epigenetics In biology, epigenetics is the study of stable phenotypic changes (known as ''marks'') that do not involve alterations in the DNA sequence. The Greek prefix '' epi-'' ( "over, outside of, around") in ''epigenetics'' implies features that are "o ...

, proline isomerization is the effect that ''cis-trans'' isomerization of the

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...

proline Proline (symbol Pro or P) is an organic acid classed as a proteinogenic amino acid (used in the biosynthesis of proteins), although it does not contain the amino group but is rather a secondary amine. The secondary amine nitrogen is in the prot ...

has on the

regulation of gene expression Regulation of gene expression, or gene regulation, includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA). Sophisticated programs of gene expression are wide ...

. Similar to

aspartic acid Aspartic acid (symbol Asp or D; the ionic form is known as aspartate), is an α-amino acid that is used in the biosynthesis of proteins. Like all other amino acids, it contains an amino group and a carboxylic acid. Its α-amino group is in the pro ...

, the

has the rare property of being able to occupy both ''cis'' and ''trans''

isomer In chemistry, isomers are molecules or polyatomic ions with identical molecular formulae – that is, same number of atoms of each element – but distinct arrangements of atoms in space. Isomerism is existence or possibility of isomers. Iso ...

s of its prolyl peptide bonds with ease.

Peptidyl-prolyl isomerase Prolyl isomerase (also known as peptidylprolyl isomerase or PPIase) is an enzyme () found in both prokaryotes and eukaryotes that interconverts the ''cis'' and ''trans'' isomers of peptide bonds with the amino acid proline. Proline has an unusua ...

, or PPIase, is an

enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. A ...

very commonly associated with proline isomerization due to their ability to catalyze the isomerization of prolines. PPIases are present in three types: cyclophilins, FK507-binding proteins, and the parvulins. PPIase enzymes

catalyze Catalysis () is the process of increasing the rate of a chemical reaction by adding a substance known as a catalyst (). Catalysts are not consumed in the reaction and remain unchanged after it. If the reaction is rapid and the catalyst recyc ...

the transition of proline between ''cis'' and ''trans'' isomers and are essential to the numerous biological functions controlled and affected by prolyl isomerization (i.e.

cell signalling In biology, cell signaling (cell signalling in British English) or cell communication is the ability of a cell to receive, process, and transmit signals with its environment and with itself. Cell signaling is a fundamental property of all cellula ...

protein folding Protein folding is the physical process by which a protein chain is translated to its native three-dimensional structure, typically a "folded" conformation by which the protein becomes biologically functional. Via an expeditious and reproduci ...

, and epigenetic modifications) Without PPIases, prolyl peptide bonds will slowly switch between ''cis'' and ''trans'' isomers, a process that can lock proteins in a nonnative structure that can affect render the protein temporarily ineffective. Although this switch can occur on its own, PPIases are responsible for most isomerization of prolyl peptide bonds. The specific amino acid that precedes the prolyl peptide bond also can have an effect on which conformation the bond assumes. For instance, when an

aromatic In chemistry, aromaticity is a chemical property of cyclic ( ring-shaped), ''typically'' planar (flat) molecular structures with pi bonds in resonance (those containing delocalized electrons) that gives increased stability compared to satur ...

amino acid is bonded to a proline the bond is more favorable to the ''cis'' conformation. Cyclophilin A uses an "electrostatic handle" to pull proline into ''cis'' and ''trans'' formations. Most of these biological functions are affected by the isomerization of proline when one isomer interacts differently than the other, commonly causing an activation/deactivation relationship. As an amino acid, proline is present in many

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

s. This aids in the multitude of effects that isomerization of proline can have in different biological mechanisms and functions.

Cell signaling

Cell signaling involves many different processes and proteins. One of the most studied cell signaling phenomena involving proline is the interactions with

p53 p53, also known as Tumor protein P53, cellular tumor antigen p53 (UniProt name), or transformation-related protein 53 (TRP53) is a regulatory protein that is often mutated in human cancers. The p53 proteins (originally thought to be, and often s ...

and prolyl isomerases, specifically

Pin1 Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 is an enzyme that in humans is encoded by the ''PIN1'' gene. Pin 1, or peptidyl-prolyl cis/trans isomerase (PPIase), isomerizes only phospho-Serine/Threonine-Proline motifs. The enzyme bi ...

