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Protease Gene Families in Populus and Arabidopsis Maribel García-Lorenzo1, Andreas Sjödin2, Stefan Jansson*2 and Christiane Funk1

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Protease Gene Families in Populus and Arabidopsis Maribel García-Lorenzo1, Andreas Sjödin2, Stefan Jansson*2 and Christiane Funk1 BMC Plant Biology BioMed Central Research article Open Access Protease gene families in Populus and Arabidopsis Maribel García-Lorenzo1, Andreas Sjödin2, Stefan Jansson*2 and Christiane Funk1 Address: 1Umeå Plant Science Centre, Department of Biochemistry, Umeå University, S – 90187 Umeå, Sweden and 2Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, S – 90187 Umeå, Sweden Email: Maribel García-Lorenzo - [email protected]; Andreas Sjödin - [email protected]; Stefan Jansson* - [email protected]; Christiane Funk - [email protected] * Corresponding author Published: 20 December 2006 Received: 14 June 2006 Accepted: 20 December 2006 BMC Plant Biology 2006, 6:30 doi:10.1186/1471-2229-6-30 This article is available from: http://www.biomedcentral.com/1471-2229/6/30 © 2006 García-Lorenzo et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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. Background neither the proteases involved in its degradation nor the Proteolysis is a poorly understood aspect of plant molec- cellular location of the process are known. In the Arabidop- ular biology. Although proteases play crucial roles in sis thaliana (hereafter Arabidopsis) genome, many genes many important processes in plant cells, e.g. responses to with sequence similarities to known proteases have been changes in environmental conditions, senescence and cell identified; the MEROPS database (release 7.30) of Arabi- death, very little information is available on the substrate dopsis proteases contains 676 entries, corresponding to specificity and physiological roles of the various plant almost 3 % of the proteome. However, protease activity proteases. Even for the most abundant plant protein, rib- has only been demonstrated for a few of the entries. Most ulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), of these putative proteases are found in extended gene Page 1 of 24 (page number not for citation purposes) BMC Plant Biology 2006, 6:30 http://www.biomedcentral.com/1471-2229/6/30 families and are likely to have overlapping functions, expansions of gene families, which should help elucidate complicating attempts to dissect the roles of the different issues concerning non-functionalization, neofunctionali- proteases in plant metabolism and development. zation and subfunctionalization. Thus, as reported here, we undertook a comparative analysis of protease gene One scenario in which proteases play a very important families in the two sequenced dicot genomes, those of the role is senescence, although it still is discussed if they actu- annual plant Arabidopsis and the tree Populus trichocarpa ally cause senescence or purely are involved in resource (hereafter Populus), with special emphasis on proteases mobilization. which may play a role in senescence. The results should help to provide a framework for further elucidation of the Senescence is the final stage of plant development and can nature and roles of these complex gene families. be induced by a number of both external and internal fac- tors such as age, prolonged darkness, plant hormones, Results biotic or abiotic stress and seasonal responses. An impor- Most protease gene families are larger in Populus than in tant function of senescence is to reallocate nutrients, Arabidopsis nitrogen in particular, to other parts of the plant before We made an analysis of all protease genes of Arabidopsis the specific structure is degraded. The understanding of and Populus. As noted above, conservation of a protein senescence is very important for biomass production. In sequence in these two species indicates that it is likely to order to understand more about the role of proteases dur- have a common function in them. Recent expansions of ing senescence in this study we compare the nuclear gene families, on the other hand, could provide indica- genome of Arabidopsis thaliana and Populus trichocarpa. The tions of different adaptive requirements (and, possibly, of close relationship of these two species in the plant king- more general differences between annual plants and dom [2] allows a direct comparison of an annual plant trees). with a tree that has to cope with highly variable adapta- tions during its long life span. Recent research has shown The results of the genome comparison between Arabidop- that leaf senescence affects the chloroplast much earlier sis and Populus are compiled in Table 1. In total, we iden- than the mitochondria or other compartments of the cell tified 723 genes coding for putative proteases in [3], we therefore chose to focus on protease families that Arabidopsis and 955 in Populus. Forty-five previously uni- express members in this plastid as well as on the papain dentified Arabidopsis genes were detected that were not protease family which consists of proteases that are well- present in the MEROPS database at the time. Like most of known to be involved in senescence. the genes in the MEROPS database, we do not know whether or not these genes code for active proteases, but In the chloroplast at least 11 different protease families due to their sequence similarity they could have protease are represented, however, several of them work as process- activity and were included in the comparison. Figure 1 ing peptidases. Only 6 families posses members that are shows a graphic representation of this comparison. Gen- known to be involved in degradation, four of these fami- erally the protease gene numbers in each family do not lies belong to the class of serine proteases, two are metal- vary greatly between the two species, although Populus has loproteases. The Deg proteases form one family (S1, more members in most subfamilies, a consequence of its chymotrypsin family) inside the serine clade and the ATP- genome history. Both lineages have undergone rather dependent Clp proteases are grouped in the S14 family. recent genome duplications [4,5] but the evolutionary The S16 family contains the so-called Lon proteases. Met- clock seems to tick almost six-fold slower in the Populus as alloproteases (MPs) are proteases with a divalent cation compared to the Arabidopsis lineage and loss of dupli- cofactor that binds to the active site; most commonly Zn2+ cated genes have been much retarded [4,5]. However, is ligated to two Histidines in the sequence HEXXH. How- some families were more expanded than others, especially ever, Zn2+ can be replaced by Co2+, Mn2+ or even Mg2+. The the A11 subfamily of aspartic proteases (the copia trans- M41 family is the group of FtsH proteases and the EGY poson endopeptidase family), which has 20 members in (ethylene-dependent gravitropism-deficient and yellow- Arabidopsis and 123 members in Populus. Since the char- green) proteases belong to the family of S2P proteases acteristic sequence of these proteases is part of the copia- (M50). transposable element, which is abundant in Populus [5,6], this expansion is likely to have been simply a consequence Comparative genomics analyses could provide valuable of the multiplication of the transposon, rather than selec- insights into the conservation, evolution, abundance and tion pressure to increase the copy number of the protease roles of the various plant protease families. For instance, per se. Therefore, this family will not be mentioned fur- such analyses should facilitate the detection of protein ther. Some subfamilies (the aspartic-type A22, cysteine- sequences that are conserved in different species, and thus type C56, serine-types S49 and S28, and metallo-types are likely to have common functions in them, and recent M1, M14 and M38) have twice as many members in Pop- Page 2 of 24 (page number not for citation purposes) BMC Plant Biology 2006, 6:30 http://www.biomedcentral.com/1471-2229/6/30 ulus compared to Arabidopsis, but in Arabidopsis these showed that of the 12 ftsH genes potentially coding for numbers are low, thus duplication could have readily fully functional proteases 10 are found in highly homolo- occurred. An interesting case is the subfamily C48, the gous pairs. While the pairs AtFtsH1/5, AtFtsH2/8 and Ulp1 (ubiquitin-like protease) endopeptidase family, AtFtsH 7/9 are targeted to the chloroplast, AtFtsH3/10 and cystein-type, which contains SUMO (small ubiquitin-like AtFtsH4 have been identified in mitochondria [18,19]. modifier) deconjugating enzymes, with 77 members in AtFtsH11, which contains only one transmembrane Arabidopsis, but only 13 in Populus. This protein family domain was recently suggested to be located in both chlo- has been shown to cleave not only the SUMO precursor, roplasts and mitochondria [19,20].
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