Protease gene families in Populus and Arabidopsis

Abstract

Background: Proteases play key roles in plants, maintaining strict protein quality control and degrading specific sets of proteins in response to diverse environmental and developmental stimuli. Similarities and differences between the proteases expressed in different species may give valuable insights into their physiological roles and evolution.

Results: We have performed a comparative analysis of protease genes in the two sequenced dicot genomes, Arabidopsis thaliana and Populus trichocarpa by using genes coding for proteases in the MEROPS database 1 for Arabidopsis to identify homologous sequences in Populus. A multigene-based phylogenetic analysis was performed. Most protease families were found to be larger in Populus than in Arabidopsis, reflecting recent genome duplication. Detailed studies on e.g. the DegP, Clp, FtsH, Lon, rhomboid and papain-Like protease families showed the pattern of gene family expansion and gene loss was complex. We finally show that different Populus tissues express unique suites of protease genes and that the mRNA levels of different classes of proteases change along a developmental gradient.

Conclusion: Recent gene family expansion and contractions have made the Arabidopsis and Populus complements of proteases different and this, together with expression patterns, gives indications about the roles of the individual gene products or groups of proteases.

Figure 1

Classification and comparison of proteases in Arabidopsis and Populus. The different colors indicate the different protease classes: threonine proteases (T), cysteine proteases (C), serine proteases (S), metalloproteases (M) and aspartic proteases (A). Each class can be divided into different families according to MEROPS, the family number is indicated between the Arabidopsis and Populus charts.

Figure 2

UPGMA (Unweighted Pair Group Method with Arithmetic Mean) tree of the FtsH protease family (M41 family in MEROPS). The names and the accession numbers for the different proteins are given in Table 2.

Figure 3

UPGMA (Unweighted Pair Group Method with Arithmetic Mean) tree of the Deg protease family (S1 family in MEROPS). The names and the accession numbers for the different proteins are given in Table 3.

Figure 4

Maximum Parsimony Tree of the Clp protease family (S14 family in MEROPS). The names and the accession numbers for the different proteins are given in Table 4.

Figure 5

UPGMA (Unweighted Pair Group Method with Arithmetic Mean) tree of the Lon protease family (S16 family in MEROPS). The names and the accession numbers for the different proteins are given in Table 5.

Figure 6

UPGMA (Unweighted Pair Group Method with Arithmetic Mean) tree of the rhomboid protease family (S54 family in MEROPS). The names and the accession numbers for the different proteins are given in Table 6.

Figure 7

Maximum Parsimony Tree of the papain-like protease family (C1 family in MEROPS). RD, Response to Dehydration; GPC, Germination-specific Cysteine protease; XCP, Xylem Cysteine Protease; XBCP, Xylem and Bark Cysteine Protease; SAG, Senescence-Associated Gene; SPCP, Sweet Potato-like Cysteine Protease; (VFCYSPRO) Vicia faba CYStein PROtease; ELSA, Early Leaf-Senescence Abundant cysteine protease; AALP, Arabidopsis Aleurine-Like Protease. The names and the accession numbers for the different proteins are given in Table 7.

Figure 8

Clustered correlation map of protease EST frequencies across 19 Populus cDNA libraries. R: roots, P: petiols, K: apical shoot, T: shoot meristem, N: bark, S: imbibed seeds, C: young leaves, Q: dormant buds, M: female catkins, L: cold-stressed leaves, I: senescing leaves, X: wood cell death, F: floral buds, V: male catkins, UB: active cambium, AB: cambial zone, G: tension wood, UA: dormant cambium, Y: virus/fungal infected leaves. For descriptions of the different libraries, see [65], or [77].

Figure 9

The twelve most common protease expression patterns during Populus leaf development. Populus DNA microarray data were processed in UPSC-BASE (Sjödin et al. 2006). Samples for microarray analysis were taken from free-growing aspen in Umeå on the following dates; May 25, June 1, June 9, June 15, June 29, July 6, July 18, July 27, August 3, August 11, August 18, August 29 and September 12 2000, and Aug 17, Aug 24, Sept 03, Sept 07, Sept 14 and Sept 17 1999. The two sample series are identified by separate lines in the profiles.