. The protein p53, along with p63 and

p73 p73 is a protein related to the p53 tumor protein. Because of its structural resemblance to p53, it has also been considered a tumor suppressor. It is involved in cell cycle regulation, and induction of apoptosis. Like p53, p73 is characterized ...

, are responsible for ensuring that alterations to the

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...

are corrected and for preventing the formation and growth of

tumors A neoplasm () is a type of abnormal and excessive growth of tissue. The process that occurs to form or produce a neoplasm is called neoplasia. The growth of a neoplasm is uncoordinated with that of the normal surrounding tissue, and persists ...

. proline residues are found throughout the p53 proteins and without the phosphorylation and isomerization of specific Serine/Threonine-Proline motifs within p53, they cannot exhibit control over their target genes. The main signalling processes that are affected by p53 are

apoptosis Apoptosis (from grc, ἀπόπτωσις, apóptōsis, 'falling off') is a form of programmed cell death that occurs in multicellular organisms. Biochemical events lead to characteristic cell changes (morphology) and death. These changes incl ...

and cell cycle arrest, both of which are controlled by specific isomerization of the prolines in p53.

History and discovery

Although isomerization of proteins has been known about since 1968 when it was discovered by C. Tanford, proline isomerization and its use as a noncovalent histone tail modification was not discovered until 2006 by Nelson and his colleagues.

As a histone tail modification

One of the most well known epigenetic mechanisms that proline isomerization plays a role in is the modification of histone tails, specifically those of

histone In biology, histones are highly basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei. They act as spools around which DNA winds to create structural units called nucleosomes. Nucleosomes in turn are wr ...

H3. Fpr4 is a PPIase, in the FK507BP group, that exhibits catalytic activity at the proline positions 16, 30, and 38 (also written P16, P30, and P38 respectively) on the N-terminal region of histone H3 in ''

Saccharomyces cerevisiae ''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungus microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been o ...

''. Fpr4's binding affinity is strongest at the P38 site, followed by P30 and then P16. However the catalytic efficiency, or the increase in isomerization rates, is highest at P16 and P30 equally, followed by P38 which exhibits a very small change in isomerization rates with the binding of Fpr4. Histone H3 has an important

lysine Lysine (symbol Lys or K) is an α-amino acid that is a precursor to many proteins. It contains an α-amino group (which is in the protonated form under biological conditions), an α-carboxylic acid group (which is in the deprotonated −C ...

residue at the 36 position (also written K36) on the N-terminal tail which can be

methylated In the chemical sciences, methylation denotes the addition of a methyl group on a substrate, or the substitution of an atom (or group) by a methyl group. Methylation is a form of alkylation, with a methyl group replacing a hydrogen atom. These t ...

by Set2, a

methyltransferase Methyltransferases are a large group of enzymes that all methylate their substrates but can be split into several subclasses based on their structural features. The most common class of methyltransferases is class I, all of which contain a Rossm ...

. Methylation of K36 is key to normal transcription elongation. Due to P38's proximity to K36, cross-talk between P38 isomerization and K36 methylation can occur. This means that isomer changes at the P38 position can affect methylation at the K36 position. In the ''cis'' position, P38 shifts the histone tail closer to the DNA, crowding the area around the tail. This can cause a decrease the ability of proteins to bind to the DNA and to the histone tail, including preventing Set2 from methylating K36. Also, this tail movement can increase the number interactions between the histone tail and the DNA, increasing likelihood of

nucleosome A nucleosome is the basic structural unit of DNA packaging in eukaryotes. The structure of a nucleosome consists of a segment of DNA wound around eight histone proteins and resembles thread wrapped around a spool. The nucleosome is the fundamen ...

