see also:

• cellular physiology - endoplasmic reticulum

• contains the genetic material (DNA), RNA to create proteins, and proteins to maintain correct folding and functioning of the nucleus components as well as transport across the nucleus membrane

• 1st discovered in the mid 1950s using an electron microscope and named in 1958
• these are minute complexes of rRNAs and proteins which interact with mRNA and tRNA to manufacture proteins from amino acids
• cytosolic ribosomes are often associated with the intracellular membranes that make up the rough endoplasmic reticulum
• each ribosome is composed of small (30S) and large (50S) components, called subunits, which are bound to each other:
  • 30S has mainly a decoding function and binds to the mRNA
    • binds to messenger RNAs and uses their sequences to determine the correct sequence of amino acids to generate a given protein
    • the start codon in all mRNA molecules has the sequence AUG
    • the stop codon is one of UAA, UAG, or UGA - there are no tRNA molecules that recognize these codons, the ribosome recognizes that translation is complete
  • 50S has mainly a catalytic function and binds to the aminoacylated tRNAs
    • amino acids are selected and carried to the ribosome by transfer RNA (tRNA) molecules, which enter the ribosome and bind to the messenger RNA chain via an anti-codon stem loop
    • for each coding triplet (codon) in the messenger RNA, there is a unique transfer RNA that must have the exact anti-codon match, and carries the correct amino acid for incorporating into a growing polypeptide chain
    • the catalytic peptidyl transferase activity that links amino acids together is performed by the ribosomal RNA
• when a ribosome finishes reading an mRNA molecule, the two subunits separate and are usually broken up but can be reused
• more than one ribosome may move along a single mRNA chain at one time (as a polysome), each “reading” a specific sequence and producing a corresponding protein molecule
• mitochondrial ribosomes of eukaryotic cells functionally resemble many features of those in bacteria, reflecting the likely evolutionary origin of mitochondria
• P-stalk ribosomes (PSRs) ¹⁾
  • an immune alert-state sub-population of ribosomes defined by the presence of the P-stalk
  • cytokines reshape the ribosome by regulating P-stalk incorporation and this is partially regulated by TGF-β-mediated phosphorylation
  • act as master regulators of cytokine-mediated processes

• the cells of all animals, plants and fungi contain specialised criss-crossing of tubes and membranes called endoplasmic reticulum (ER)
• endoplasmic reticulum is essentially a factory in which proteins, lipids and hormones are manufactured, folded into their three-dimensional structure and modified
• ER also controls calcium concentrations in the cell and forms the basis for the cellular transport system, feeds misfolded proteins to intracellular disposal and renders toxins that have entered the cell harmless
• ER within a cell is constantly being remodeled via a process of ER-phagy (self-digestion which degrades faulty or unneeded ER)
  • ER-phagy is driven by the protein ubiquitin which:
    • changes the shape of part of the FAM134B protein and causes the FAM134B clusters to become more stable and the ER to bulge out more at these sites. The stronger membrane curvature then leads to further stabilization of the clusters and, moreover, attracts additional membrane curvature proteins. So the effect of ubiquitin is self-reinforcing. ²⁾
    • also effects the membrane curvature protein called ARL6IP1 which is also part of the ER-phagy processes
• role in ferroptosis mediated cellular death:
  • the first cellular membranes susceptible to lipid peroxidation are the endoplasmic reticulum-mitochondrial contact sites (EMCSs). EMCSs not only expand rapidly in response to lipid peroxidation, but also play a key role in spreading the damaging lipids to mitochondria. In turn, this causes an increase in the production of reactive oxygen species (ROS) and fragmentation of these energy-producing organelles, which amplifies cellular damage.
  • disrupting the physical link between the endoplasmic reticulum and mitochondria significantly reduced the accumulation of harmful lipid peroxides. This “untethering” effect effectively shields cells from undergoing ferroptosis. Conversely, enhancing and stabilizing the ER-mitochondria connections intensifies PL peroxidation and accelerates cell death.³⁾

• mitochondria provide power to the cell
• mitochondria have their own DNA (“mtDNA”), a small circular strand with about three dozen genes which is a remnant from bacteria which settled in our single celled ancestors 1.5 billion years ago
• mtDNA is packaged by proteins and forms uniform, evenly-spaced membrane-less droplets within mitochondria called nucleoids
  • when stressed, these droplets can fuse together forming larger droplets which may be a cause of cellular senescence⁴⁾
• NUMTs
  • mitochondrial DNA has occasionally “jumped” out of the mitochondria and into human chromosomes creating DNA insertions called nuclear-mitochondrial segments - NUMTs (“pronounced new-mites”) which have been accumulating in our chromosomes for millions of years - most humans have hundreds of these inherited NUMTs which seem to be benign
  • a new inherited NUMT becomes integrated into the human genome about once in every 4,000 births.
  • in addition, somatic NUMTs can occur during a lifetime within neurons, esp. the prefrontal cortex in response to cellular stress, and these seem to signal a shorter human lifespan and aging ⁵⁾
• a newly discovered protein HKDC1 has been found to be crucial in maintaining the health of mitochondria and lysosomes
• mitophagy is the controlled removal of damaged mitochondria
  • there are various mitophagy pathways, and the most well-characterized of these depends on proteins called PINK1 and Parkin and this process is dependent upon HKDC1 which co-localizes with a protein called TOM20, which is located in the outer membrane of the mitochondria. A protein called TFEB controlls the expression of the gene which encodes HKDC1, and this is up-regulated during periods of mitochondrial or cellular stress. HKDC1 also interacts with the protein VDAC and then TRPML to repair lysosomes. HKDC1 thus helps prevent DNA damage induced cellular senescence by maintaining mitochondrial and lysosomal homeostasis. ⁶⁾

