Neutral invertases in grapevine and comparative analysis with Arabidopsis, poplar and rice

Abstract

Neutral invertases (NIs, EC 3.2.1.26) cleave sucrose to glucose and fructose. They are encoded by a small gene family of 9 members in the Arabidopsis genome, 8 in rice, 16 in poplar and 9 in Vitis vinifera (L.). The grapevine NIs were identified in the 8.4X genome assembly of the quasi-homozygous line PN40024. In addition, alleles of three NIs were sequenced in the heterozygous cultivar 'Cabernet Sauvignon'. Analyses of sequence variation between alleles, homoeologous and paralogous copies in grapevine and their orthologues in Arabidopsis, poplar and rice are provided. In grapevine, NIs were classified into four alpha NIs and five beta NIs and subsequently grouped into hierarchical clades using a combination of evidence including amino acid identity, exon/intron structure, rate of synonymous substitutions (K (s)) and chromosomal distribution. Estimation of K (s) proved the ancient origin of all NIs and the lack of expansion by gene duplication past the event of polyploidisation. We then focused on transcription analysis of five NIs for which evidence of expression was available from expressed sequence tag databases. Among these, four NIs consisted of pairs of homoeologous copies, each pair lying on a pair of chromosomes duplicated by polyploidy. Unequal expression of homoeologous genes was observed by quantitative RT-PCR in leaf, flower, seed and root tissues. Since NIs might play significant roles in fruit and wine quality, NIs expression was monitored in flesh and skin of 'Merlot' berries and shown in parallel with the suite of changes that accompany fruit ripening, including glucose and fructose accumulation.

Comparative genomic analysis of mitogen activated protein kinase gene family in grapevine

“…In fact, the annotated genome sequence of Vitis vinifera become available (Velasco et al, 2007), suggesting that grapevine has a potential as a model organism for fruit trees. In addition, with the availability of complete grapevine sequences, it has become imperative to compare the functions of gene families, particularly those having vital functions with the gene families characterized from Arabidopsis (The French-Italian Public Consortium for Grapevine Genome Characterization, 2007;Matus et al, 2008;Nonis et al, 2008).…”

“…Although some supercontigs are still being correctly assembled and oriented in each chromosome (Matus et al, 2008), the completion of the grapevine genome has made it possible to identify gene family through the analysis of sequence similarity with Arabidopsis genome. In fact, terpene synthase gene family (The French-Italian Public Consortium for Grapevine Genome Characterization, 2007), MYB R2R3 subfamily (Matus et al, 2008) and invertase (Nonis et al, 2008) have been identified by In-silico analysis based on Arabidopsis genome. Recently, putative rice and poplar MAPKs, which are placed into four subgroups that are identified earlier in Arabidopsis based on the sequence similarity, have been revealed through in-silico analysis of current rice and poplar genome databases Nicole et al, 2006;Reyna and Yang, 2006;Liu and Xue, 2007).…”

Metabolism of soluble sugars in developing melon fruit: a global transcriptional view of the metabolic transition to sucrose accumulation

“…The plant neutral invertases have generally been attributed a cytosolic localization, consistent with the neutral pH activity optimum and absence of glycosylation, and have recently been classified into two subgroups, a and b, with the a subgroup associated with organelles, plastids and mitochondria, while the b subgroup has been attributed a non-organellar localization (Ji et al 2005;Murayama and Handa 2007;Nonis et al 2008;Vargas et al 2008). Figure 2 indicates that the four expressed genes represent the three subgroups of neutral invertase: CmNIN3 is most similar to the b-type cytosolic form, CmNIN1 and CmNIN4 are a-type, mitochondrial and CmNIN2 encodes for an a-type plastidic enzyme.…”

“…2). Melon representatives of the three clades of NIN (Ji et al 2005;Murayama and Handa 2007;Nonis et al 2008;Vargas et al 2008), two clades of UGE (Barber et al 2006;Rösti et al 2007), two groups of FK , three groups of SUS Núñez et al 2008;Subbaiah et al 2006) and two groups of HK (Claeyssen and Rivoal 2007;Granot 2008;Olsson et al 2003) were all identified. The SPS gene family, which has been divided into three subfamilies, A, B and C (Komatsu et al 1999;Langenkämper et al 2002;Lutfiyya et al 2007) is the only exception.…”

“…Trees were developed using the public www.phylogeny.fr program(Dereeper et al 2008). Accession numbers of the genes/enzymes presented are a Acid (AAG) and neutral (NAG) a-galactosidases; b Acid (AIN) AAM28822), LeLIN9 (AM050394), LeTIV (M81081); c a and b type neutral invertases according toNonis et al 2008; d UDPglucose epimerases (UGE); Arabidopsis according toBarber et al 2006: AtUGE1 (At1G12780), AtUGE2 (At4G23920), AtUGE3 (At1G63180), AtUGE4 (At1G64440), AtUGE5 (At4G10690); e Sucrose phosphate syntheses (SPS), Arabidopsis according toLutfiyya et al 2007: AtSPS1F (At5G20280), AtSPS2F (At5G11110), AtSPS3F (At1G04920), AtS-PS4F (At4G10120) and citrus: CuSPS1 (AB005023), CuSPS2 (AB006319), CuSPS3 (AB006660); f Cytosolic and plastidic fructokinases (FK), tomato according toDamari-Weissler et al 2006: LeFK1 (U64817), LeFK2 (U64818), LeFK3 (AY323226), LeFK4 (AY099454); g Invertase inhibitors (INH), Arabidopsis: AtC/VIF (At1G47960) AtC/ VIF2 (At5G64620), tobacco: NtCIF (Y12805), NtVIF (Y12806) and tomato LeCIF (AJ010943); h Sucrose synthases (SUS), Arabidopsis according toBieniawska et al 2007: AtSUS1 (At5G20830), AtSUS2 (At5G49190), AtSUS3 (At4G02280), AtSUS4 (At3G43190), AtSUS5 (At5G37180), AtSUS6 (At1G73370) and maize SUS: ZmSUS1 (NP_001105323), ZmSUS2 (NP_001105194), ZmSUS-SH1(NP_00110 5411); i Phosphoglucomutases (PGM), Arabidopsis: AtPGMcyt1 (At1G70730), AtPGMcyt2 (At1G23190), AtPGMpl1 (At5G51820); j Phosphoglucoisomerases (PGI), Arabidopsis: AtPGIcyt (At5G42740), AtPGIpl (At4G24620); k Mitochondrial and plastidic hexokinase (HK) according toKarve et al 2008, Arabidopsis: AtHXK1 (At4G29130), AtHXK2 (At2G19860), AtHXK3 (At1g47840), and ''hexokinase-like'' AtHKL1 (At1G50460), AtHKL2 (At3G20040), AtHKL3 (At4G37840), tomato: LeHK1 (AJ401153), LeHK2 (AF208543), LeHK3 (…”