, a research scientist in the Guttman laboratory, agrees.

"Our ability to interrogate the human RNA targets of SARS-CoV-2 proteins allowed us to identify these mechanisms without prior evidence," he says. "The methods and practices we developed here will allow us to apply these same processes to emergent diseases and even currently existing viruses where we lack a deep understanding of mechanism."

The paper is titled "SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses."


How does it work?

In order to synthesize proteins, the ribosome translates mRNA (messenger RNA) strands, which have themselves been transcribed from the DNA sequence, into the corresponding protein sequence. The sequence of the nucleotides (adenine, guanine, cytosine and uracil) in an mRNA strand corresponds to a particular sequence of amino acids, the building blocks of all proteins.

Every set of 3 nucleotides (called a codon) on an mRNA strand “codes” for, or corresponds to, 1 amino acid. As the mRNA strand passes through the ribosome, the ribosome sequentially adds on each amino acid that the mRNA sequence demands, binding the amino acids together to form a long protein strand (sometimes called a polypeptide). The RNA molecules which are responsible for delivering the amino acids to the ribosome are called tRNA (transfer RNA). Once the entire sequence has been translated, the ribosome releases the newly formed protein so it can be on its merry way!

And a lil’ something you didn’t know about the ribosome.

Not only does the ribosome perform one of the most vital functions needed to sustain life, but it also happens to serve as a detailed fossil record of the origins and evolution of life as we know it!

How can this be? Scientists (shout out to my research mentor, Dr. Loren Williams!) have found that the ribosome itself has evolved over its billions of years of existence by a process of gradual accretion – meaning new bits of proteins and RNA have been added onto the surface of previous versions of the ribosome to make newer, bigger, better ribosomes over time. As such, the most highly evolved ribosomes, such as those in our own H. sapiens cells, are larger than more primitive ribosomes, such as those used by bacterial E. coli cells. But if you peel away the “newest” layers of ribosomes in more evolved species, the precise shape of the ribosomes which their ancestors used is preserved in the core of the bigger, modern molecule! Much like we can see what a tree once looked like by observing its rings, we are able to map the evolutionary history of the ribosome by using computational modeling to dissect it down to its ancient core.

Because the process of translating DNA into protein is perhaps one of the most central functions in biology—without which life as we understand it would not exist—when we learn about the origins of the ribosome by investigating its layers as we would a molecular fossil, we are also learning key insights about the origin of life itself!


Structure

Ribosomes are made of proteins and ribonucleic acid (abbreviated as RNA), in almost equal amounts. It comprises of two sections, known as subunits. The tinier subunit is the place the mRNA binds and it decodes, whereas the bigger subunit is the place the amino acids are included.

Both subunits comprise of both ribonucleic acid and protein components and are linked to each other by interactions between the proteins in one subunit and the rRNAs in the other subunit. The ribonucleic acid is obtained from the nucleolus, at the point where ribosomes are arranged in a cell.

The structures of ribosomes include:

  • Situated in two areas of the cytoplasm.
  • Scattered in the cytoplasm and a few are connected to the endoplasmic reticulum.
  • Whenever joined to the ER they are called the rough endoplasmic reticulum.
  • Free and the bound ribosomes are very much alike in structure and are associated with protein synthesis.
  • Around 37 to 62% of RNA is comprised of RNA and the rest is proteins.
  • Prokaryotes have 70S ribosomes respectively subunits comprising the little subunit of 30S and the bigger subunit of 50S. Eukaryotes have 80S ribosomes respectively comprising of little (40S) and substantial (60S) subunits.
  • Ribosomes seen in the chloroplasts of mitochondria of eukaryotes are comprised of big and little subunits composed of proteins inside a 70S particle.
  • Share a center structure which is very much alike to all ribosomes in spite of changes in its size.
  • RNA is arranged in different tertiary structures. The RNA in the bigger ribosomes is into numerous continuous infusions as they create loops out of the center of the structure without disturbing or altering it.
  • Contrast between those of eukaryotic and bacteria are utilized to make antibiotics that can crush bacterial disease without damaging human cells.

