Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014

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EcoCyc Highlights

This page collects older "Highlights from..." features from the EcoCyc front page, grouped by release.

18.0 release highlights

  • E. coli can utilize sulfoquinovose, a common organo-sulfur compound in nature, as its sole source of carbon and energy. Denger et al. recently described the degradation pathway for sulfoquinovose. Learn more about this pathway here.

  • In a surprising twist, activation of the GhoTS toxin/antitoxin system is itself controlled by the MqsRA toxin/antitoxin system. The GhoS antitoxin is a site-specific endoribonuclease that cleaves ghoT mRNA. The ghoS mRNA is in turn a target of the MqsR toxin. Thus, when MqsR is not inhibited by its antitoxin MqsA, it degrades ghoS mRNA, which in turn allows translation of the ghoT mRNA and production of the GhoT toxin.

  • The characterisation of an E. coli inner membrane glycolipid with enzyme-like activity that is essential for membrane protein integration was first reported by Nishiyama et al. in 2012. More recently Moser et al. have shown that this membrane protein integrase (MPIase) is a novel chaperone that drives protein integration into membranes by modulating the dimer orientation of SecYEG translocase.

17.5 release highlights

  • Kim et al. recently showed that carboxy-S-adenosyl-L-methionine is an intermediate in the biosynthesis of the 5-(carboxymethoxy)uridine modification of the wobble nucleotide of certain tRNAs. The two reactions of the 5-(carboxymethoxy)uridine biosynthesis pathway are catalyzed by CmoA and CmoB.

  • Experimental work by Kreth et al. suggested that E. coli K-12 contains both inducible and constitutive systems for the import of pyruvate plus an additional system for pyruvate efflux. New transport reactions for pyruvate uptake and export have been added to EcoCyc.

  • The multidrug resistance protein MdtM was reported by Holdsworth et al. to be a low-affinity cation:H+ antiporter with a role in alkaline pH homeostasis.

17.1 release highlights

  • 1,4-dihydroxy-2-naphthoyl-CoA thioesterase, EC 3.1.2.28, is an enzyme of the menaquinone biosynthesis pathway. It had long been an orphan activity: the gene encoding the enzyme had been unknown. Recently, Chen et al. showed that ydiI encodes this enzyme and renamed the gene menI.

  • The membrane protein DauA (for "dicarboxylic acid uptake system A") was reported by Karinou et al. to be an aerobic succinate transporter active at acidic pH.

  • WaaH and EptC were shown by Klein et al. to catalyse glucuronic acid and phosphoethanolamine modification to E. coli LPS under low phosphate conditions.

17.0 release highlights

  • The role of the inner membrane proteins PgaC and PgaD in biofilm formation has been further described and a novel mechanism of cyclic-di-GMP mediated exopolysaccharide control elucidated. Steiner et al. have shown that the second messenger molecule c-di-GMP binds specifically to a PgaCD complex, mediating a productive interaction that results in the formation of an active glycosyltransferase complex.

  • Fried et al. report that the YpdAB Two-Component Signal Transduction System pathway acts to stimulate nutrient scavenging as a result of carbon starvation and thus plays a role in the carbon control network of E. coli K-12.

  • Cardiolipin is an anionic phospholipid that is found in most bacteria and in mitochondrial membranes. The third (and final) cardiolipin synthase of E. coli, ClsC, was recently identified by Tan et al.. Unlike ClsA and ClsB, it uses phosphatidylethanolamine as the source of the phosphatidyl group for transfer to the terminal free hydroxyl group of phosphatidylglycerol.

16.5 release highlights

  • Selkrig et al. have reported the characterization of a novel ‘translocation and assembly module’ that spans the inner and outer membranes of E. coli K-12 and is responsible for the efficient secretion of adhesin protein. This newly described complex comprises the inner membrane protein TamB (YtfO) and the outer membrane protein TamA (YtfM).

  • The release of solutes through mechanosensitive ion channels functions to protect bacterial cells against hypo-osmotic shock. Edwards et al. have recently reported experimental characterization of two mechanosensitive channels encoded by the genes ynaI and ybiO. This latest report brings the total number of known mechanosensitive channels in E. coli K-12 to seven, experimental evidence from Edwards et al. suggests that this represents the full complement.

  • With the discovery of RlmJ as the enzyme responsible for methylation of A2030 in 23S ribosomal RNA by Golovina et al., the set of methyltransferases that modify E. coli ribosomal RNAs is now complete.

  • The mechanism of ribosomal silencing has been an active area of research. A recent addition to the set of proteins that regulate the assembly or activity of the ribosome is RsfS. Häuser et al. discovered that RsfS is able to inhibit the assembly of a functional 70S ribosome during stationary phase.

