Root of the Tree: The Significance, Evolution, and Origins of the Ribosome.

[NNadir]

The paper having the title of this post is here: Root of the Tree: The Significance, Evolution, and Origins of the Ribosome (Jessica C. Bowman, Anton S. Petrov, Moran Frenkel-Pinter, Petar I. Penev, and Loren Dean Williams, Chem. Rev. 2020, 120, 11, 4848–4878)

I go through a number of scientific papers in the course of a day, but seldom am I inspired to read any in their entirety. I just go to the "good parts" and most often leave unimportant details out. (I'm the same with books; but recently, in the age of Covid and the cloture of libraries, I find myself reading some books cover to cover.) I almost never read a journal issue cover to cover, but I may find myself inspired to read one now. The current issue of Chemical Reviews is devoted largely to Scientific Reviews of the origin of life, a subject that has fascinated me ever since my high school biology teacher described the Miller Urey experiment. I didn't know doodley squat about chirality then, but nevertheless, the interest in the prebiotic origins - and for that matter the abiotic origin of chirality - have fascinated me during my long life. What better time is there to muse on the origins of life as one's own life winds down. I hope I find and have the time to read this issue in its entirety.

This particular paper is really striking, inasmuch as it touches on the key structure at the interface of the two main classes of molecules that have been the subject of speculation as the originating molecules, peptides/proteins/amino acids and nucleic acids: The ribosome.

This is a very long paper, and I can only excerpt a tiny portion, but if one finds a way to these papers, and one is interested in this mysterious topic, "why and how life?," one may find some fascinating discussion.

All cells contain ribosomes, the cellular structures that translate DNA/RNA into the proteins that basically run life's machinery. (Thomas Cech and others found that RNA can also catalyze molecular transitions.)

The partnership between RNA and protein dominates biology. The durability of this ancient partnership is documented in the universal tree of life (TOL), which is the lineage of the translation system. Woese and Fo 1,2) sketched out a universal TOL revealing the blueprint of the common origins and biochemical interrelatedness of all living systems. This TOL contains three primary branches, which are the bacterial, archaeal, and eukaryotic superkingdoms of life. More recent determinations of the TOL, using concatenated sequences of ribosomal proteins (rProteins), increased the resolution and accuracy of the tree.(3,4) TOLs now incorporate reconstructed genomes of unculturable organisms from a variety of environments.(5,6) In the most recent TOLs, eukarya branches from within archaea.(6,7) The last universal common ancestor of life (LUCA) lies at the first branch point of the TOL. Extant biology is the crown. The origin of life occurred within the root of the TOL. As a system to organize and frame vast amounts of information, the TOL is on par with the Periodic Table.

The ribosome, made from RNA and protein, is responsible for synthesizing all protein in living systems. The ribosome is composed of a small ribosomal subunit (SSU) that decodes mRNA and a large ribosomal subunit (LSU) that catalyzes peptidyl transfer. To make a protein, the ribosome initiates, interprets an mRNA codon (decodes), transfers an amino acid from a tRNA to a nascent peptide, translocates, repeats the last three of these steps over and over again, and ultimately terminates synthesis at an mRNA stop codon.(8?12) In Bacteria, new peptide bonds are formed at a rate of ?20 amino acid additions per second. The functional core of the SSU is the decoding center (DCC) and the functional core of the LSU is the peptidyl transferase center (PTC). The distribution of ribosomal functions within rRNA secondary structures is shown in Figure 1. Aminoacyl-tRNA synthetases (aaRSs) enforce the genetic code by joining amino acids to their cognate tRNAs...

...2.1. Universality of the Ribosome

Genes encoding the translation machinery dominate the universal gene set of life (UGSL),(13?15) which is the set of protein-encoding genes that are shared as orthologues throughout the TOL and are found in essentially every living system. Koonin’s version of the UGSL contains around 65 genes.(14) Fifty-three of these are directly involved in translation, including 34 genes for rProteins (Figure 2) and genes for aaRSs and translation factors. The Pace(13) and Doolittle(15) versions of the UGSL are very similar to that of Koonin. The USGL is larger and even more translation-centric if it is expanded to include nontranslated genes such as those encoding rRNAs and tRNAs. A few constituents of the USGL are involved in transcription and even fewer in replication. There are no genes for metabolism, membrane biosynthesis or proton pumps in the UGSL.

The universality of translation across living systems extends beyond sequence homology to three-dimensional structures. Ribosomal and other translational components are universal in three-dimensions for all living systems (Figures 3, 4, and 5).(17?20) The extreme structural conservation of the DCC and the PTC(21?23) is illustrated in Figure 3. All ribosomes, from large bacterial to even larger archaeal ribosomes to gigantic mammalian ribosomes, are built upon the same basal structure, which we call the universal common core. The universal common core has a mass of nearly 2 million Daltons.(18,19)...

