Aryl Coenzyme A Ligases, a Subfamily of the Adenylate-Forming Enzyme Superfamily

Abstract

Aryl-CoA ligases belong to class I of the adenylate-forming enzyme superfamily (ANL superfamily) and catalyze the formation of thioester bonds between aromatic compounds and Coenzyme A (CoA) and occur in nearly all forms of life. These ligases are involved in various metabolic pathways degrading benzene, toluene, ethylbenzene, and xylene (BTEX) or polycyclic aromatic hydrocarbons (PAHs). They are often necessary to produce the central intermediate benzoyl-CoA that occurs in various anaerobic pathways. The substrate specificity is very diverse between enzymes within the same class, while the dependency on Mg 2+ , ATP and CoA as well as oxygen insensitivity are characteristics shared by the whole enzyme-class. Some organisms employ the same aryl-CoA ligase when growing aerobically and anaerobically, while others induce different enzymes depending on the environmental conditions. Aryl-CoA ligases can be divided into two major groups, benzoate:CoA ligase-like enzymes and phenylacetate:CoA ligase-like enzymes. They are widely distributed between the phylogenetic clades of the ANL superfamily and show closer relations within the subfamilies than to other aryl-CoA ligases. This, together with residual CoA-ligase activity in various other enzymes of the ANL superfamily, leads to the conclusion that CoA ligases might be the ancestral proteins from which all other ANL superfamily enzymes developed.

The benzoyl-CoA pathway serves as a genomic marker to identify the oxygen requirements in the degradation of aromatic hydrocarbons

“…We constructed MEME motifs to improve the ortholog search. Other works have described MEME motifs found in the adenylate-forming enzyme superfamily Class I ( Marahiel et al, 1997 ; Clark et al, 2018 ; Arnold et al, 2021 ), which includes groups of conserved residues and structural features consistent with our results. A comparison of our predicted motifs with the reported motifs showed that BCL-motif-1 is located in the N-terminus and is associated with a phosphate loop (P-loop).…”

“…The genomes of T. aromatica ( bclA ), B. xenovorans LB400 (badA), Azoarcus spp. ( bzdA ), and R. palustris ( badA ) presented experimental evidence of BCL-encoding genes ( Egland et al, 1995 ; Schühle et al, 2003 ; Kawaguchi et al, 2006 ; Bains and Boulanger, 2007 ; Valderrama et al, 2012 ; Arnold et al, 2021 ) ( Supplementary Table S1 ). We used this information to search for orthologous sequences of BCLs in bacterial genomes.…”

“…Genes encoding the lower metabolic pathways for converting benzoyl-CoA are part of the genomic context. These pathways are often arranged as operons ( Egland et al, 1995 ; Porter and Young, 2014 ; Arnold et al, 2021 ). Therefore, instead of considering three upstream and downstream genes, as proposed in our previous work ( Martinez-Amador et al, 2019 ; Soto-Avila et al, 2021 ), we extended the inspection of genes in the genomic context to 10 upstream and 10 downstream genes from the BCL.…”

“…Six sequences were selected as a tree outgroup. The sequences were taken from aryl-CoA ligases used in Arnold et al (2021) original work, which used these sequences to construct a neighbor-joining phylogenetic tree of amino acid sequences from the adenylate-forming enzyme superfamily. Our ultimate tree, which grouped 148 sequences, was visualized using the iTol tool ( Letunic and Bork, 2021 ).…”

“…The BCL enzymes belong to the Class I superfamily of adenylate-forming enzymes (ANL superfamily) and subclass Ib, which include acyl and aryl coenzyme A (CoA) synthetases/ligases ( Schmelz and Naismith, 2009 ; Clark et al, 2018 ; Arnold et al, 2021 ). Using ATP, it catalyzes the formation of a thioester bond between aromatic compounds and coenzyme A (CoA, CoASH).…”