Chemical Tagging of Protein Lipoylation

Abstract

Protein lipoylation is a post‐translational modification of emerging importance in both prokaryotes and eukaryotes. However, labeling and large‐scale profiling of protein lipoylation remain challenging. Here, we report the development of iLCL (iodoacetamide‐assisted lipoate‐cyclooctyne ligation), a chemoselective reaction that enables chemical tagging of protein lipoylation. We demonstrate that the cyclic disulfide of lipoamide but not linear disulfides can selectively react with iodoacetamide to produce sulfenic acid, which can be conjugated with cyclooctyne probes. iLCL enables tagging of lipoylated proteins for gel‐based detection and cellular imaging. Furthermore, we apply iLCL for proteomic profiling of lipoylated proteins in both bacteria and mammalian cells. In addition to all of the eight known lipoylated proteins, we identified seven candidates for novel lipoylated proteins. The iLCL strategy should facilitate uncovering the biological function of protein lipoylation.

CPLM 4.0: an updated database with rich annotations for protein lysine modifications

“…These ‘relatively minor modifications’ were generally regarded as constitutive and inert marks in histones ( 4 ), until the discovery of GCN5 as the first histone acetyltransferase (HAT) from Tetrahymena thermophile , a ciliated protozoan, by C. David Allis and James E. Brownell in 1996 ( 5 , 6 ). Later, it was demonstrated that the lysine residue is particularly active and can be regulated by a variety of PLMs, including acylation modifications such as acetylation ( 7 ), crotonylation ( 8 ), succinylation ( 9 ) and lactylation ( 10 ), ubiquitin and ubiquitin-like (Ub/Ubl) conjugations such as ubiquitination ( 11 ) and sumoylation ( 12 ), and other types of PLMs such as methylation ( 13 ) and lipoylation ( 14 ). PLMs occurred at histone lysine residues constitute the ‘histone code’ together with other histone modifications, and play a critical role in transcriptional regulation and gene expression ( 15 , 16 ).…”

Functionalised Cofactor Mimics for Interactome Discovery and Beyond

“…Recently, proteomic profiling of lipoylation has also been performed by functionalising lipoamide in situ, utilising the reactivity of the lipoamide 1,2-dithiolane ring to chemoselectively conjugate cyclooctyne probes to lipoamide-bound proteins in bacterial and mammalian lysates. [52] The minimalist photocrosslinker was also exploited in the recently developed ATP mimetic 2.10, which was found to enrich 59 known ATP-binding proteins in A549 cell membrane fractions, as well as highly abundant cytosolic ATP binders from cell lysates. [53] A contrasting chemical proteomics method, thermal proteome profiling (TPP), [54] which examines the stabilisation of proteins induced by ligand binding, has also been recently used to profile ATPbinding proteins, finding 315 of 7859 of proteins annotated with GO terms relating to this cofactor.…”

Funktionalisierte Cofaktor‐Analoga für die Erforschung von Interaktomen und darüber hinaus

“…Diese Sonde wurde in Proteomik‐Experimenten verwendet, wobei eine neue Delipoylierungsfunktion von Sirt2 aufgedeckt wurde. Kürzlich wurde das Proteom‐Profiling der Lipoylierung auch durch die Funktionalisierung von Liponamid in situ durchgeführt, wobei die Reaktivität des 1,2‐Dithiolan‐Rings des Liponamids genutzt wurde, um chemoselektiv Cyclooctin‐Sonden an Liponamid‐gebundene Proteine in bakteriellen und Säugetier‐Lysaten zu konjugieren [52] …”