16.1 release highlights

  • The discovery of the regulatory functions of small RNAs encoded in the E. coli genome continues apace. Two groups, Thomason et al. and Jørgensen et al., independently discovered that the small RNA McaS regulates the expression of curli as well as flagellar motility and biofilm formation.

  • The first hypochlorite-specific transcription factor has been described by Gebendorfer et al.. YjiE regulates genes involved in cysteine, methionine biosynthesis, sulfur metabolism, iron acquisition and homeostasis.

  • Although the cell division machinery of E. coli has been the subject of investigation for many years, new proteins involved in the process continue to be discovered. Durand-Heredia et al. recently described the cell division factor ZapD, which promotes bundling of the FtsZ polymers at mid-cell.

16.0 release highlights

  • A recent publication by Spira et al. in BMC Microbiology highlights the genetic heterogeneity, particularly in the rpoS gene, that can result from storage and transfer of E. coli strains between laboratories.

  • NMN amidohydrolase, EC 3.5.1.42, is involved in NAD recycling and salvage. It has long been an orphan enzymatic activity: no gene encoding the enzyme had been cloned from any organism. Recently, however, Galeazzi et al. have shown that ygaD (now renamed pncC) encodes the E. coli enzyme.

  • Ribosomal RNA is extensively modified. Basturea et al. have now identified the last missing enzyme for 16S rRNA modification, RsmJ, which attaches a methyl group to N2 of G1516. In addition, Kimura et al. have shown that RlmL has dual activity, methylating both G2069 and G2445 of 23S rRNA. Now only a single methyltransferase activity, responsible for modifying A2030 of 23S rRNA, remains unidentified. Enzymes responsible for two additional non-methyl modifications of 23S rRNA also remain unknown.

  • Phosphonates are compounds with a direct carbon-phosphorous bond. Although C-P bonds are very stable, phosphonates can be used as a source of phosphorous by a variety of microbes. However, the biochemical pathway for phosphonate degradation had remained enigmatic. Kamat et al. have now elucidated the chemical steps of the methylphosphonate degradation pathway, paving the way for its possible utilization in bioremediation.

15.5 release highlights

  • The function of the inner membrane protein RseP has been expanded. Formerly characterised for its role in the activation of the sigmaE stress response, Saito et al. have reported that it is also involved in the degradation of remnant signal proteins left in the inner membrane (a function previously ascribed to the SppA protein of E. coli).

  • New functions have been added to the periplasmic protein RcnB (formerly YohN) - implicated in the maintenance of intracellular levels of nickel and cobalt, and the membrane-associated protein YidD - required for the efficient insertion and maturation of YidC-dependent inner membrane proteins.

  • Glyoxalase III is an enzyme involved in the degradation of methylglyoxal. The gene encoding the glyoxalase III activity in E. coli was long unknown. Subedi et al. recently showed that glyoxalase III is in fact identical with the protein known as Hsp31.

15.1 release highlights

  • Biochemical characterization and a crystal structure of the periplasmic protein, Spy, has been recently reported by Quan et al.. Spy is a periplasmic chaperone with a unique cradle structure and it is strongly induced by conditions that induce protein unfolding. Spy acts to prevent protein aggregation; it also supports protein refolding in the absence of an energy cofactor – exactly how this is achieved remains a question for further research.

  • Three previously uncharacterized inner membrane proteins have been identified as transporters. Kurihara et al. reported that PlaP (formerly YeeF) functions as a low affinity putrescine symporter; AlaE (formerly YgaW) was characterized by Hori et al. as an inducible L-alanine exporter, and YjbB was reported to be involved in the export of inorganic phosphate by Motomura et al..

  • Epoxyqueuosine reductase is the final enzyme of the pathways that synthesize queuosine, a 7-deazapurine-modified nulceoside that is present in certain tRNAs. Miles et al. showed that the enzyme is encoded by yjeS and renamed the gene to queG. All enzymes of queuosine biosynthesis have now been found, although 7-carboxy-7-deazaguanine synthase (QueE) has only been characterized in Bacillus subtilis.

15.0 release highlights

  • As the target of the β-lactam class of antibiotics, the peptidoglycan synthesizing enzymes are always of great interest. Two groups of researchers recently reported the characterization of the outer membrane lipoproteins LpoA (formerly YraM) and LpoB (formerly YcfM), showing that they form complexes with and regulate the activity of, the peptidoglycan synthetases, PBP1A and PBP1B.

  • New ways of rescuing a stalled ribosome have recently been described. Chadani et al. discovered that the ArfA (formerly YhdL) protein is functionally redundant with SsrA-tagging and trans-translation of peptides encoded by mRNAs that lack an in-frame stop codon. Unlike in the SsrA-trans-translation system, ribosome rescue by ArfA does not involve targeted degradation of the translated peptide. Handa et al. discovered that the YaeJ protein is able to hydrolyze peptidyl-tRNAs generated by translation of non-stop mRNAs or mRNAs containing clusters of rare codons.

