We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one-step method for inactivation of chromosomal genes and primers designed to create in-frame deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in high-throughput studies, two independent mutants were saved for every deleted gene. These mutants-the 'Keio collection'-provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome-wide testing of mutational effects in a common strain background, E. coli K-12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase (http://ecoli.aist-nara.ac.jp/).

Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 nontransposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.

A major quantitative trait locus (QTL) controlling response to photoperiod, Hd1 , was identified by means of a mapbased cloning strategy. High-resolution mapping using 1505 segregants enabled us to define a genomic region of ‫ف‬ 12 kb as a candidate for Hd1 . Further analysis revealed that the Hd1 QTL corresponds to a gene that is a homolog of CON-STANS in Arabidopsis. Sequencing analysis revealed a 43-bp deletion in the first exon of the photoperiod sensitivity 1 ( se1 ) mutant HS66 and a 433-bp insertion in the intron in mutant HS110. Se1 is allelic to the Hd1 QTL, as determined by analysis of two se1 mutants, HS66 and HS110. Genetic complementation analysis proved the function of the candidate gene. The amount of Hd1 mRNA was not greatly affected by a change in length of the photoperiod. We suggest that Hd1 functions in the promotion of heading under short-day conditions and in inhibition under long-day conditions. INTRODUCTIONThe transition of the apical meristem from vegetative to reproductive growth is a critical event in the life cycle of a plant. In rice, the timing of this transition affects the timing of heading. This timing, or heading date, is one of the critical traits considered for adapting rice to different cultivation areas and cropping seasons. Rice is a short-day (SD) plant; its heading is promoted by short photoperiods. The response of the plant to length of day (referred to as photoperiod sensitivity [PS]) and its basic vegetative growth determine the heading date of rice. Many genetic studies of heading date have been performed, and several genes controlling PS in rice have been genetically identified, including Se1 ( Lm ), Se3 to Se7 , and E1 to E3 (Yokoo et al., 1980;Yamagata et al., 1986;Poonyarit et al., 1989;Sano, 1992;Yokoo and Okuno, 1993;Tsai, 1995; Kinoshita, 1998). However, only one gene involving photoperiod response in rice has been cloned, Se5 (Izawa et al., 2000). Little is known about the structure and function of PS genes in rice at the molecular level. In contrast, several genes involved in flowering time have been isolated, allowing clarification of part of the genetic control pathway in Arabidopsis (reviewed by Levy and Dean, 1998; Fowler et al., 1999; Kobayashi et al., 1999;Sheldon et al., 1999). Identification of the genes involved in flowering time has made it possible to determine the genetic control pathways for the response to photoperiod and vernalization in Arabidopsis (reviewed by Levy and Dean, 1998;Samach and Coupland, 2000). In addition, homologs of Arabidopsis genes for flowering time also function in Brassica napus (Robert et al., 1998).The major genes or quantitative trait loci (QTLs) for heading date have been mapped by using DNA markers in rice (Mackill et al., 1993; Li et al., 1995;Xiao et al., 1996;Lin et al., 1998;Tamura et al., 1998). Four QTLs for heading date involved in PS were mapped precisely as single Mendelian factors by using advanced backcross progeny (Yamamoto et al., , 2000Lin et al., 2000). A major gene controlling PS, Se1 , first was ide...

Analysis of cellular components at multiple levels of biological information can provide valuable functional insights. We performed multiple high-throughput measurements to study the response of Escherichia coli cells to genetic and environmental perturbations. Analysis of metabolic enzyme gene disruptants revealed unexpectedly small changes in messenger RNA and proteins for most disruptants. Overall, metabolite levels were also stable, reflecting the rerouting of fluxes in the metabolic network. In contrast, E. coli actively regulated enzyme levels to maintain a stable metabolic state in response to changes in growth rate. E. coli thus seems to use complementary strategies that result in a metabolic network robust against perturbations.

The legume Lotus japonicus has been widely used as a model system to investigate the genetic background of legume-specific phenomena such as symbiotic nitrogen fixation. Here, we report structural features of the L. japonicus genome. The 315.1-Mb sequences determined in this and previous studies correspond to 67% of the genome (472 Mb), and are likely to cover 91.3% of the gene space. Linkage mapping anchored 130-Mb sequences onto the six linkage groups. A total of 10 951 complete and 19 848 partial structures of protein-encoding genes were assigned to the genome. Comparative analysis of these genes revealed the expansion of several functional domains and gene families that are characteristic of L. japonicus. Synteny analysis detected traces of whole-genome duplication and the presence of synteny blocks with other plant genomes to various degrees. This study provides the first opportunity to look into the complex and unique genetic system of legumes.

Protein-protein interactions play key roles in protein function and the structural organization of a cell. A thorough description of these interactions should facilitate elucidation of cellular activities, targeted-drug design, and whole cell engineering. A large-scale comprehensive pull-down assay was performed using a His-tagged Escherichia coli ORF clone library. Of 4339 bait proteins tested, partners were found for 2667, including 779 of unknown function. Proteins copurifying with hexahistidine-tagged baits on a Ni 2+

With the goal of solving the whole-cell problem with Escherichia coli K-12 as a model cell, highly accurate genomes were determined for two closely related K-12 strains, MG1655 and W3110. Completion of the W3110 genome and comparison with the MG1655 genome revealed differences at 267 sites, including 251 sites with short, mostly single-nucleotide, insertions or deletions (indels) or base substitutions (totaling 358 nucleotides), in addition to 13 sites with an insertion sequence element or defective prophage in only one strain and two sites for the W3110 inversion. Direct DNA sequencing of PCR products for the 251 regions with short indel and base disparities revealed that only eight sites are true differences. The other 243 discrepancies were due to errors in the original MG1655 sequence, including 79 frameshifts, one amino-acid residue deletion, five amino-acid residue insertions, 73 missense, and 17 silent changes within coding regions. Errors in the original MG1655 sequence (o1 per 13 000 bases) were mostly within portions sequenced with out-dated technology based on radioactive chemistry.

A major quantitative trait locus (QTL) controlling response to photoperiod, Hd1 , was identified by means of a mapbased cloning strategy. High-resolution mapping using 1505 segregants enabled us to define a genomic region of ‫ف‬ 12 kb as a candidate for Hd1. Further analysis revealed that the Hd1 QTL corresponds to a gene that is a homolog of CON-STANS in Arabidopsis. Sequencing analysis revealed a 43-bp deletion in the first exon of the photoperiod sensitivity 1 (se1) mutant HS66 and a 433-bp insertion in the intron in mutant HS110. Se1 is allelic to the Hd1 QTL, as determined by analysis of two se1 mutants, HS66 and HS110. Genetic complementation analysis proved the function of the candidate gene. The amount of Hd1 mRNA was not greatly affected by a change in length of the photoperiod. We suggest that Hd1 functions in the promotion of heading under short-day conditions and in inhibition under long-day conditions.