Evolution of the regulatory subunits for the heteromeric acetyl-CoA carboxylase

Abstract

The committed step for de novo fatty acid (FA) synthesis is the ATP-dependent carboxylation of acetyl-coenzyme A catalysed by acetyl-CoA carboxylase (ACCase). In most plants, ACCase is a multi-subunit complex orthologous to prokaryotes. However, unlike prokaryotes, the plant and algal orthologues are comprised both catalytic and additional dedicated regulatory subunits. Novel regulatory subunits, biotin lipoyl attachment domain-containing proteins (BADC) and carboxyltransferase interactors (CTI) (both three-gene families in Arabidopsis) represent new effectors specific to plants and certain algal species. The evolutionary history of these genes in autotrophic eukaryotes remains elusive, making it an ongoing area of research. Analyses of potential protein-protein and co-occurrence interactions, informed by gene network patterns using the STRING database, in Arabidopsis thaliana and Chlamydomonas reinhardtii unveil intricate gene associations with ACCase, suggesting a complex interplay between FA synthesis and other cellular processes. Among both species, a higher number of co-expressed genes was identified in Arabidopsis, indicating a wider potential regulatory network of ACCase in plants. This review investigates the extent to which these genes arose in autotrophic eukaryotes and provides insights into their evolutionary trajectory. This article is part of the theme issue 'The evolution of plant metabolism'.

Keywords: ACCase; acetyl-CoA carboxylase; fatty acid synthesis; metabolic regulation.

Figure 1.

Schematic representation of the heteromeric acetyl-CoA carboxylase (hetACCase) complex and its regulatory interactors. The complex is formed by the association of subunits, including biotin carboxylase (BC), biotin carboxyl carrier proteins (BCCP), biotin lipoyl attachment domain-containing proteins (BADC), and the carboxyltransferase (CT) subunits α and β, which form heterodimers. BADC proteins are non-biotinylated and act as regulatory subunits of ACCase. Protein-interaction inhibitor II (PII) and carboxyltransferase interactors (CTI) negatively regulate ACCase activity. Gene names of all negative regulators are highlighted in red. The enzymatic reaction represents the biotin carboxylation process, which is energy-dependent and uses HCO₃ ⁻ as the carbon source. Additionally, αCT and βCT subunits facilitate the carboxyl transfer to acetyl-CoA, resulting in the formation of malonyl-CoA. This malonyl-CoA molecule serves as a substrate for fatty acid synthesis. Regulatory subunits can be influenced by multiple abiotic factors. For instance, BADC3 is affected by pH changes and light-dark cycle [6], light-dependent activation of CTI [7], and PII is influenced by nitrogen levels [8] as well as the presence of 2-oxoglutarate, pyruvate, or oxaloacetate in the carbon metabolism pathway during fatty acid synthesis in plastids [9]. This figure was created using icons from BioRender (https://biorender.com/).

Figure 2.

Co-occurrence of the ACCase genes. Boxes indicate whether the given species contains an orthologue to Arabidopsis thaliana ACCase genes (red, yes; white, no). Abbreviations for heteromeric ACCase catalytic subunits: BC, biotin carboxylase; BCCP1/2, biotin carboxyl carrier protein isoform 1 or 2; αCT, carboxyltransferase alpha subunit; βCT, carboxyltransferase beta subunit; and regulatory subunits: BADC3, BADC2, BADC1, biotin attachment domain-containing proteins; CTI1, CTI2, CTI3, carboxyltransferase interactors; PII: protein-interaction inhibitor II. The asterisks (*) indicate isoforms for which multiple hits were found; the box reflects the isoform with the highest sequence similarity to the Arabidopsis reference gene. Detailed accession numbers can be found in the eletronic supplementary material, table S1. The phylogenetic tree was created using the BLAST taxonomy tool (https://www.ncbi.nlm.nih.gov/Taxonomy/CommonTree/wwwcmt.cgi).

Figure 3.

Phylogenetic analysis of plant ACCase. Phylogenetic trees among heteromeric ACCase catalytic subunits are shown in: (a) biotin carboxylase (BC), (b) biotin carboxyl carrier protein 1 and 2 of (BCCP1 and BCCP2, respectively); (c) carboxyltransferase alpha subunit (αCT); (d) carboxyltransferase beta subunit (βCT). Phylogenetic trees among regulatory subunits are shown in: (e) protein interaction inhibitor II (PII); (f) biotin attachment domain-containing proteins (BADC 1/2/3) and (g) carboxyltransferase interactors (CTI1/2/3). Asterisks (*) indicate the presence of more than one subunit. The analysis involved amino acid sequences from Arabidopsis thaliana, Musa acuminata, Ceratopteris richardii, Selaginella moellendorffii, Physcomitrella patens, Zygnema circumcarinatum, Zygnema cf. cylindricum , Mesotaenium endlicherianum , Closterium sp. , Klebsormidium nitens, Volvox carteri, Chlamydomonas reinhardtii, Dunaliella salina, Chromochloris zofingiensis, Coccomyxa subellipsoidea, Botryococcus braunii, Auxenochlorella protothecoides, Ostreobium quekettii, Cyanidioschyzon merolae, Cyanidiococcus yangmingshanensis, Galdieria sulphuraria, Porphyra umbilicalis , Gracilaria domingensis , Chondrus crispus, Nannochloropsis gaditana, Nannochloropsis salina, Aureococcus anophagefferens, Pelagomonas calceolata, Parmales sp. scaly parma, Dactylococcopsis salina, Synechococcus sp., Prochlorococcaceae cyanobacterium, Anabaena sp., Nostoc parmelioides and Microcystis aeruginosa.The species with different colours represent distinct categories: pink for land plants (eudicots, monocots, ferns, lycophyte and mosses), green for green algae, blue for heterokont algae, red for red algae, and orange for cyanobacteria. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test 2000 replicates is shown next to the branches.

Figure 4.

Gene network analysis of the ACCase genes using the STRING database. Yellow nodes represent all ACCase subunits, green nodes represent genes related to fatty acid synthesis (FAS) and grey nodes represent the other genes that are not yet known to be related to the fatty acid synthesis. (a) Gene network analysis of the ACCase genes in Arabidopsis thaliana and; (b) gene network analysis of the ACCase genes in Chlamydomonas reinhardtii. The networks are constructed based on protein–protein interactions (PPIs) and gene co-expression patterns, with a minimum required interaction score of 0.2 for significance.