• have enzyme systems which help to clean up organelles and proteins within the cell that are no longer required

• cytonemes are thin, long, hair-like projections on cells which are important during neural development
• they connect cells, communicating across vast distances by transport of signaling molecules
• during development, one way cells know when to adopt a specific fate is by responding to distinct thresholds of signaling proteins called morphogens
  • “cells will respond differently to these signals across a signaling gradient, taking on different characteristics in response to high and low concentrations of a particular morphogen. A good gradient is necessary for development; a bad gradient can spell disaster.” ⁷⁾
• prevented signaling proteins from entering cytonemes disrupts neural development in mouse models, causing major neurological defects

• many proteins within the cell are for regulating cellular functions, providing transport systems across cell membranes or as enzymes to break down substances
• others are manufactured for export out of the cell as hormones, neurotransmitters, transporters and other functions
• examples:
  • sirtuins
    • a nicotinamide adenine dinucleotide (NAD+)-dependent protein lysine deacylase enzyme family that regulates many life-essential functions and play a crucial role in various age-related diseases and in regulating metabolism and stress responses
  • morphogens
    • signaling proteins which are used in cytonemes to send signals to other cells, especially during development
  • E3 ubiquitin ligases
    • there are over 670 E3 genes each of which produce different E3 ligase proteins⁸⁾
    • these ligases act as cellular ‘gatekeepers’, deciding which proteins should be activated, silenced and destroyed by attaching ubiquitin onto proteins to ‘tag’ them, helping the cell control what proteins do and whether they are repaired, relocated, or destroyed

• sodium, potassium and calcium in particular have crucial roles in the function of cells

• glucose
• fatty acids
• ketones
• ATP, etc

• these are the essential building blocks for manufacturing protein

• see cytokines

• spermidine
  • a compound present in all living cells
• acylspermidines
  • a family of metabolites derived from modifications of diverse proteins, many of which play essential roles in growth and cell survival
  • some of these interact with sirtuin enzymes and are involved in vital biochemical processes, including central energy metabolism and amino acid metabolism and impact cellular life span and cell proliferation ⁹⁾

• electrical fields on cell surfaces appear to play critical roles in the differentiation of embryonic cells and their role and positional development within tissues and organs

• the acoustic signal transduction pathway is initiated at focal adhesions, induces Ptgs2 response via FAK phosphorylation, and increases PGE2 activity against the EP4 receptor, activating a gene set, which consequently, the cells reinforced focal adhesions and expanded their adhesion areas.¹⁰⁾
  • this response appears to be markedly higher in 3T3-L1 preadipocytes
    • adipocyte differentiation is affected by PGE2 via EP4 receptor signalling24,25. Ptgs2 expression is suppressed in developed white adipose tissues, which is directly related to reduced PGE2 production and increased fat mass in the tissue - this suggests the potential for regulating adipocyte activity through acoustic stimulation

• cellular senescence is a permanent cell cycle arrest that can be triggered by both internal and external genotoxic stressors, such as telomere dysfunction and DNA damage
• impaired ceramide transport¹¹⁾
  • ceramides, a group of fat molecules, are produced inside cells' endoplasmic reticulum (ER) and transported by the ceramide transfer protein to the cell's Golgi complex. There, they are converted into another class of lipids known as sphingomyelin.
  • ceramides are essential to cell function, but only at the right levels and in the right location.
  • if this ceramide transport process becomes impaired, causing ceramides to accumulate inside the ER, it can trigger a ER stress response that can ultimately push the cell into replicative senescence
  • ceramides are also involved in apoptosis - during apoptosis, ceramides build up at the mitochondria and weaken mitochondrial membranes. It's a fatal wound that the cell cannot recover from.
• the execution of senescence is mainly by two pathways, p16/RB and p53/p21, which lead to CDK4/6 inhibition and RB activation to block cell cycle progression
  • the regulation of p53/p21 signaling in response to DNA damage and other insults is well-defined
    • p53 signals p21 which blocks CDK2-cyclin E and CDK4/6 kinases - Cyclin D leading to RB activation which promotes G1 cell cycle arrest and senescence
  • p16/RB process but its regulation remained poorly understood:
    • during natural aging, there is a gradual accumulation of p16-expressing senescent cells in tissues
    • PR55α/PP2A in blocking p16/RB signaling and IR-induced cellular senescence was discovered in 2023 ¹²⁾
      • ectopic PR55α expression in normal pancreatic cells inhibits p16 transcription, increases RB phosphorylation, and blocks IR-induced senescence
      • PR55α function in the regulation of p16 and senescence is p53-independent as it was unaffected by the mutational status of p53
      • PR55α only affects p16 expression but not p14 (ARF) expression, which is also transcribed from the same CDKN2A locus but from an alternative promoter
      • in normal human tissues, levels of p16 and PR55α proteins were inversely correlated and mutually exclusive
      • p16 protein blocks CDK4/6 kinases - Cyclin D leading to RB activation which promotes G1 cell cycle arrest and senescence