Structural Analysis of Arabidopsis thaliana Chromosome 5. VII. Sequence Features of the Regions of 1,013,767 bp Covered by Sixteen Physically assigned P1 and TAC Clones

Sixteen Pl and TAC clones assigned to Arabidopsis thaliana chromosome5 were sequenced, and their sequence features were analyzedusing various computer programs. The total length of the sequencesdetermined was 1,013,767 bp. Together with the nucleotide sequencesof 109 clones previously reported, the regions of chromosome5 sequenced so far now total 9,072,622 bp, which presumablycovers approximately one-third of the chromosome. A similaritysearch against the reported gene sequences predicted the presenceof a total of 225 protein-coding genes and/or gene segmentsin the newly sequenced regions, indicating an average gene densityof one gene per 4.5 kb. Introns were identified in 72.4% ofthe potential protein genes for which the entire gene structurewas predicted, and the average number per gene and the averagelength of the introns were 3.3 and 163 bp, respectively. Thesesequence features are essentially identical to those in thepreviously reported sequences. The sequence data and gene informationare available on the World Wide Web database KAOS (Kazusa Arabidopsisdata Opening Site) at http://www.kazusa.or.jp/arabi/.     

Gene profiling of the red light signalling pathways in roots

Red light, acting through the phytochromes, controls numerousaspects of plant development. Many of the signal transductionelements downstream of the phytochromes have been identifiedin the aerial portions of the plant; however, very few elementsin red-light signalling have been identified specifically forroots. Gene profiling studies using microarrays and quantitativeReal-Time PCR were performed to characterize gene expressionchanges in roots of Arabidopsis seedlings exposed to 1 h ofred light. Several factors acting downstream of phytochromesin red-light signalling in roots were identified. Some of thegenes found to be differentially expressed in this study havealready been characterized in the red-light-signalling pathwayfor whole plants. For example, PHYTOCHROME KINASE 1 (PKS1),LONG HYPOCOTYL 5 (HY5), EARLY FLOWERING 4 (ELF4), and GIGANTEA(GI) were all significantly up-regulated in roots of seedlingsexposed to 1 h of red light. The up-regulation of SUPPRESSOROF PHYTOCHROME A RESPONSES 1 (SPA1) and CONSTITUTIVE PHOTOMORPHOGENIC1-like (COP1-like) genes suggests that the PHYA-mediated pathwaywas attenuated by red light. In addition, genes involved inlateral root and root hair formation, root plastid development,phenylpropanoid metabolism, and hormone signalling were alsoregulated by exposure to red light. Interestingly, members ofthe RPT2/NPH3 (ROOT PHOTOTROPIC 2/NON PHOTOTROPIC HYPOCOTYL3) family, which have been shown to mediate blue-light-inducedphototropism, were also differentially regulated in roots inred light. Therefore, these results suggest that red and bluelight pathways interact in roots of seedlings and that manyelements involved in red-light-signalling found in the aerialportions of the plant are differentially expressed in rootswithin 1 h of red light exposure. Key words: Arabidopsis, gene profiling, microarray, photomorphogenesis, red light, roots     

Large-scale comparison of protein sequence alignment algorithms with structure alignments

Sequence alignment programs such as BLAST and PSI-BLAST are used routinely in pairwise, profile-based, or intermediate-sequence-search (ISS) methods to detect remote homologies for the purposes of fold assignment and comparative modeling. Yet, the sequence alignment quality of these methods at low sequence identity is not known. We have used the CE structure alignment program (Shindyalov and Bourne, Prot Eng 1998;11:739) to derive sequence alignments for all superfamily and family-level related proteins in the SCOP domain database. CE aligns structures and their sequences based on distances within each protein, rather than on interprotein distances. We compared BLAST, PSI-BLAST, CLUSTALW, and ISS alignments with the CE structural alignments. We found that global alignments with CLUSTALW were very poor at low sequence identity (<25%), as judged by the CE alignments. We used PSI-BLAST to search the nonredundant sequence database (nr) with every sequence in SCOP using up to four iterations. The resulting matrix was used to search a database of SCOP sequences. PSI-BLAST is only slightly better than BLAST in alignment accuracy on a per-residue basis, but PSI-BLAST matrix alignments are much longer than BLAST's, and so align correctly a larger fraction of the total number of aligned residues in the structure alignments. Any two SCOP sequences in the same superfamily that shared a hit or hits in the nr PSI-BLAST searches were identified as linked by the shared intermediate sequence. We examined the quality of the longest SCOP-query/ SCOP-hit alignment via an intermediate sequence, and found that ISS produced longer alignments than PSI-BLAST searches alone, of nearly comparable per-residue quality. At 10-15% sequence identity, BLAST correctly aligns 28%, PSI-BLAST 40%, and ISS 46% of residues according to the structure alignments. We also compared CE structure alignments with FSSP structure alignments generated by the DALI program. In contrast to the sequence methods, CE and structure alignments from the FSSP database identically align 75% of residue pairs at the 10-15% level of sequence identity, indicating that there is substantial room for improvement in these sequence alignment methods. BLAST produced alignments for 8% of the 10,665 nonimmunoglobulin SCOP superfamily sequence pairs (nearly all <25% sequence identity), PSI-BLAST matched 17% and the double-PSI-BLAST ISS method aligned 38% with E-values <10.0. The results indicate that intermediate sequences may be useful not only in fold assignment but also in achieving more complete sequence alignments for comparative modeling.     