  • Two research groups, Durand-Heredia et al. and Hale et al., reported that ZapC (formerly YcbW) is a cell division protein that binds FtsZ and promotes lateral interactions/bundling between FtsZ protofilaments.

14.6 release highlights

  • At least three pathways (alanine biosynthesis I, alanine biosynthesis II, and alanine biosynthesis III) contribute to the synthesis of alanine in E. coli. The evidence for alanine biosynthesis II initially came from cell extract studies and the isolation of the still-unsequenced gene alaB during a screen for genes able to complement an alanine auxotroph (Wang et al., 1987). Recently, the two major glutamate-pyruvate aminotransferases AlaA and AlaC were identified by Kim et al.. AlaA and AlaC together account for 90% of glutamic-pyruvic transaminase (GPT) activity in the cell.

  • The "predicted rRNA methylase" YibK was found to be the methyltransferase responsible for 2'-O-methylation of the wobble nucleotide 34 (cytidine or uridine) ribose in both tRNALeu isoacceptors by Benítez-Páez et al.. The gene was re-named to trmL.

  • A new toxin/antitoxin system, RnlA/RnlB, part of the putative integrated lambdoid prophage CP4-57, was described by Koga et al.. Interestingly, the toxin component, RnlA, was previously identified as RNase LS, an antagonist of bacteriophage T4 infection. The antitoxin, RnlB, interacts directly with RnlA and suppresses RNase LS activity.

14.5 release highlights

  • NADH:ubiquinone oxidoreductase I (NDH-1) is an NADH dehydrogenase that catalyzes the transfer of electrons from NADH to the quinone pool in the cytoplasmic membrane and is able to generate a proton electrochemical gradient. The study of this enzyme is of great interest, because it is considered to be a structurally minimal form of a proton-pumping NADH:ubiquinone oxidoreductase and serves as a model for the more complex mitochondrial enzyme. Recently, Efremov et al. solved a crystal structure of the membrane domain of NDH-1 and postulated a plausible mechanism of electron transfer and its coupling to proton translocation. Proton translocation may be induced by movement of the long amphipathic α-helix of the NuoL subunit that is aligned parallel to the membrane.

  • New functions were assigned for the inner membrane proteins YfgF, reported to be a cyclic di-GMP phosphodiesterase by Lacey et al., and YbdG, characterised as a low abundance mechanosensitive channel of miniconductance by Schumann et al..

  • Despite its importance, the origin of the pimeloyl moiety, an essential precursor for the synthesis of biotin, has long been enigmatic. Lin et al. have now shown that its synthesis involves enzymes of the fatty acid elongation cycle as well as the BioC and BioH enzymes. The new 7-keto-8-aminopelargonate biosynthesis I pathway summarizes these findings.

14.1 release highlights

  • In 2006, a new metabolic pathway for utilization of pyrimidines as the sole source of nitrogen was discovered by Loh et al.. Recently, Kim et al. and Mukherjee et al. have characterized the pyrimidine oxygenase that catalyzes the first step of this pathway.

  • The characterisation of several chaperone-usher fimbrial operons (sfmACDHF, ycbQRSTUVF, yraHIJK, yadCKLMhtrEecpDyadN, yehABCD, and yfcOPQRSTUV) in E. coli K-12 was recently reported by Korea et al. (PMID 20345943). These operons are cryptic under normal laboratory conditions, but induced expression in strains lacking the normal type I fimbrial genes resulted in phenotypes that included biofilm formation, adhesion to eukaryotic epithelial cells and microscopically observable pili.

  • Three groups of investigators, Boehm et al., Paul et al. and Fang et al., have identified YcgR as a regulator of flagellar motility in response to the small signaling molecule cyclic di-GMP.

14.0 release highlights

  • With a single exception, all enzymes that methylate various sites in the 16S ribosomal RNA have now been identified. The most recent additions were RsmH and RsmI, which were found to be responsible for methylation of C1402 at N4 of cytosine and the 2'-O position of the ribose moiety, respectively. You can read the original publication here.

  • Crystal structures of a number of proteins that are thought to form a carboxysome-like proteinaceous microcompartment that functions in ethanolamine utilization were recently reported by Tanaka et al. (PMID 20044574). The structures of EutS, EutL, EutK and EutM are suggestive of their functions, and we are looking forward to their functional characterization in E. coli.

  • The YtfQ protein has been identified as a galactofuranose binding protein - the periplasmic component of a predicted ABC-type transporter (YtfQRT/YjfF). You can read the original publication here.

