RegulonDB (http://regulondb.ccg.unam.mx/) is the primary reference database offering curated knowledge of the transcriptional regulatory network of Escherichia coli K12, currently the best-known electronically encoded database of the genetic regulatory network of any free-living organism. This paper summarizes the improvements, new biology and new features available in version 6.0. Curation of original literature is, from now on, up to date for every new release. All the objects are supported by their corresponding evidences, now classified as strong or weak. Transcription factors are classified by origin of their effectors and by gene ontology class. We have now computational predictions for σ54 and five different promoter types of the σ70 family, as well as their corresponding −10 and −35 boxes. In addition to those curated from the literature, we added about 300 experimentally mapped promoters coming from our own high-throughput mapping efforts. RegulonDB v.6.0 now expands beyond transcription initiation, including RNA regulatory elements, specifically riboswitches, attenuators and small RNAs, with their known associated targets. The data can be accessed through overviews of correlations about gene regulation. RegulonDB associated original literature, together with more than 4000 curation notes, can now be searched with the Textpresso text mining engine.

RegulonDB (http://regulondb.ccg.unam.mx/) is the primary reference database of the best-known regulatory network of any free-living organism, that of Escherichia coli K-12. The major conceptual change since 3 years ago is an expanded biological context so that transcriptional regulation is now part of a unit that initiates with the signal and continues with the signal transduction to the core of regulation, modifying expression of the affected target genes responsible for the response. We call these genetic sensory response units, or Gensor Units. We have initiated their high-level curation, with graphic maps and superreactions with links to other databases. Additional connectivity uses expandable submaps. RegulonDB has summaries for every transcription factor (TF) and TF-binding sites with internal symmetry. Several DNA-binding motifs and their sizes have been redefined and relocated. In addition to data from the literature, we have incorporated our own information on transcription start sites (TSSs) and transcriptional units (TUs), obtained by using high-throughput whole-genome sequencing technologies. A new portable drawing tool for genomic features is also now available, as well as new ways to download the data, including web services, files for several relational database manager systems and text files including BioPAX format.

Proteins of 50 or fewer amino acids are poorly characterized in all organisms. The corresponding genes are challenging to reliably annotate, and it is difficult to purify and characterize the small protein products. Due to these technical limitations, little is known about the abundance of small proteins, not to mention their biological functions. To begin to characterize these small proteins in Escherichia coli, we assayed their accumulation under a variety of growth conditions and after exposure to stress. We found that many small proteins accumulate under specific growth conditions or are stress induced. For some genes, the observed changes in protein levels were consistent with known transcriptional regulation, such as ArcA activation of the operons encoding yccB and ybgT. However, we also identified novel regulation, such as Zur repression of ykgMO, cyclic AMP response protein (CRP) repression of azuC, and CRP activation of ykgR. The levels of 11 small proteins increase after heat shock, and induction of at least 1 of these, YobF, occurs at a posttranscriptional level. These results show that small proteins are an overlooked subset of stress response proteins in E. coli and provide information that will be valuable for determining the functions of these proteins.

The thiCOGE genes of Rhizobium etli code for enzymes involved in thiamin biosynthesis. These genes are transcribed with a 211-base untranslated leader that contains the thi box, a 38-base sequence highly conserved in the 5 regions of thiamin biosynthetic and transport genes of Gram-positive and Gram-negative organisms. A deletion analysis of thiC-lacZ fusions revealed an unexpected relationship between the degree of repression shown by the deleted derivatives and the length of the thiC sequences present in the transcript. Three regions were found to be important for regulation: (i) the thi box sequence, which is absolutely necessary for high-level expression of thiC; (ii) the region immediately upstream to the translation start codon of thiC, which can be folded into a stem-loop structure that would mask the Shine-Dalgarno sequence; and (iii) the proximal part of the coding region of thiC, which was shown to contain a putative Rho-independent terminator. A comparative phylogenetic analysis revealed a possible folding of the thi box sequence into a hairpin structure composed of a hairpin loop, two helixes, and an interior loop. Our results show that thiamin regulation of gene expression involves a complex posttranscriptional mechanism and that the thi box RNA structure is indispensable for thiCOGE expression.T hiamin pyrophosphate (TPP), also known as cocarboxylase, is the cofactor of key enzymes of carbon metabolism such as pyruvate dehydrogenase, ␣-ketoglutarate dehydrogenase, transketolase, pyruvate decarboxylase, and others. TPP is made by the enzymatic coupling of two independently synthesized precursors, 4-amino-5-hydroxymethyl-2-methyl pyrimidine pyrophosphate and 5-(2-hydroxyethyl)-4-methyl thiazole monophosphate (1).In Escherichia coli and Salmonella enterica serovar Typhimurium, several genes are known to participate in TPP biosynthesis (2). thiC and thiD are required for 4-amino-5-hydroxymethyl-2-methyl pyrimidine pyrophosphate synthesis (3, 4), whereas dxs (5, 6), thiF, thiS, thiG, thiH, and thiI are involved in 5-(2-hydroxyethyl)-4-methyl thiazole monophosphate synthesis (3,7,8). In addition, the product of the thiE gene couples 4-amino-5-hydroxymethyl-2-methyl pyrimidine pyrophosphate and 5-(2-hydroxyethyl)-4-methyl thiazole monophosphate to give thiamin monophosphate, which undergoes another phosphorylation catalyzed by the product of the thiL gene to form TPP, the biologically active form of vitamin B 1 (9, 10). A salvage enzyme (thiamin kinase) encoded by thiK, which incorporates exogenous thiamin into TPP (11), also exists. In both organisms the thi genes are located throughout the chromosome and are arranged in three operons and four single gene loci (2). thiCEFSGH, thiMD (ThiM and ThiD are involved in salvage of 5-(2-hydroxyethyl)-4-methyl thiazole and 4-amino-5-hydroxymethyl-2-methyl pyrimidine from the culture medium, respectively; ThiD also catalyzes the phosphorylation of 4-amino-5-hydroxymethyl-2-methyl pyrimidine monophosphate and thiBPQ (which code for an ABC type transport system for t...

In susceptible insects, Cry toxin specificity correlates with receptor recognition. In previous work, we charac