List of "biological primitives"/bionumbers in aging (and ways to measure them)

In flies, loss of function mutations in genes encoding components of Polycomb Repressive Complex 2 (PRC2)—an H3K27me3 specific methyltransferase complex—result in decreased levels of H3K27me3 and increased lifespan

PTM crosstalk relevant to longevity is histone bivalency where two histone PTMs that normally oppose each other (H3K4me3 and H3K27me3) act synergistically in combination to promote a unique intermediate state of chromatin that appears “poised” for gene activation

SIRT6 T294 phosphorylation site is particularly interesting given the role of SIRT6 in regulating lifespan. A more thorough phylogenetic analysis of T294 reveals that it is only present in a few long-lived groups such as old-world primates, cetaceans, beavers, tree squirrels, as well as David’s myotis bat; however, the majority of mammals appear to lack this site. Consistent with its potentially important role, phosphorylation of T294 is the most highly observed modification of human SIRT6 (cataloged in the PhosphoSitePlus database);[94] yet, several studies failed to reveal its role. T294 resides outside of the highly conserved sir-tuin catalytic domain within a proline-rich region that bridges to a less conserved C-terminus that may facilitate protein–protein interactions.[95] Substitution of T294 with glutamic acid (T294E) that in many cases would mimic a constitutive phosphorylation did not affect SIRT6 nuclear (or nucleolar) localization.[96] Similarly, alanine substitution (T294A) did not reduce SIRT6’s ability to stimulate DNA repair after oxidative stress

Since PTMs are not directly genetically encoded, engineering these features in vivo was beyond reach until recently. Novel engineering strategies such as protein ligation/splicing, non-natural amino acid mutagenesis, or inactive CRISPR/Cas9-fusion protein-based localization of epigenetic modifiers may permit the engineering of designer PTMs/proteoforms in vivo.[104] We expect that future proteomics studies of longevity will incorporate these approaches to correlate PTMs/proteoforms with lifespan.

Moreover, an AP site is a location in DNA that has neither a purine or a pyrimidine base due to DNA damage, they are the most prevalent type of endogenous DNA damage in cells. AP sites can be generated spontaneously or after the cleavage of modified bases, like 8-OH-Gua

Moreover, oxidative DNA damage like 8-oxo-dG contributes to carcinogenesis through the modulation of gene expression, or the induction of mutations.[54] On the condition that 8-oxo-dG is repaired by BER, parts of the repair protein is left behind which can lead to epigenetic alterations, or the modulation of gene expression

The term G4 DNA was originally reserved for these tetramolecular structures that might play a role in meiosis.[5] However, as currently used in molecular biology, the term G4 can mean G-quadruplexes of any molecularity. Longer sequences, which contain two contiguous runs of three or more guanine bases, where the guanine regions are separated by one or more bases, only require two such sequences to provide enough guanine bases to form a quadruplex. These structures, formed from two separate G-rich strands, are termed bimolecular quadruplexes. Finally, sequences which contain four distinct runs of guanine bases can form stable quadruplex structures by themselves, and a quadruplex formed entirely from a single strand is called an intramolecular quadruplex.[17]

#bionumbers
Guanine (G) bases in G-quadruplex have the lowest redox potential causing it to be more susceptible to the formation of 8-oxoguanine (8-oxoG), an endogenous oxidized DNA base damage in the genome. Due to Guanine having a lower electron reduction potential than the other nucleotides bases,[53]8-oxo-2’-deoxyguanosine (8-oxo-dG), is a known major product of DNA oxidation

#DNArepair
AP site damage was found to be predominant in PQS regions of the genome, where formation of G-quadruplex structures is regulated and promoted by the DNA repair process, base excision repair (BER).[49] Base excision repair processes in cells have been proved to be reduced with aging as its components in the mitochondria begin to decline, which can lead to the formation of many diseases such as Alzheimer’s disease (AD).[50] These G-quadruplex structures are said to be formed in the promoter regions of DNA through superhelicity, which favors the unwinding of the double helical structure of DNA and in turn loops the strands to form G-quadruplex structures in guanine rich regions.[51] The BER pathway is signalled when it indicates an oxidative DNA base damage, where structures like, 8-Oxoguanine-DNA glycosylase 1 (OGG1), APE1 and G-quadruplex play a huge role in its repair. These enzymes participate in BER to repair certain DNA lesions such as 7,8-dihydro-8-oxoguanine (8-oxoG), which forms under oxidative stress to guanine bases.[52]

https://sci-hub.st/https://www.nature.com/articles/s41591-020-01182-9

). The cellular turnover time
is defined based on cell death and not on cell differentiation. For
example, in our analysis of blood cells, we included their time as
undifferentiated progenitors in their overall cell lifespan (Methods).
We found that the total turnover rate of the human body is
0.33 ± 0.02 × 1012 (330 ± 20 billion) cells d−1 (equal to about 4million
cells s−1). About 86% of these cells are blood cells, mostly of bone
marrow origin. Almost all of the remaining 14% are gut cells. The
three major contributors to the cellular turnover of the human body
are jointly responsible for about 96% of the total turnover: eryth -
rocytes (RBCs), neutrophils and intestinal and stomach epithelia.

