In eukaryotes As the building-blocks for the
organelle, production of rRNA is ultimately the
rate-limiting step in the synthesis of a
ribosome. In the
nucleolus, rRNA is synthesized by
RNA polymerase I using the specialty genes (
rDNA) that encode for it, which are found repeatedly throughout the
genome. The genes coding for 18S, 28S and 5.8S rRNA are located in the
nucleolus organizer region and are transcribed into large precursor rRNA (pre-rRNA) molecules by
RNA polymerase I. These pre-rRNA molecules are separated by external and internal spacer sequences and then
methylated, which is key for later assembly and
folding. After separation and release as individual molecules, assembly proteins bind to each naked rRNA strand and fold it into its functional form using cooperative assembly and progressive addition of more folding proteins as needed. The exact details of how the folding proteins bind to the rRNA and how correct folding is achieved remains unknown. The rRNA complexes are then further processed by reactions involving exo- and endo-nucleolytic cleavages guided by
snoRNA (small nucleolar RNAs) in complex with proteins. As these complexes are compacted together to form a cohesive unit, interactions between rRNA and surrounding ribosomal
proteins are constantly remodeled throughout assembly in order to provide stability and protect
binding sites. This process is referred to as the "maturation" phase of the rRNA lifecycle. The modifications that occur during maturation of rRNA have been found to contribute directly to control of
gene expression by providing physical regulation of translational access of
tRNA and
mRNA. Some studies have found that extensive
methylation of various rRNA types is also necessary during this time to maintain
ribosome stability. The genes for 5S rRNA are located inside the
nucleolus and are transcribed into pre-5S rRNA by
RNA polymerase III. The pre-5S rRNA enters the
nucleolus for processing and assembly with 28S and 5.8S rRNA to form the LSU. 18S rRNA forms the SSUs by combining with numerous
ribosomal proteins. Once both subunits are assembled, they are individually exported into the
cytoplasm to form the 80S unit and begin initiation of
translation of
mRNA. Ribosomal RNA is
non-coding and is never translated into
proteins of any kind: rRNA is only
transcribed from
rDNA and then matured for use as a structural building block for ribosomes. Transcribed rRNA is bound to
ribosomal proteins to form the subunits of
ribosomes and acts as the physical structure that pushes
mRNA and
tRNA through the
ribosome to process and translate them. • Certain angiogenic
ribonucleases, such as
angiogenin (ANG), can translocate and accumulate in the
nucleolus. When the concentration of ANG becomes too high, some studies have found that ANG can bind to the
promoter region of
rDNA and unnecessarily increase rRNA transcription. This can be damaging to the nucleolus and can even lead to unchecked transcription and
cancer. • During times of cellular glucose restriction,
AMP-activated protein kinase (AMPK) discourages
metabolic processes that consume energy but are non-essential. As a result, it is capable of phosphorylating
RNA polymerase I (at the Ser-635 site) in order to down-regulate rRNA synthesis by disrupting
transcription initiation. • Impairment or removal of more than one
pseudouridine or 29-O-methylation regions from the ribosome decoding center significantly reduces rate of rRNA
transcription by reducing the rate of incorporation of new
amino acids. • Formation of
heterochromatin is essential to silencing rRNA transcription, without which ribosomal RNA is synthesized unchecked and greatly decreases the lifespan of the organism.
In prokaryotes Similar to
eukaryotes, the production of rRNA is the
rate-limiting step in the
prokaryotic synthesis of a
ribosome. In
E. coli, it has been found that rRNA is
transcribed from the two promoters P1 and P2 found within seven different
rrn operons. The P1
promoter is specifically responsible for regulating rRNA synthesis during moderate to high bacterial growth rates. Because the transcriptional activity of this
promoter is directly proportional to the growth rate, it is primarily responsible for rRNA
regulation. An increased rRNA concentration serves as a negative feedback mechanism to ribosome synthesis. High NTP concentration has been found to be required for efficient
transcription of the
rrn P1 promoters. They are thought to form stabilizing complexes with
RNA polymerase and the
promoters. In
bacteria specifically, this association of high NTP concentration with increased rRNA synthesis provides a molecular explanation as to why ribosomal and thus protein synthesis is dependent on growth-rate. A low growth-rate yields lower rRNA / ribosomal synthesis rates while a higher growth rate yields a higher rRNA / ribosomal synthesis rate. This allows a cell to save energy or increase its
metabolic activity dependent on its needs and available resources. In
prokaryotic cells, each rRNA gene or
operon is transcribed into a single RNA precursor that includes 16S, 23S, 5S rRNA and
tRNA sequences along with transcribed spacers. The RNA processing then begins before the
transcription is complete. During processing reactions, the rRNAs and
tRNAs are released as separate molecules.
Prokaryotic regulation Because of the vital role rRNA plays in the
cell physiology of
prokaryotes, there is much overlap in rRNA
regulation mechanisms. At the transcriptional level, there are both positive and negative effectors of rRNA transcription that facilitate a cell's maintenance of
homeostasis: • An UP element upstream of the
rrn P1 promoter can bind a subunit of
RNA polymerase, thus promoting
transcription of rRNA. •
Transcription factors such as FIS bind upstream of the
promoter and interact with
RNA polymerase which facilitates
transcription. • Anti-termination factors bind downstream of the
rrn P2
promoter, preventing premature transcription termination. • Due to the
stringent response, when the availability of
amino acids is low, ppGpp (a negative effector) can inhibit
transcription from both the P1 and P2
promoters. == Degradation ==