The point of the review is the understanding that this structure, the ribosome, is rather universal and is thus an essential point to consider in the origins of life.

Now I'll share some "science porn" with the captions...



The caption:

Figure 1. Functional regions of rRNA. (a) Information mapped onto the E. coli SSU rRNA secondary structure. CPK indicates the central pseudoknot; FPK is the functional pseudoknot. (b) Information mapped onto the E. coli LSU rRNA secondary structure. A plurality of LSU rRNA is assigned to the exit tunnel (cyan), indicating that it performs a principal function of the LSU. The second shell of the exit tunnel provides buttressing for the first shell of the exit tunnel. Regions of multiple function, for example, rRNA that contributes to both the A-site and the PTC, are striped with two colors. Strand termini and select helices are indicated. Domains are indicated on the SSU rRNA. Domains are not indicated on the LSU rRNA where they have no physical significance. Interactions with ribosomal proteins are not included.

The caption:

Figure 2. The Tree of Life mapped with universal and superkingdom-specific ribosomal proteins. The line width of the TOL is weighted by the total number of rProteins in a given superkingdom. Universal rProteins are listed in white text in the black region at the bottom. Bacteria-specific rProteins are in the blue region on the right, and Archaea-specific rProteins are in the lime-green region in the center. Eukarya-specific rProteins are in the red region on the left. All Archaea-specific rProteins are found in Eukarya, and thus, no rProteins are unique to Archaea. This rProtein nomenclature is consistent with the TOL; rProteins in Eukarya that are of archaeal ancestry are labeled as archaeal. This rProtein naming scheme, by incorporating evolutionary relationships into rProtein names, is intended to facilitate understanding of the evolution of the translation system. Adapted with permission from ref (16), where a dictionary of various rProtein naming schemes can be found.

The caption:

Figure 4. The universal common core of rRNA mapped onto the secondary and three-dimensional structures of rRNAs of a bacterium and an archaeon. The SSU (left) contains the 16S rRNA and the LSU (right) contains the 23S and 5S rRNAs. Red (SSU) and blue (LSU) indicate common core rRNA. Black or gray indicate rRNA that is not part of the common core and is variable in structure or absent from some species. (a) The rRNA of the bacterium E. coli. (b) The rRNA of the archaeon P. furiosus. Some sites of insertion of microexpansion segments are indicated by dashed lines in the archaeon secondary structure. Each three-dimensional structure is viewed from the solvent exposed surface of the assembled ribosome, with the subunit interface directed into the page. E. coli, PDB 4V9D, and P. furiosus, PDB 4V6U. Adapted with permission from ref (19).

The caption:

Figure 5. The universal common core mapped onto the secondary and three-dimensional structures of rRNAs of the eukaryote S. cerevisiae. The SSU (left) contains the 18S rRNA, and the LSU (right) contains the 26S, 5.8S, and 5S rRNAs. Red (SSU) and blue (LSU) indicate common core rRNA, as in the previous figure. Some sites of insertion of expansion segments are indicated by dashed lines. S. cerevisiae: PDB 4V88. Adapted with permission from ref (19).

And where bugs like us fit in to this key:




The caption:

Figure 11. Secondary structures of ES7 mapped onto the canonical eukaryotic TOL. Colors indicate the extent of conservation of ES7 rRNA. Blue is Helix 25, part of the universal common core. Green rRNA is universal to all eukaryotes except those with reduced genomes. Yellow is universal to metazoans. Red is tentacle rRNA. Tentacles reach extreme lengths in birds and mammals.

And how all this life might have arisen from simplicity:



The caption:

Figure 17. The coevolution of LSU rRNA, SSU rRNA, tRNA, and proteins. Six phases of the accretion model lead to the LUCA ribosome. In phase 1, RNAs form stem-loops and minihelices that begin to accrete. In phase 2, the PTC is formed and catalyzes condensation in the absence of coding. The SSU may have a single-stranded RNA binding function. In phase 3, the subunits gain mass. At the end of phase 3, the interface is acquired and the subunits associate, mediated by the expansion of tRNA from a minihelix to the modern L-shape. LSU and SSU evolution is independent and uncorrelated during phases 1–3. In phase 4, evolution of the subunits is correlated. The ribosome is a noncoding diffusive ribozyme in which proto-mRNA and the SSU act as positioning cofactors. In phase 5, the ribosome expands to an energy-driven, translocating, decoding machine. In phase 6, the ribosome matures, marking completion of the common core with a proteinized surface (the proteins are omitted for clarity). The colors of the rRNA and rProtein phases are the same as in Figures 13c,d, and 15. mRNA is shown in light green. The A-site tRNA is magenta, the P-site tRNA is cyan, and the E-site tRNA is dark green. Adapted with permission from ref (114).

A little beauty on a beautiful day.

I wish you a pleasant, safe, and healthy afternoon.

[jeffreyi]

1. Science porn indeed!

Thx for taking the time to post all this...