Plant Carbonic Anhydrases: Structures, Locations, Evolution, and Physiological Roles

Abstract

Carbonic anhydrases (CAs) are zinc metalloenzymes that catalyze the interconversion of CO₂ and HCO₃^- and are ubiquitous in nature. Higher plants contain three evolutionarily distinct CA families, αCAs, βCAs, and γCAs, where each family is represented by multiple isoforms in all species. Alternative splicing of CA transcripts appears common; consequently, the number of functional CA isoforms in a species may exceed the number of genes. CAs are expressed in numerous plant tissues and in different cellular locations. The most prevalent CAs are those in the chloroplast, cytosol, and mitochondria. This diversity in location is paralleled in the many physiological and biochemical roles that CAs play in plants. In this review, the number and types of CAs in C₃, C₄, and crassulacean acid metabolism (CAM) plants are considered, and the roles of the α and γCAs are briefly discussed. The remainder of the review focuses on plant βCAs and includes the identification of homologs between species using phylogenetic approaches, a consideration of the inter- and intracellular localization of the proteins, along with the evidence for alternative splice forms. Current understanding of βCA tissue-specific expression patterns and what controls them are reviewed, and the physiological roles for which βCAs have been implicated are presented.

Keywords: alternative splicing; carbonic anhydrase; physiological role; regulation.

Figure 1

Structures of α, β, and γ Carbonic Anhydrase Proteins with Their Active Site Architecture. (A) The human CAII monomer (Mangani and Håkansson, 1992) mostly consists of β strands and contains a single active site with three zinc coordinating histidine residues. (B) The Pisum sativum βCA octamer (Kimber and Pai, 2000) contains eight active sites where each zinc is coordinated by two cysteines and a histidine. (C) The Methanosarcina thermophila γCA (Iverson et al., 2000) forms a trimer with three active sites. Although the γCA active site also contains three histidine resides, one monomer provides the H81 and H122 residues, while a second monomer provides the H117 residue to form the γCA active site. Red boxes indicate the enlarged locations of each protein structure to display their active-site architecture. CA protein structures and active-site images were generated using Jmol (http://www.jmol.org/).

Figure 2

Relative Expression of Carbonic Anhydrases in Sorghum bicolor Organs. (A) α, (B) β, and (C) γ carbonic anhydrase expression in different organs of Sorghum bicolour taken from MOROKOSHI - The Sorghum Transcriptome Database (Makita et al., 2015), in fragments per kilobase of transcript per million mapped reads (FPKM). Note that the y axis for the βCA expression is different than that of the αCA or γCA graphs.

Figure 3

Multiple Sequence Alignment of C-termini of β Carbonic Anhydrase Proteins from Different Plants. Sequences were aligned using Clustal Omega (http://www.ebi.ac.uk/Tools/msa/clustalo/; Sievers et al., 2011). Sequences for Physcomitrella patens (Lang et al., 2005;Rensing et al., 2005, Zimmer et al., 2013), Selaginella moellendorffii (Banks et al., 2011), Medicago truncatula (Young et al., 2011, Tang et al., 2014), Vitis vinifera (Jaillon et al., 2007), Populus trichocarpa (Tuskan et al., 2006, Du et al., 2015, Ye and Zhong, 2015), Brachypodium distachyon (Vogel et al., 2010), Oryza sativa (Ouyang et al., 2007), Setaria italic (Bennetzen et al., 2012), Sorghum bicolor (Makita et al., 2015) were obtained from Phytozome (https://phytozome.jgi.doe.gov). Sequences for Arabidopsis thaliana were obtained from TAIR (Lamesch et al., 2011). Sequences for Ananas comosus were obtained from CoGe (https://genomevolution.org; Ming et al., 2015).

Figure 4

Alternative Splicing of β Carbonic Anhydrase Genes in Arabidopsis thaliana and Neurachne munroi. Blue lines indicate genomic DNA with larger boxes representing exons. Green and magenta boxes indicate exons present in different splice forms, with green representing open reading frame sequence and magenta representing untranslated regions. Asterisks indicate that the Neurachne munroi CA1 and CA2 genomic DNA sequences are incomplete; for each gene, exon 4 and the downstream exons are present in both splice forms, as represented by the green arrows. Data from DiMario et al. (2016) and Clayton et al. (2016).

Figure 5

Schema Illustrating the Physiological Functions of β Carbonic Anhydrases in Plant Cells and Organs. In leaf mesophyll cells of C₄ plants, a cytosolic βCA catalyzes the first step in C₄ photosynthesis. βCAs are involved in a CO₂ sensing pathway in guard cells and implicated in stomatal development. A number of roles have been attributed to βCAs found in leaf mesophyll cells of C₃ plants, including involvement in refixation of respiratory CO₂, stress responses, amino acid and lipid biosynthesis, and seedling establishment. In nitrogen-fixing root nodules of legumes, βCAs are implicated in different functions during nodule maturation, including roles in primary metabolism and gas exchange. Note: the roles of βCA in C₃ guard cells and C₃ leaf mesophyll cells are likely to be performed by homologs in the corresponding cell types of C₄ plants. See text for details and references.