formation and potentially leading to the creation of higher-order chromatin structure. In ''trans'', P38 leads to the opposite effects: allowing for Set2 to methylate K36. Set2 is only affected by isomerization of P38 when creating a trimethylated K36 (commonly written as K36me3), however, and not K36me2. Fpr4 also binds to P32 in H4, though its effects are minimal. In mammalian cells, the isomerization of H3P30 interacts with the

phosphorylation In chemistry, phosphorylation is the attachment of a phosphate group to a molecule or an ion. This process and its inverse, dephosphorylation, are common in biology and could be driven by natural selection. Text was copied from this source, wh ...

of H3S28 (serine in the 28 position of histone H3) and the methylation of H3K27. hFKBP25 is a PPIase that is a

homolog In biology, homology is similarity due to shared ancestry between a pair of structures or genes in different taxa. A common example of homologous structures is the forelimbs of vertebrates, where the wings of bats and birds, the arms of prima ...

for Fpr4 in mammalian cells and is found to commonly be associated with the presence of HDACs. Cyp33 is a cyclophilin that has the ability to isomerize H3 proline residues at P16 and P30 positions. Histones H2A and H2B also have multiple proline residues near amino acids that when modified affect the activity surrounding the histone.

Interactions with H3K4me3 and H3K14ac

The isomerization of the peptide bond between histone H3's alanine 15 and proline 16 is affected by the

acetylation : In organic chemistry, acetylation is an organic esterification reaction with acetic acid. It introduces an acetyl group into a chemical compound. Such compounds are termed ''acetate esters'' or simply '' acetates''. Deacetylation is the oppo ...

at K14 and can control the

methylation In the chemical sciences, methylation denotes the addition of a methyl group on a substrate, or the substitution of an atom (or group) by a methyl group. Methylation is a form of alkylation, with a methyl group replacing a hydrogen atom. These t ...

states of K4. K4me3 represses gene transcription and depends upon the Set1

complex subunit Spp1 being balanced with the Jhd2

demethylase Demethylases are enzymes that remove methyl (CH3) groups from nucleic acids, proteins (particularly histones), and other molecules. Demethylases are important epigenetic proteins, as they are responsible for transcriptional regulation of the genom ...

s for proper function. Acetylation of K14 allows for a state change in P16 and primarily promotes the ''trans'' state of P16. This ''trans'' isomer of P16 reduces K4 methylation, which results in transcription repression. Isomerization of P16 has downstream effects of controlling protein binding to acetylated K18. When P16 is in the ''trans'' conformation, Spt7 is allowed to bind to K18ac, increasing transcription.

Interactions with gene regulatory proteins

RNA polymerase II

Proline isomerization of certain prolines in RNA polymerase II is key in the process of recruiting and placing processing factors during transcription. PPIases target

RNA polymerase II RNA polymerase II (RNAP II and Pol II) is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA. It is one of the three RNAP enzymes found in the nucleus of eukaryoti ...

by interacting with the Rpb1 carboxy terminal domain, or CTD. Proline isomerization is then used as part of the mechanism of the CTD to recruit co-factors required for co-transcriptional

RNA processing Transcriptional modification or co-transcriptional modification is a set of biological processes common to most eukaryotic cells by which an RNA primary transcript is chemically altered following transcription from a gene to produce a mature, f ...

, regulating RNA polymerase II activity.

Nrd1 Nardilysin is a protein that in humans is encoded by the ''NRD1'' gene. Interactions NRD1 has been shown to interact with Heparin-binding EGF-like growth factor Heparin-binding EGF-like growth factor (HB-EGF) is a member of the EGF family of ...

is a protein that is responsible for many of the transcriptional activities of RNAP II, specifically through the

- dependent termination pathway. This pathway requires the parvulin Ess1, or Pin1 depending on the organism, to isomerize the pSer5-Pro6 bond in the CTD. Without the ''cis'' conformation of the pSer5-Pro6 bond, created by Ess1/Pin1, Nrd1 cannot bind to RNAP II. Any variation from this process leads to a decrease in Nrd1 binding affinity, lowering the ability of RNAP II to process and degrade noncoding RNAs.