Interestingly, proteins enriched in the insoluble fraction of
CMA-deficient brains display a 20-fold higher supersaturation
score indicating that they are part of the metastable proteome
(the one at risk of aggregation). Furthermore, we noted that
proteins containing KFERQ-like motifs are at higher risk of
misfolding, indicating a tight relationship between the col-
lapse of the metastable proteome and CMA deficiency. These
findings support the idea that the protein inclusions observed
in the brains of CKL2A-/- mice originate from the inability to
timely degrade soluble forms of prone-to-aggregate proteins
that leads to their subsequent precipitation.

The properties of the residues that constitute the motif, rather than the specific amino acids, determine whether the CMA-targeting chaperone HSC70 can bind to this region9. The motif is always flanked by a glutamine on one of the sides (as the pentapeptide functions as a targeting sequence in both directions) and contains one or two of the positive residues K and R, one or two of the hydrophobic residues F, L, Ior V andone of the negatively charged E or D residues. Approximately 40% of proteins in the mammalian proteome contain a canonical KFERQ-like motif. In addition, in some substrate proteins, the same targeting motif can be generated through post-translational modifications, thus expanding the number of potential CMA substrates. Phosphorylation of S, T or Y present in a motif containing only four of the canonical residues and missing the negatively charged one can complete the motif and convert the protein to a CMA substrate2326. In some instances, Q can be replaced by K, which upon acetylation acquires properties similar to Q, thus completing the motif 27,28. Ubiquitylation or acetylation of the same K could, in theory, become a switch between proteasomal and lysosomal degradation. Characteristics of canonical or putative CMA motifs and recommendations for motif validation are described in Box 1.

https://www.ncbi.nlm.nih.gov/books/NBK9879/

effects of protein crowding - https://www.pnas.org/content/117/46/28614

Strikingly, amphisomes displayed the similar motility pattern: reduced retrograde (18.04% ± 1.74%), but not anterograde transport in the same axons of AD neurons (Figure 2F,G). We also quantified the average retrograde velocity and run length of Rab7-marked organelles in WT and hAPP mutant neurons (Figure 2H). Consistent with previous studies (Castle et al., 2014; Deinhardt et al., 2006), the average retrograde velocity and run length of Rab7-associated LEs in WT neurons were 0.40 ± 0.01 μm/sec and 56.97 ± 2.02 μm, respectively, which were significantly reduced in AD neurons (velocity: 0.10 ± 0.007 μm/sec, p<1×10−14; run length: 17.95 ± 1.18 μm, p<1×10−12). Altogether, these observations indicate that aberrant accumulation of amphisomes in distal AD axons may result from impaired retrograde transport. Moreover, we showed increased levels of APP (2.05 ± 0.29; p=0.015952) and C99 (6.13 ± 1.07; p=0.008705), but not C83 (1.18 ± 0.10; p=0.16055) in mutant hAPP Tg neurons relative to those of neurons from WT littermates (Figure 2—figure supplement 1C,D).

We also examined the co-localization of LC3 with Rab5-labeled early endosomes in cultured neurons from mutant hAPP Tg mice. We found that about 46% of LC3-labeled AVs co-localized with early endosomes within the axon of mutant hAPP neurons (45.58% ± 2.24%; n = 47, v = 875) (Figure 2—figure supplement 1H). However, Rab5-marked early endosomes moved either a short distance, or in an oscillatory pattern along axons (Figure 2—figure supplement 1I). While our observation is consistent with the results from previous studies (Cai et al., 2010; Chen and Sheng, 2013), the motility of axonal early endosomes showed no significant change in mutant hAPP neurons relative to that of WT neurons (WT: 67.53% ± 1.97; hAPP: 70.93% ± 2.31%; p=0.268) (Figure 2—figure supplement 1J). A recent study reported that nascent AVs gain retrograde transport motility by recruiting LE-loaded dynein-Snapin motor-adaptor complexes after fusion with Rab7-associated LEs to form amphisomes (Cheng et al., 2015a, 2015b). Thus, our data supports the notion that fusion of AVs with Rab5-endosomes could be a transitional process before they further mature into Rab7-positive amphisomes to gain long-distance retrograde transport motility.

RNA and proteins: