Ribosomal RNA strands code what Proteins ?

[Widdekind]

Ribosomes are molecularly massive structures, composed of 3 RNA strands, cradled in a cluster of 56 proteins. Those 3 RNA strands (16S + 5S,23S), and their corresponding complimentary anti-strands (16S + 5S,23S), code for what poly-peptides, i.e. would generate what proteins, if "fed" to other ribosomes ?

[CharonY]

They cannot be translated, if that is what you mean. The lack the typical signal sequences of mRNA and presumably their tertiary structure will also inhibit translation. However, you could just look at the sequence and translate them using the genetic code, if you wanted to. I have no idea what information you would like to gain from that.

[Widdekind]

for an RNA-world scenario, primitive molecular "trans-life" could possibly have been self-catalyzing complexes of RNA + Protein, similar to Ribosomes; ergo perhaps Ribosomal RNA codes for Ribosomal Proteins ?

[ecoli]

for an RNA-world scenario, primitive molecular "trans-life" could possibly have been self-catalyzing complexes of RNA + Protein, similar to Ribosomes; ergo perhaps Ribosomal RNA codes for Ribosomal Proteins ?

 

As CharonY suggested, you seem to be assuming that ribosomal RNA gets translated into protein, but it doesn't.

 

Ribosomal RNA forms complexes with ribosomal proteins, but there's no sequence similarity (not sure about the literature on this, but I assume the prevailing hypothesis is that the protein subunits got 'added' later)

[Widdekind]

From Science Daily 2012, non-Ribosomal Proteins pre-date Ribsomes.

 

"some early proteins were made before the evolution of the ribosome as a protein-manufacturing system... proteins were more ancient than the ribosomal machinery that today produces most of them

 

the proteins that catalyze non-ribosomal protein synthesis -- a complex and apparently universal assembly-line process of the cell that does not involve RNA molecules, and can still retain high levels of specificity -- are more ancient than ribosomal proteins... ribosomes were not the first biological machines to synthesize proteins...

 

RNA molecules began as co-factors that aided in protein synthesis and fine-tuned it, resulting in the elaborate machinery of the ribosome that exists today."

Non-ribosomal protein (NRP) synthesis "resembles fatty-acid synthesis"; perhaps primitive pre-cellular life employed pathways, for the biosynthesis, of fats, carbs, & proteins, which were all similar, and all before the later evolution, of Ribosomes (Cells, Genes) ? NRPs are often "siderophores", i.e. "iron carriers", that "cradle" bio-valuable Fe⁺⁺⁺ ions. By naive extrapolation, all primitive NRPs "cradled" bio-valubale metalic ions -- implying that they were bio-catalysts, i.e. enzymes, for other bio-chemical reactions. (Indeed, modern proteins are often enzymes.)

 

NRPs are synthesized, individually & uniquely, by conventional proteins (called NRP-Synthetase enzymes), themselves assembled by ribosomes, from DNA-to-RNA "blue-prints". According to said article, the fact that the NRP-S sequences were "remembered", and re-encoded into DNA genes, is note-worthy. By what mechanism, would ancient NRP-S "proto-genes" have existed, to be remembered?

 

Proteins

 

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Ribsomes ===(mRNA)=== DNA

 

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NRP-S

 

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NRP

By naive extrapolation, all primitive NRPs were enzymes (above), each "custom built", by its own NRP-S, coded by its own gene. If so, then Ribosomes centralized the assembly process; whereas before, myriad genes coded myriad NRP-S, bio-sythesizing myriad NRPs; after, myriad genes all "went to/thru the ribosome", which bio-synthesized the myriad Proteins. I.e. Ribosomes are a "universal NRP-S", capable of bio-synthesizing any Protein, so "stream-lining production", through a "central production hub".

 

Now, again according to said article, Ribosomes have been evolving bigger & bigger, with larger & larger Proteins; and longer & longer RNA strands. Ipso facto, anciently, proto-Ribosomes were small clusters, of P+RNA. And, the "active site", where mRNA attaches, on arrival from the DNA, is not the oldest part of Ribosomes; ergo, proto-Ribosomes did not communicate, with mRNA / DNA:

 

proto-Ribsome

 

(P+RNA)

 

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NRP-S

 

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NRP

Now, Ribosomes are composed of multiple "modules", each a conglomerate of P+RNA. And, before they joined, they were separate. Since we also need a "proto-gene" system, to "blue-print" all the NRP-S (which then, each individually & separately bio-syntheisze one unique NRP); we recognize, that bundles of P+RNA resemble primitive Viruses, i.e. "Protein-armored RNA". Perhaps ancient "proto-Genes", were "Protein-reinforced RNA" strands? Then ancient proto-life would have represented "armadas", of P+RNA molecules ("ships"), each the template, of a NRP-S Protein enzyme, each of which, in turn, assembled NRP "nano-tools"?

 

(P+RNA)

............

(P+RNA)

............

(P+RNA)

 

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.....................

||

.....................

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NRP-S

...............

NRP-S

...............

NRP-S

 

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.....................