MLL1

Cyp33 in mammals causes isomerization in

MLL1 Histone-lysine ''N''-methyltransferase 2A also known as acute lymphoblastic leukemia 1 (ALL-1), myeloid/lymphoid or mixed-lineage leukemia 1 (MLL1), or zinc finger protein HRX (HRX) is an enzyme that in humans is encoded by the ''KMT2A'' gene. ML ...

. MLL1 is a multiprotein complex that regulates gene expression and chromosomal translocations involving this gene often lead to leukemia. MLL's target genes include HOXC8, HOXA9, CDKN1B, and C-MYC. MLL also has two binding domains: a Cyp33 RNA-recognition motif domain (RRM), and a PHD3 domain that binds to H3K4me3 or Cyp33 RRM. Cyp33 has the ability to downregulate the expression of these genes through proline isomerization at the peptide bond between His1628 and Pro1629 within MLL. This bond lies in a sequence between the PHD3 finger of MLL1 and the bromeodomain of MLL1, and its isomerization mediates the bonding of the PHD3 domain and the Cyp33 RRM domain. When these two domains are bonded transcription is repressed through recruitment of histone deacetylases to MLL1 and inhibition of H3K4me3.

Phosphatase recruitment

Phosphorylated amino acids are crucial for the modulation of the binding of

transcription factor In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The fu ...

s and other gene

regulatory protein Regulation of gene expression, or gene regulation, includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA). Sophisticated programs of gene expression are wide ...

s. Pin1's effect on isomerization of proline residues leads to an increase or decrease in recruitment of phosphatases, namely Scp1 and Ssu72 and their recruitment to the RNAP II CTD. The ''cis-''Pro formation is associated with an increase in Ssu72. Scp1 on recognizes ''trans''-Pro formations, and is not affected by such isomerization. Pin1 also triggers the activation of the

DSIF In gene expression, DSIF (DRB Sensitivity Inducing Factor) is a protein that can either negatively or positively affect transcription by RNA polymerase II (Pol II). In one case of negative regulation, it can interact with negative elongation factor ...

complex and NELF, which are responsible for pausing RNAP II in mammalian cells, and their conversion into positive elongation factors, facilitating elongation. This potentially could be an isomerization dependent process.

Regulation of mRNA stability

, a parvulin, regulates mRNA stability and expression in certain eukaryotics mRNAs. These mRNAs are GM-CSF, P''th'', and TGFβ and each of them have AREs, or AU-rich cis-elements. The ARE binding protein KSRP has a Pin1 binding site. Pin1 binds to this site and dephosphorylates the serine and isomerizes the peptide bond between Ser181 and Pro182. This isomerization causes the decay of P''th'' mRNA. KSRP, and other ARE binding proteins like AUF1, are thought to affect the other mRNAs through mechanisms similar to P''th'', with the requirement of a phosphorylated serine bonded to a proline in a specific conformation. Pin1 also triggers proline isomerization of Stem-Loop Binding Protein (SLBP), allowing it to control the dissociation of

SLBP Histone RNA hairpin-binding protein or stem-loop binding protein (SLBP) is a protein that in humans is encoded by the ''SLBP'' gene. Species distribution SLBP has been cloned from humans, ''C. elegans'', ''D. melanogaster'', '' X. laevis'', a ...

from histone mRNA. This leads to Pin1 being able to affect histone mRNA decay. Pin1 affects many other genes in the form of gene silencing through the disruption of cell pathways, making it important in mRNA turnover by modulating RNA binding protein activity.

Difficulties with research

Currently there are no existing compounds that can mimic the peptide bond of proline to other amino acids while maintaining only a ''cis'' or ''trans'' configuration because most mimics found will eventually change from one isomer to another. This makes research on the direct effect of each of the isomers on biological mechanisms more difficult. Also, the actual isomerization of proline is a slow process, meaning that any studying of the effects of the different isomers of proline takes a large amount of time to complete.

References

{{Reflist Epigenetics Gene expression Glucogenic amino acids Isomerism Stereochemistry