Identification of dynamin as an interactor of rice GIGANTEA by tandem affinity purification (TAP)

GIGANTEA (GI), CONSTANS (CO) and FLOWERING LOCUS T (FT) regulatephotoperiodic flowering in Arabidopsis. In rice, OsGI, Hd1 andHd3a were identified as orthologs of GI, CO and FT, respectively,and are also important regulators of flowering. Although GIhas roles in both flowering and the circadian clock, our understandingof its biochemical functions is still limited. In this study,we purified novel OsGI-interacting proteins by using the tandemaffinity purification (TAP) method. The TAP method has beenused effectively in a number of model species to isolate proteinsthat interact with proteins of interest. However, in plants,the TAP method has been used in only a few studies, and no novelproteins have previously been isolated by this method. We generatedtransgenic rice plants and cell cultures expressing a TAP-taggedversion of OsGI. After a two-step purification procedure, theinteracting proteins were analyzed by mass spectrometry. Sevenproteins, including dynamin, were identified as OsGI-interactingproteins. The interaction of OsGI with dynamin was verifiedby co-immunoprecipitation using a myc-tagged version of OsGI.Moreover, an analysis of Arabidopsis dynamin mutants indicatedthat although the flowering times of the mutants were not differentfrom those of wild-type plants, an aerial rosette phenotypewas observed in the mutants. We also found that OsGI is presentin both the nucleus and the cytosol by Western blot analysisand by transient assays. These results indicate that the TAPmethod is effective for the isolation of novel proteins thatinteract with target proteins in plants.     

The FLOWERING LOCUS T/TERMINAL FLOWER 1 family in Lombardy poplar

Genes in the FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1)family have been shown to be important in the control of theswitch between vegetative and reproductive growth in severalplant species. We isolated nine members of the FT/TFL1 familyfrom Lombardy poplar (Populus nigra var. italica Koehne). Sequenceanalysis of the members of the FT/TFL1 family revealed considerablehomology within their coding regions both among family membersand to the members of the same family in Arabidopsis, tomatoand grapevine. Moreover, members of this family in all fourspecies examined display a common exon–intron organization.Phylogenetic analysis revealed that the genes fall into fourdifferent clades: two into the TFL1 clade; five into the FTclade; and one each into the MOTHER OF FT AND TFL1 and BROTHEROF FT AND TFL1 clades. One gene in the TFL1 clade, PnTFL1, isexpressed in vegetative meristems, and transgenic Arabidopsisthat ectopically expressed PnTFL1 had a late-flowering phenotype.The expression patterns of two genes in the FT clade, PnFT1and PnFT2, suggested a role for them in the promotion of flowering,and transgenic Arabidopsis that ectopically expressed eitherPnFT1 or PnFT2 had an early-flowering phenotype.     

Touch-Inducible Genes for Calmodulin and a Calmodulin-Related Protein Are Located in Tandem on a Chromosome of Arabidopsis thaliana

Genes for calmodulin and calmodulin-related proteins in Arabidopsisare up-regulated by a variety of physical stimuli, which includerain, wind and touch [Braam and Davis (1990) Cell 60: 357].We have isolated five genes for calmodulin (AtCALl, 2, 3, 5,6) and one gene for a calmodulin-related protein (AtCAL4) froman Arabidopsis genomic library. Touch stimulus of Arabidopsisplants induces the accumulation of mRNA transcribed from AtCAL4andAtCAL5, but not from the other isolated genes. The two touch-induciblegenes are arrayed in tandem with a short intergenic region of700 bp but they show different organ-specific patterns of expression. (Received April 27, 1995; Accepted July 20, 1995)