The gene for 2-phosphoglycolate phosphatase (gph) in Escherichia coli is located in the same operon as dam and at least five other diverse genes

Physiological and transcriptional studies reveal Cr(VI) reduction mechanisms in the exoelectrogen Cellulomonas fimi Clb-11

A facultative exoelectrogen, Cellulomonas fimi strain Clb-11, was isolated from polluted river water. This strain could generate electricity in microbial fuel cells (MFCs) with carboxymethyl cellulose (CMC) as the carbon source, and the maximum output power density was 12.17 ± 2.74 mW·m^-2. In addition, Clb-11 could secrete extracellular chromate reductase or extracellular electron mediator to reduce Cr(VI) to Cr(III). When the Cr(VI) concentration was less than 0.5 mM in Luria-Bertani (LB) medium, Cr(VI) could be completely reduced by Clb-11. However, the Clb-11 cells swelled significantly in the presence of Cr(VI). We employed transcriptome sequencing analysis to identify genes involved in different Cr(VI) stress responses in Clb-11. The results indicate that 99 genes were continuously upregulated while 78 genes were continuously downregulated as the Cr(VI) concentration increased in the growth medium. These genes were mostly associated with DNA replication and repair, biosynthesis of secondary metabolites, ABC transporters, amino sugar and nucleotide sugar metabolism, and carbon metabolism. The swelling of Clb-11 cells might have been related to the upregulation of the genes atoB, INO1, dhaM, dhal, dhak, and bccA, which encode acetyl-CoA C-acetyltransferase, myo-inositol-1-phosphate synthase, phosphoenolpyruvate-glycerone phosphotransferase, and acetyl-CoA/propionyl-CoA carboxylase, respectively. Interestingly, the genes cydA and cydB related to electron transport were continuously downregulated as the Cr(VI) concentration increased. Our results provide clues to the molecular mechanism of Cr(VI) reduction by microorganisms in MFCs systems.

The Synechocystis sp. PCC 6803 Genome Encodes Up to Four 2-Phosphoglycolate Phosphatases

Photorespiratory phosphoglycolate (2PG) metabolism is essential for cyanobacteria, algae, and plants. The first enzyme of the pathway, 2PG phosphatase (PGPase), is known from plants and algae but was scarcely investigated in cyanobacteria. In silico analysis revealed four candidate genes (slr0458, slr0586, sll1349, and slr1762) in the genome of the model cyanobacterium Synechocystis sp. PCC 6803 that all belong to the 2-haloacid dehalogenase (HAD) superfamily and could possibly encode PGPase proteins. However, in contrast to known algal and plant PGPases, the putative cyanobacterial PGPases belong to another HAD subfamily implying that PGPases in eukaryotic phototrophs did not originate from cyanobacterial PGPases. To verify their function, these four genes were inactivated both individually and in combination. A mild high-CO₂-requiring (HCR) growth phenotype typical for photorespiratory mutants was observed only in Δsll1349. Combinatorial inactivation enhanced the HCR phenotype in specific double and triple mutants. Heterologous expression of the putative cyanobacterial PGPases in E. coli led to higher PGPase activities in crude cell extracts, but only the purified Slr0458 protein showed PGPase activity. Hence, we propose that a consortium of up to four photorespiratory PGPases may initiate photorespiratory 2PG metabolism in Synechocystis. We suggest that redundancy of this essential enzyme activity could be related to the highly adaptive lifestyle of cyanobacteria such as Synechocystis sp. PCC 6803, which allows them to grow under very diverse conditions.

Aminoacyl-tRNA Synthetases in the Bacterial World

Aminoacyl-tRNA synthetases (aaRSs) are modular enzymes globally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation. Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g., in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show huge structural plasticity related to function and limited idiosyncrasies that are kingdom or even species specific (e.g., the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS). Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably between distant groups such as Gram-positive and Gram-negative Bacteria. The review focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation, and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulated in last two decades is reviewed, showing how the field moved from essentially reductionist biology towards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRS paralogs (e.g., during cell wall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointed throughout the review and distinctive characteristics of bacterium-like synthetases from organelles are outlined.

Transcriptional Profiling of a Cross-Protective Salmonella enterica serovar Typhimurium UK-1 dam Mutant Identifies a Set of Genes More Transcriptionally Active Compared to Wild-Type, and Stably Transcribed across Biologically Relevant Microenvironments

Vaccination with Salmonella enterica serovar Typhimurium lacking DNA adenine methyltransferase confers cross-protective immunity against multiple Salmonella serotypes. The mechanistic basis is thought to be associated with the de-repression of genes that are tightly regulated when transiting from one microenvironment to another. This de-repression provides a potential means for the production of a more highly expressed and stable antigenic repertoire capable of inducing cross-protective immune responses. To identify genes encoding proteins that may contribute to cross-protective immunity, we used a Salmonella Typhimurium DNA adenine methyltransferase mutant strain (UK-1 dam mutant) derived from the parental UK-1 strain, and assessed the transcriptional profile of the UK-1 dam mutant and UK-1 strain grown under conditions that simulate the intestinal or endosomal microenvironments encountered during the infective process. As expected, the transcriptional profile of the UK-1 dam mutant identified a set of genes more transcriptionally active when compared directly to UK-1, and stably transcribed in biologically relevant culture conditions. Further, 22% of these genes were more highly transcribed in comparison to two other clinically-relevant Salmonella serovars. The strategy employed here helps to identify potentially conserved proteins produced by the UK-1 dam mutant that stimulate and/or modulate the development of cross-protective immune responses toward multiple Salmonella serotypes.

