Homocysteine Editing, Thioester Chemistry, Coenzyme A, and the Origin of Coded Peptide Synthesis †

Abstract

Aminoacyl-tRNA synthetases (AARSs) have evolved “quality control” mechanisms which prevent tRNA aminoacylation with non-protein amino acids, such as homocysteine, homoserine, and ornithine, and thus their access to the Genetic Code. Of the ten AARSs that possess editing function, five edit homocysteine: Class I MetRS, ValRS, IleRS, LeuRS, and Class II LysRS. Studies of their editing function reveal that catalytic modules of these AARSs have a thiol-binding site that confers the ability to catalyze the aminoacylation of coenzyme A, pantetheine, and other thiols. Other AARSs also catalyze aminoacyl-thioester synthesis. Amino acid selectivity of AARSs in the aminoacyl thioesters formation reaction is relaxed, characteristic of primitive amino acid activation systems that may have originated in the Thioester World. With homocysteine and cysteine as thiol substrates, AARSs support peptide bond synthesis. Evolutionary origin of these activities is revealed by genomic comparisons, which show that AARSs are structurally related to proteins involved in coenzyme A/sulfur metabolism and non-coded peptide bond synthesis. These findings suggest that the extant AARSs descended from ancestral forms that were involved in non-coded Thioester-dependent peptide synthesis, functionally similar to the present-day non-ribosomal peptide synthetases.

Demethylation of methionine and keratin damage in human hair

“…Previous work has shown that proteins carry Hcy residues linked via an amide bond (Hcy-protein) (Sikora et al 2014 ) or a disulfide bond ( S -Hcy-protein) (Lim et al 2003 ; Jacovina et al 2009 ). Three mechanisms can account for the generation of Hcy-proteins: (1) modification of protein lysine residues by Hcy-thiolactone (Jakubowski 1999 ); (2) a nitric oxide (NO)-mediated mechanism affording S -NO-Hcy, which is a substrate for aminoacylation of tRNA Met by methionyl-tRNA synthetase, forming S -NO-Hcy-tRNA Met , which in turn participates in protein biosynthesis on ribosomes by delivering S -NO-Hcy at positions normally occupied by Met (Jakubowski 2000a , b , 2001 , 2017 ); (3) iron-catalyzed de-methylation of protein Met residues to Hcy (Mozziconacci et al 2013 ). S -Hcy-proteins are generated in a red-ox mechanism involving free Hcy (Jakubowski 1999 , 2000a , b ; Lim et al 2003 ).…”

“…Although in metabolically active tissues Hcy can be incorporated into proteins via amide or peptide bonds by pathways mediated by Hcy-thiolactone or S -NO-Hcy, respectively, both dependent on methionyl-tRNA synthetase (Jakubowski 2011 , 2012 , 2017 ), these pathways cannot be operational in metabolically inactive tissues such as hair. Thus, another mechanism must be responsible for Hcy-keratin accumulation in human hair.…”

“…Homocysteine (Hcy) is a universal intermediate in the metabolism of two major sulfur-containing amino acids methionine (Met) and cysteine. While Met and cysteine (Cys) are canonical coded amino acids that are incorporated into proteins by the ribosomal biosynthetic apparatus, Hcy is not (Jakubowski 2017 ). However, although Hcy is a non‐coded amino acid, proteins carry Hcy residues linked via an isopeptide bond to lysine (Lys) residues ( N -Hcy-protein) (Jakubowski 1999 , 2002 ; Sikora et al 2014 ) or via a disulfide bond to cysteine residues ( S -Hcy-protein) (Lim et al 2003 ; Jacovina et al 2009 ).…”

“…However, although Hcy is a non‐coded amino acid, proteins carry Hcy residues linked via an isopeptide bond to lysine (Lys) residues ( N -Hcy-protein) (Jakubowski 1999 , 2002 ; Sikora et al 2014 ) or via a disulfide bond to cysteine residues ( S -Hcy-protein) (Lim et al 2003 ; Jacovina et al 2009 ). Proteins can also carry Hcy bound by a peptide bond than can be formed translationally by a nitric oxide-dependent mechanism (Jakubowski 2000a , b , 2001 , 2017 ) or post-translationally by metal-dependent demethylation of a protein methionine residue (Mozziconacci et al 2013 ). However, although about a dozen individual proteins that contain Hcy N-linked to lysine residues or S-linked to cysteine residues have been identified in vivo in humans or animals (Jakubowski 2013 ), proteins that carry Hcy bound by a peptide bond have not yet been identified.…”

Homocysteine: Its Possible Emerging Role in At-Risk Population Groups

“…The transsulfuration path starts to function when the concentrations of Hcy and methionine increase, for example by post-prandial protein intake [14], or cysteine is needed. In humans, during protein synthesis, Hcy instead of methionine could be wrongly selected in the reaction catalyzed by methionyl-tRNA synthetase (MetRS), producing a reactive toxic metabolite of Hcy known as Hcy-thiolactone [15,16]. This compound is able to chemically modify proteins and to impair their normal function, generating N-homocysteinylated (N-Hcy) proteins.…”