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A team of Russian scientists has determined which proteins can be safely lost in the ribosome, a composition of macromolecules found within all living cells.

The researchers are from the Skolkovo Institute of Science and Technology (Skoltech) and the Kharkevich Institute for Information Transmission Problems, both in Moscow, Russia. Their report appears in the latest journal Molecular Biology and Evolution.

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Some Ribosomes Are Incomplete, Yet They Remain Stable

Ribosomes are considered "universal cellular machines." They are found in both eukaryotes (cells with membrane-bound organelles, i.e. nucleus) and prokaryotes (those that do not). These molecular machines are responsible for synthesizing biological proteins in a process called "translation."

Ribosomes are generally made up of small and large ribosomal subunits. Each subunit has ribosomal ribonucleic acid (rRNA) proteins and ribosomal proteins (RPs).

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While these traits are generally similar across cells, previous studies have reported that there are strains of bacteria that continue to function even without a complete set of ribosomal proteins. The research team was led by Mikhail Gelfand, Skoltech Professor and Vice President For Biomedical Research, set out to analyze 214 samples of relatively small bacterial genomes.

The team was able to identify a set of "missing" proteins. Only nine ribosomal proteins were totally conserved, and the rest of the 48 other ribosomal proteins were missing in at least one bacterial strain from the sample.

"Tiny genomes are characteristic of endosymbionts, bacteria that live within other bacteria or eukaryotic cells," Gelfand explained. He added that in this relatively static environment, plus "weak selection," this genome information tends to lose to some non-essential genes. He likened it to some multicellular parasites that lack entire organs, yet still continue to function.

Gelfand also addressed the common preconception that the ribosome is the most conserved organelle with a standard and consistent protein set. Even in the current record for simplicity among bacteria, 121 genes, the Skoltech professor noted that it is impossible to "encode all fifty-something" RPs, which explains why some of these proteins are missing. In their study, researchers were able to show that determining the missing proteins are not random.


A Practice of Bacterial Decluttering

Evidence shows that the ribosomal proteins belonging to the small subunit were more conserved than those in the large subunit. Also, most of the lost ribosomal proteins were those located on the surface of the ribosome. Because of this, the proteins have fewer contacts with other parts of the ribosome.

The report also noted that these proteins were incorporated into the rest of the macromolecular machine later in evolution, suggesting that bacteria implements a "last in, first out" criteria in dropping ribosomal proteins.

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Another interesting point in the study is that the top three bacteria with the shortest genomes in the dataset also have the most missing ribosomal proteins. This suggests a positive correlation between the number of remaining RPs and the bacteria's genome size.

The researchers, however, noted that while ribosomal proteins leave a "downsizing" or "decluttering" bacterial genome, they are still among the last to leave. This is mainly because they are still a part of the ribosome, which is an essential part of most cells.