Lignification enzymes associated with the membranes

the proteomic analyses and were selected as candidates (MA_10434957g0010, MA_62683g0010, MA_9415070g0020, and MA_40328g0010). All were co-expressed with monolignol biosynthesis based on the analysis of the ConGenIE data and the data by Blokhina et al. (2019). Two ABCB transporters (MA_138894g0010 and MA_635039g0010) were selected as candidates based solely on their co-expression with monolignol bait genes in ConGenIE and Norwood datasets.

Without a doubt, many of the ABC transporters that I have mentioned here likely play a role in phytohormone transport, as that is one of the important functions of ABC transporters in plants (Borghi et al., 2019). It has been pointed out that local concentrations of hydrophobic molecules may threaten the integrity of the membranes, and ABC transporters may expel these hydrophobic compounds from membranes (Lefèvre and Boutry, 2018). The concentration of phenolic compounds needed to destabilise the structure of the membrane may, however, not be biologically relevant. More modestly, effects on membrane ion permeabilities (Hossain et al., 2021) or the inhibition of membrane enzymes (Sikkema et al., 1995) could have an effect. In addition, a role for phenylpropanoid transporters in the regulation of the phenylpropanoid pathway has been suggested (Biała et al., 2017; Biała and Jasiński, 2018). Even pathway intermediates could be transported, similarly to the way that ABCG10 transports 4-coumarate and liquiritigenin, which are intermediates of the medicarpin biosynthetic pathway (Biała et al., 2017). However, it is not known if such regulatory transport of monolignol biosynthesis intermediates or monolignols exists.

Interestingly, an amino acid permease family (AAP) protein encoded by MA_18076g0010 was also co-expressed with the monolignol biosynthesis baits (II).

AAPs are proton symporters for amino acids at the PM (Fischer et al., 2002). Lignin biosynthesis requires the transport of various intermediates for monolignol biosynthesis pathway within the cell, and this transporter could be involved in the transport of phenylalanine or shikimate, for example, from the plastid.

3.5. Lignification enzymes associated with the membranes

cells, and 278 were found in developing phloem (II). The majority of the detected proteins (430) were present only in the developing xylem, which was technically the material from which it was the easiest to isolate membrane proteins. Yet, specific proteins in the phloem (82) and in the cell culture (36) were also detected. In the co- expression analyses, 63 genes were co-expressed with the monolignol biosynthesis bait genes in all the four datasets, supporting their role in lignification. The membrane proteomes were compared to this small set of co-expressed genes and twenty of the co- expressed genes were detected in the proteomics, too. This observation suggests that many lignification-related proteins are connected to membranes.

3.5.1. Monolignol pathway enzymes in proteomics

Proteins corresponding to six of the 12 monolignol biosynthesis genes that were used as baits in the co-expression experiments were found in the membrane preparations (II). In addition, proteins encoded by two additional monolignol biosynthesis genes, MA_202753g0010 (C4H) and MA_667858g0010 (CCoAOMT), were detected in the xylem membranes, and further found to be co-expressed with the baits in our datasets.

The detection of the enzymes encoded by the bait genes in proteomic data supports the proposal of Jokipii-Lukkari et al. (2018) that the enzymes encoded by these genes are involved in monolignol production in the developing xylem of Norway spruce. The data suggest also that these Norway spruce monolignol pathway enzymes could be associated with membranes, like many of their homologues in poplar and in Arabidopsis (see chapter “Monolignol biosynthesis”). Three C4H enzymes and one C3'H enzyme were found in the membrane proteomic data, and it is tempting to speculate that they could serve as anchors for a metabolon, as has been proposed for Arabidopsis (Bassard et al., 2012). In a tandem affinity purification experiment, Bassard et al. (2012) detected several proteins that were attached to CH4 and/or C3'H, and homologues of these can be found in spruce membrane proteome, some of which even co-express with bait genes (II: Supplemental table 1). Firstly, cytochrome b5 (MA_21175g0010) and NADH-cytochrome b5 reductase 1 (MA_8687g0010) were present in many of the membrane preparations. Cytochrome b5 has a role as an electron shuttle protein in S-lignin biosynthesis in Arabidopsis (Gou et al., 2019).

Secondly, a membrane-steroid binding protein, MSBP (MA_82655g0010), was

present in the membrane preparations. MSBP proteins are components of ER membranes and connect cytochrome P450 proteins (Bassard et al., 2012; Gou et al., 2018). Reticulon family proteins that were previously detected as being attached to P450 proteins (Bassard et al., 2012) were also present in spruce membranes (MA_10434136g0010, MA_10436218g0010, MA_654072g0010). Thirdly, a small, PM-localised Rac/Rop family GTPase, Rac1, interacts with CCR1 in rice, and plays a role in regulating lignin and phenolics biosynthesis during pathogen defence (Kawasaki et al., 2006). Three homologues to OsRac1 were also present in membranes preparations (MA_11461g0010, MA_36432g0010, and MA_948089g0010).

However, no CCR enzymes were detected in the proteomic data.

COMT encoded by MA_10432099g0010 was detected in the xylem membrane proteome, and its gene expression followed the other lignification enzymes (II), indicating that this enzyme could be involved in monolignol biosynthesis in developing xylem. No membrane associations have been described for COMT thus far. The abundance of a poplar homologue (COMT2) is the highest of all monolignol enzymes (Shuford et al., 2012). If that was the case with this spruce COMT as well, it is possible that it was detected as a soluble contaminant in the membrane samples.

3.5.2. Plastids – or xyloplasts

In developing xylem, the building blocks for lignin biosynthesis originate from sucrose, which is transported through the phloem, delivered via ray parenchyma cells, and finally arrives in developing tracheids/tracheary elements that can enzymatically convert sucrose into several sugar phosphates (reviewed by Mahboubi and Niittylä, 2018). One important sink of these sugars is in SCW polysaccharide synthesis, but some are also broken down via glycolysis to produce phosphoenolpyruvate.

Phosphoenolpyruvate is then taken up by plastids via phosphoenolpyruvate/phosphate transport proteins (PPT, Fischer et al., 1997). The shikimate pathway occurs within plastids and uses phosphoenylpyruvate to synthesise phenylalanine and shikimate for use in the monolignol biosynthesis pathway (Tohge et al., 2013; Pascual et al., 2016). This means that plastids are important upstream cellular machineries needed for lignification within the xylem. Despite their importance for lignification, the plastids within developing xylem have been poorly

studied, as noted by Pinard and Mizrachi (2018). The authors propose that a term

´xyloplasts´ be used for these organelles. The results in study II show that eight genes encoding enzymes of the shikimate pathway are co-expressed with the monolignol biosynthesis baits across different datasets. However, only one of these was present in the proteomic data, phosphor-2-dehydro-3-deoxyheptonate aldolase 1 (MA_10436001g0020).