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.....................

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NRP

...................

NRP

...................

NRP

Then, by fortuitous conglomeration, (P+RNA) "proto-Genes" began sticking together, accreting into "proto-Chromosomes", one of which became the Ribosome?

 

(P+RNA):(P+RNA):(P+RNA) -------> Ribosome

At some point, DNA evolved, i.e. "ruggedized RNA" (via removal of an O) that no longer needed "Protein scaffolding"; DNA was, somehow, "spun-off".

 

Perhaps "Ribosomes" date to the dawn of "cells", i.e. pre-ribosomal-proteins reflect pre-celular, molecular life? According to Science Daily 2008,

 

"evolution in the ribosome, where genetic information is translated into proteins...

 

protein translation had to be well developed when the evolution of modern cells started... So the evolution of cells and the evolution of translation are really linked to one another...

 

correlations between some ribosomal protein and RNA signatures...is evidence that the ribosomal RNA and proteins co-evolved...

 

the ribosome constitutes the core of the cellular translation mechanism, which is the sine qua non of gene expression, which is the essence of life as we know it"

[CharonY]

Urks, sorry to say, but this is a muddled piece of unfounded assumptions and more or less random intuitive leaps.

First of all, there are certain peptides that considered secondary metabolites and synthesizsed independent of the ribsomal machinery. They are not related to what is discussed in the article (initial peptide synthesis is arguably of much lower complexity than what we see today).

 

The article deals with the evolution of ribosomes. Thus, using sequence analyses they tried to figure out, which part(s) were first in the facilitation of translation. I.e. they argue that the early machinery could not be pure RNA-complexes but were early on RNA-protein complexes that coevolved and progressively increased protein quality. The result was a dominance of proteins derived from this apparatus and essentially replacing whatever worked before.

 

Thus the authors conclude that an earlier form of peptide synthesis must have existed. Although they did not elaborate that in the article.

 

It should be noted that one of the reasons why a pure RNA world appears attractive is that AFAIK we do not really have good data on self-replicating peptides. I cam across a paper once, but it is pretty much controversial. But then it is not really my field.

Edited April 4, 2012 by CharonY

[Widdekind]

First of all, there are certain peptides that considered secondary metabolites and synthesizsed independent of the ribsomal machinery.

Today, after four billion years of losing competition to Ribosomes, extra-Ribosomal Proteins (NRPs) are limited to the "molecular margins" of bio-chemistry, i.e. "secondary metabolites". But, the "relic remnants" of the NRP system, seen today, are (plausibly) a "dim echo" of the original system -- many of whose functions were replaced, by Ribosomally-generated Proteins, over the aeons. I.e. some Ribosomal Proteins, today, (plausibly) perform the functions that, 4Gya, NRPs performed (less well).

 

The result was a dominance of proteins derived from this apparatus and essentially replacing whatever worked before.

The "earlier form of peptide synthesis [which] must have existed" was referenced, in passing, as the "Non-Ribosomal Protein" (NRP) system. Wikipedia has an entry on the topic, which I cited.

 

Ipso facto, the article implies:

 

• an archaic NRP system existed >4Gya
  
• NRPs are assembled from NRP-S, which today are standard gene-encoded, Ribosomally-assembled, Proteins
  
• i.e., today, w.h.t.: DNA ---> Ribosomes ---> NRP-S ---> NRP
  
• ergo, archaically, w.h.t.: proto-ribosomes ---> NRP-S ---> NRP
  

Prima facie, implied proto-Ribosomes were "proto-Genes", composed of fragile RNA, augmented by Protein scaffolding for molecular structural support; numerous such (RNA+P) existed (originally individually, later conglomerating into multi-gene complexes), coding for numerous NRP-S/NRP molecules; with the evolution, of DNA, Genes were "backed up" onto superior DNA, and the (RNA+P) complexes remained, only to translate between DNA vs. Proteins; many NRP-S/NRP pathways were superceded, over the aeons,

 

DNA --->

Ribosomes

---> NRP-S ---> NRP

........................

\------> Protein

until today only a few "molecular fossils" remain.

 

could you recover the source you mentioned, or anything on NRPs (the Wikipedia article discusses only a single class of NRPs).

Edited April 5, 2012 by Widdekind

[CharonY]

What we see today in form of NRP does not have in any shape or form similarities to what the article alludes to. They involve multi-step enzymatic pathway that are impossible with today's well-established machinery. Just because a word sounds like what you mean, it does not necessarily mean it.

 

Earliest form is almost inevitably a simple self-replicating machinery. Reading up keywords on wiki and building up a story is a shortcut to the speculations section.

[Widdekind]

What we see today in form of NRP does not have in any shape or form similarities to what the article alludes to. They involve multi-step enzymatic pathway that are impossible with today's well-established machinery.

are you denying, that NRPs, are assembled, by NRP-Ss, which are themselves gene-encoded Proteins, assembled on Ribosomes ?

[CharonY]

Nope. And if you re-read your own statement it would be pretty clear that these pathways are absolutely not related to what the authors imply.