Package deal

Pick up any biology textbook and you will find an account of the discovery of the structure of DNA in the 1950s, and how scientists worked out that certain kinds of RNA serve as a copy of that information. For many years, it was thought that all this genetic information was carried inside cells. But within a few decades, researchers began to challenge this simple view.

In 1983, a couple of years before Tosar was born, two papers were published describing the presence of tiny vesicles outside cells 4 , 5 . Soon after publication, the co-author of one of these seminal papers, biochemist Rose Johnstone, coined the term exosome. However, these discoveries faded into history, and it wasn’t until 1996, when researchers at Utrecht University discovered exosomes being churned out by immune cells 6 , that the field started to blossom.

But even then, some scientists pushed back against the suggestion that these vesicles contained RNA. Many simply refused to accept that living cells were systematically releasing genetic material. Jan Lötvall, who studies exosomes at the University of Gothenburg in Sweden, remembers the scepticism he faced when, in 2007, he reported that exosomes could shuttle RNA between cells 7 . He recalls that others scoffed at his suggestion that living cells not only release genetic material but also receive these packages from other cells. This sort of signalling between cells was a concept that people struggled to accept. Biologists knew about nerves pinging each other with electrical signals, and chemical messengers such as hormones triggering distant cells. But the idea that packages of nucleic acids were shared between cells suggested a whole new realm of cellular communication. “I lost grants when we published this,” Lötvall says. Funders were reluctant to support the follow-up experiments he proposed. Now, however, the paper has been referenced upwards of 5,000 times and is a seminal study in the field.

Cayota heard about Lötvall’s findings on extracellular genetic material and decided to encourage members of his lab, including Tosar, who was embarking on his graduate studies, to hunt for signs of this, too. Meanwhile, other scientists started producing data hinting that ribosomal components might be present outside cells. In 2009, a group at Pohang University of Science and Technology in South Korea found signs of ribosomal subunits inside the EVs that are present in the fluid around colorectal cancer cells 8 . The following year, a group at Harvard Medical School in Boston, Massachusetts, found ribosomal components in vesicles in human urine 9 . And last year, researchers found indirect evidence of ribosomes in the extracellular space. They discovered strands of extracellular messenger RNA, or ex-mRNA, that were longer than expected. This, the scientists wrote, “indicated that ex-mRNA fragments are ribosome protected”, meaning that some physical association with ribosomes might have shielded them from degrading enzymes 10 .

Tosar’s search for extracellular ribosomes outside of vesicles built on this work. What is notable about his research, however, is that he found not just fragments of ribosomes, but also evidence of fully intact ones. His peers say that Tosar is forming a case for researchers to pay more attention to the potential significance of genetic machinery in the extracellular space. “I think it’s a very big deal,” says molecular biologist Kenneth Witwer, who studies exRNA at Johns Hopkins University in Baltimore, Maryland, and who has collaborated with Tosar in the past. “He’s someone I really respect as a thinker.”

Roger Alexander, a senior scientist at the Pacific Northwest Research Institute in Seattle, Washington, has also noticed Tosar’s work. “He’s leading the charge in what I think is a very important area that has not gotten enough attention in our field,” Alexander says. “There’s a lot of interesting biology and clinical potential there.”


Abstract

Historically, the ribosome has been viewed as a complex ribozyme with constitutive rather than intrinsic regulatory capacity in mRNA translation. However, emerging studies reveal that ribosome activity may be highly regulated. Heterogeneity in ribosome composition resulting from differential expression and post-translational modifications of ribosomal proteins, ribosomal RNA (rRNA) diversity and the activity of ribosome-associated factors may generate 'specialized ribosomes' that have a substantial impact on how the genomic template is translated into functional proteins. Moreover, constitutive components of the ribosome may also exert more specialized activities by virtue of their interactions with specific mRNA regulatory elements such as internal ribosome entry sites (IRESs) or upstream open reading frames (uORFs). Here we discuss the hypothesis that intrinsic regulation by the ribosome acts to selectively translate subsets of mRNAs harbouring unique cis-regulatory elements, thereby introducing an additional level of regulation in gene expression and the life of an organism.