13.6 release highlights

  • YjdL peptide transporter. Despite decades of study, E. coli still includes many genes without assigned functions. In a recent paper, YjdL was characterized as a dipeptide transporter. Click here to learn more about this recently characterized protein.

13.5 release highlights

  • Methylthioadenosine degradation. E. coli is generally very efficient, making full use of all its metabolic inputs. In the case of spermidine and aminopropylcadaverine synthesis, methylthioribose is generated as an apparent waste product. Inside the cell, these biosynthetic processes actually generate methylthioadenosine, which is converted into methylthioribose, which is then excreted. To learn more about this conversion process, click here and check out the new pathway.

13.1 release highlights

  • Putrescine transporter PuuP. Putrescine, a product of organic decomposition, can be used by E. coli in the synthesis of spermidine, aminobutanal, and other metabolites, and more generally to feed carbon and nitrogen into the cell's metabolic network. Recently, the mechanism by which putrescine makes its way into the cell was clarified, as its importer was characterized as a proton-dependent transporter. For more about PuuP and the role of putrescine in the cell, click here and start exploring.

13.0 release highlights

  • Rod shape-determining membrane protein. An E. coli cell is a tiny rod, usually a little more than twice as long as it is wide. Unraveling the basis of cell shape is an ongoing area of active research. Since our last release, the protein formerly known as YfgA has been identified as a key player in regulating the length of the long axis of the E. coli cell. This protein straddles the cell membrane, forming helical filaments along the cell periphery and quite possibly interacting with the machinery of peptidoglycan synthesis to directly impact cell shape. Click here to read about the newly renamed RodZ, and its role in making sure E. coli maintains its shape.

12.5 release highlights

  • NADH to cytochrome bo oxidase electron transfer. The proton-motive force across the cytoplasmic membrane is essential for life, powering ATP synthesis and the action of proton-driven symporters. As shown in this pathway, two NADH:ubiquinone oxidoreductase and cytochrome bo terminal oxidase work together to transfer electrons from NADH to oxygen, using the energy from those electrons to pump protons across the cytoplasmic membrane and generate the proton-motive force. This pathway is one of eleven new electron transfer pathways in the 12.5 release, capitalizing on our recently added ability to represent electron transfer half reactions and combine them to generate pathways. Click here to learn more about this fundamental pathway of energy generation.

12.1 release highlights

  • Membrane-bound lytic murein transglycosylase F. Even after years of research, many E. coli gene functions are still unknown, and researchers continue to identify novel gene functions and round out our knowledge of this fundamental model organism. This EcoCyc release includes a number of newly identified gene functions, such as the characterization of yfhD as a murein transglycosylase. The newly renamed mltF joins an already large group of transglycosylases that catalyze the breakdown of peptidoglycan. Click here or click through from the MltF entry to see that reaction and the many other enzymes that catalyze it as well.

12.0 release highlights

  • Control of the hisLGDCBHAFI operon by attenuation. Attenuation offers an additional level of regulation of gene expression, above and beyond control of transcriptional activation by transcription factors. The hisLGDCBHAFI operon is a classic example of transcriptional attenuation modulated by the eventual downstream product of the enzymes coded for by the genes within the operon. We've recently added the capability to formally represent attenuation within EcoCyc. For other examples, take a look at the dual attenuation control of ilvBN and the complex case of bglGFB.

11.6 release highlights

  • Fructose degradation. Fructose is one of many possible carbon sources for E. coli. The newly introduced pathway of fructose degradation describes the critical linkage between fructose uptake and conversion of fructose into a form usable by glycolysis. Click through to this concise pathway to see how investing a little bit of energy up front lets E. coli thrive on this hexose sugar.

11.5 release highlights

  • Methylerythritol phosphate biosynthesis. The five-carbon isoprene unit is the building block of thousands of important natural products. Whereas humans and other mammals synthesize their isoprene from acetyl-CoA via the mevalonate pathway, E. coli and many other microbes use an alternate pathway that starts with D-glyceraldehyde-3-phosphate and pyruvate to achieve the same end. These different isoprene generation systems are relevant for basic biology, drug development against pathogens, and synthetic engineering, and provide a good starting point for learning about how evolution can give us more than one path to the same goal. Click through to the MEP and mevalonate pathways to learn more about these two parallel routes to the all-important isoprene.
  • Chitobiose degradation. Chitin is the second most abundant biopolymer after cellulose, giving form to arthropods and fungi the world over. The major breakdown product of chitin, chitobiose, is imported into the cell by the chitobiose PTS transporter and then degraded into an end product that can eventually feed into glycolysis and beyond. Click through to the pathway to see how this transformation occurs, and then keep clicking to track the eventual fate of chitobiose as a carbon source for E. coli.