Hibernation Factor
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A hibernation factor is a
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
used by cells to induce a dormant state by slowing or halting the cellular
metabolism Metabolism (, from ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cellular processes; the co ...
. This can occur during periods of stress, randomly in order to allocate "designated survivors" in a population, or when bacteria cease growth (enter stationary phase). Hibernation factors can do a variety of things, including dismantling cellular machinery and halting gene expression, but the most important hibernation factors bind to the
ribosome Ribosomes () are molecular machine, macromolecular machines, found within all cell (biology), cells, that perform Translation (biology), biological protein synthesis (messenger RNA translation). Ribosomes link amino acids together in the order s ...
and halt
protein production Protein production is the biotechnological process of generating a specific protein. It is typically achieved by the manipulation of gene expression in an organism such that it expresses large amounts of a recombinant gene. This includes the ...
, which consumes a large fraction of the energy in a cell.


Ribosome hibernation

Ribosome hibernation occurs when ribosome hibernation factors bind to the ribosome and halt protein production. Ribosome hibernation is almost ubiquitous in
bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
, as well as in the
plastids A plastid is a membrane-bound organelle found in the cells of plants, algae, and some other eukaryotic organisms. Plastids are considered to be intracellular endosymbiotic cyanobacteria. Examples of plastids include chloroplasts (used for photo ...
of plants, and may also be present in
eukaryotes The eukaryotes ( ) constitute the domain of Eukaryota or Eukarya, organisms whose cells have a membrane-bound nucleus. All animals, plants, fungi, seaweeds, and many unicellular organisms are eukaryotes. They constitute a major group of ...
. Ribosome hibernation factors can simply inactivate ribosomes (RaiA, Balon), link pairs into inactive dimers called 100 S ribosomes (RMF and HPF), or interfere at various stages of the translation cycle (RsfS, YqjD, SRA, and EttA). One indicator of ribosome hibernation is the presence of a large number of 100S ribosomes, which can constitute up to 60% of the ribosomes in a cell at a time.


RMF, RaiA, and HPF

Three proteins, RMF, RaiA, and HPF, are only found in the large class of bacteria
gammaproteobacteria ''Gammaproteobacteria'' is a class of bacteria in the phylum ''Pseudomonadota'' (synonym ''Proteobacteria''). It contains about 250 genera, which makes it the most genus-rich taxon of the Prokaryotes. Several medically, ecologically, and scienti ...
. RMF (Ribosome modulation factor) is a small protein, typically produced under nutrient starvation and stress conditions, that is the main factor in the formation of 100S ribosomes. During the formation process, RMF binds together 70S (standard) ribosomes to form 90S ribosome dimers. These 90S dimers are converted by HPF (hibernation promoting factor) to form mature 100S dimers. A third protein, RaiA (ribosome-associated inhibitor A) is thought to both inactivate 70S ribosomes alone and stabilize them, preventing them from being converted into 100S ribosomes. Most non-gammaproteobacteria, as well as some plant plastids, instead contain a HPF homologue that can form 100S ribosomes by itself.


Balon

Balon (Spanish "ball", after homologue Pelota) is a hibernation factor protein found in the cold-adapted bacterium '' Psychrobacter urativorans.'' The protein was discovered accidentally by a researcher who unintentionally left a sample of ''P. urativorans'' in an ice bucket for too long, cold-shocking it, through subsequent cryo-EM scans of the organism's ribosomes. Unlike other factors, Balon can bind to the ribosome while protein production is in process. This is important for rapid response to stress because in some cells, protein production can take up to 20 minutes to complete. Balon does this by rather than physically blocking the A site of the ribosome, as other hibernation factors do, binding near to but not across the channel, allowing it to attach to the ribosome independent of whether protein production is taking place. Genetic relatives of Balon have been found in 20% of bacterial genomes catalogued in public databases, but are absent from ''
Escherichia coli ''Escherichia coli'' ( )Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Escherichia'' that is commonly fo ...
'' and ''
Staphylococcus aureus ''Staphylococcus aureus'' is a Gram-positive spherically shaped bacterium, a member of the Bacillota, and is a usual member of the microbiota of the body, frequently found in the upper respiratory tract and on the skin. It is often posi ...
'', the most widely used models for cellular dormancy.


RsfS

RsfS (Ribosome silencing factor S) inhibits translation by preventing the
30S The prokaryotic small ribosomal subunit, or 30Svedberg, S subunit, is the smaller subunit of the 70S ribosome found in prokaryotes. It is a complex of the 16S ribosomal RNA (rRNA) and 19 proteins. This complex is implicated in the binding of tr ...
and
50S 50 S is the larger subunit of the 70S ribosome of prokaryotes, i.e. bacteria and archaea. It is the site of inhibition for antibiotics such as macrolides, chloramphenicol, clindamycin, and the pleuromutilins. It includes the 5S ribosom ...
subunits of the ribosome from binding to each other again after they split during ribosome recycling. It has also been suggested to be a ribosome biogenesis factor rather than a hibernation factor.


SRA

SRA (Stationary-phase-induced Ribosome-Associated protein) is not well understood as of 2018. It is a small protein of 45 amino acids and is tightly associated with the 30S ribosomal subunit. It increases from an average of 0.1 molecules per ribosome to 0.4 per ribosome during the transition to stationary phase and remains so for several days.


YqjD

YqjD is an inner membrane protein specific to stationary phase. It binds to 70S and 100S ribosomes and has been proposed as of 2018 to mediate the localization (moving) of hibernating ribosomes to the cell membrane. While cells lacking YqjD do not have altered growth rates of ribosome composition, artificially high levels of it quickly halts growth depending on the protein's ribosome-binding capability.


EttA

EttA (Energy-dependent translational throttle A) is an ATP-binding protein of the ABC-F family which is thought to modulate translation rate based on the energy level of a cell. When ADP (degraded ATP, indicating low energy) levels are high, the protein inhibits ribosome activity, allowing translation at high ATP levels. EttA interferes specifically after the formation of the first
peptide bond In organic chemistry, a peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another, along a peptide or protein cha ...
in the new protein and before the first translocation step induced by
EF-G EF-G (elongation factor G, historically known as translocase) is a prokaryotic elongation factor involved in mRNA translation. As a GTPase, EF-G catalyzes the movement (translocation) of transfer RNA (tRNA) and messenger RNA (mRNA) through th ...
.


References

{{reflist Molecular biology Metabolism