Aminoacyl-tRNA Synthetases in the Bacterial World

Aminoacyl-tRNAsynthetases (aaRSs) are modular enzymesglobally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation.Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g.,in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show hugestructural plasticity related to function andlimited idiosyncrasies that are kingdom or even speciesspecific (e.g.,the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS).Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably betweendistant groups such as Gram-positive and Gram-negative Bacteria.Thereview focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation,and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulatedin last two decades is reviewed,showing how thefield moved from essentially reductionist biologytowards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRSparalogs (e.g., during cellwall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointedthroughout the reviewand distinctive characteristics of bacterium-like synthetases from organelles are outlined.

The DamX protein of Escherichia coli and Salmonella enterica

We recently showed that disruption of damX causes bile sensitivity in Salmonella enterica. The damX gene is part of an operon that contains genes with heterogeneous functions: DNA adenine methylation, biosynthesis of aromatic compounds, carbohydrate metabolism, and tRNA charging. The damX gene encodes a protein with a predicted size of 46 kDa. In Salmonella, DamX is found in the inner membrane of both dividing and non-dividing cells. The DamX protein contains a peptidoglycan-binding SPOR domain, and accumulates in the E. coli septal ring. E. coli mutants lacking DamX are bile-sensitive like their Salmonella counterparts.

Identification of the Salmonella enterica damX gene product, an inner membrane protein involved in bile resistance

The damX gene product of Salmonella enterica serovar Typhimurium is a protein located in the inner membrane. DamX migrates as a 70-kDa protein in SDS-PAGE even though the predicted protein size is 46 kDa. Synthesis of DamX protein occurs in both exponential- and stationary-phase cultures. Disruption of damX causes severe sensitivity to bile. Lack of the outer membrane protein AsmA suppresses bile sensitivity in Salmonella damX mutants.

Biosynthesis of the Aromatic Amino Acids

This chapter describes in detail the genes and proteins of Escherichia coli involved in the biosynthesis and transport of the three aromatic amino acids tyrosine, phenylalanine, and tryptophan. It provides a historical perspective on the elaboration of the various reactions of the common pathway converting erythrose-4-phosphate and phosphoenolpyruvate to chorismate and those of the three terminal pathways converting chorismate to phenylalanine, tyrosine, and tryptophan. The regulation of key reactions by feedback inhibition, attenuation, repression, and activation are also discussed. Two regulatory proteins, TrpR (108 amino acids) and TyrR (513 amino acids), play a major role in transcriptional regulation. The TrpR protein functions only as a dimer which, in the presence of tryptophan, represses the expression of trp operon plus four other genes (the TrpR regulon). The TyrR protein, which can function both as a dimer and as a hexamer, regulates the expression of nine genes constituting the TyrR regulon. TyrR can bind each of the three aromatic amino acids and ATP and under their influence can act as a repressor or activator of gene expression. The various domains of this protein involved in binding the aromatic amino acids and ATP, recognizing DNA binding sites, interacting with the alpha subunit of RNA polymerase, and changing from a monomer to a dimer or a hexamer are all described. There is also an analysis of the various strategies which allow TyrR in conjunction with particular amino acids to differentially affect the expression of individual genes of the TyrR regulon.

Identification of a large noncoding RNA in extremophilic eubacteria

We have discovered a large and highly conserved RNA motif that typically resides in a noncoding section of a multigene messenger RNA in extremophilic Gram-positive eubacteria. RNAs of this class adopt an ornate secondary structure, are large compared with most other noncoding RNAs, and have been identified only in certain extremophilic bacteria. These ornate, large, extremophilic (OLE) RNAs have a length of approximately 610 nucleotides, and the 35 representatives examined exhibit extraordinary conservation of nucleotide sequence and base pairing. Structural probing of the OLE RNA from Bacillus halodurans corroborates a complex secondary structure model predicted from comparative sequence analysis. The patterns of structural conservation, and its unique phylogenetic distribution, suggest that OLE RNA carries out a complex and critical function only in certain extremophilic bacteria.

YbiV from Escherichia coli K12 is a HAD phosphatase

The protein YbiV from Escherichia coli K12 MG1655 is a hypothetical protein with sequence homology to the haloacid dehalogenase (HAD) superfamily of proteins. Although numerous members of this family have been identified, the functions of few are known. Using the crystal structure, sequence analysis, and biochemical assays, we have characterized YbiV as a HAD phosphatase. The crystal structure of YbiV reveals a two-domain protein, one with the characteristic HAD hydrolase fold, the other an inserted alpha/beta fold. In an effort to understand the mechanism, we also solved and report the structures of YbiV in complex with beryllofluoride (BeF3-) and aluminum trifluoride (AlF3), which have been shown to mimic the phosphorylated intermediate and transition state for hydrolysis, respectively, in analogy to other HAD phosphatases. Analysis of the structures reveals the substrate-binding cavity, which is hydrophilic in nature. Both structure and sequence homology indicate YbiV may be a sugar phosphatase, which is supported by biochemical assays that measured the release of free phosphate on a number of sugar-like substrates. We also investigated available genomic and functional data in an effort to determine the physiological substrate.

Structure- and function-based characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum

The protein TA0175 has a large number of sequence homologues, most of which are annotated as unknown and a few as belonging to the haloacid dehalogenase superfamily, but has no known biological function. Using a combination of amino acid sequence analysis, three-dimensional crystal structure information, and kinetic analysis, we have characterized TA0175 as phosphoglycolate phosphatase from Thermoplasma acidophilum. The crystal structure of TA0175 revealed two distinct domains, a larger core domain and a smaller cap domain. The large domain is composed of a centrally located five-stranded parallel beta-sheet with strand order S10, S9, S8, S1, S2 and a small beta-hairpin, strands S3 and S4. This central sheet is flanked by a set of three alpha-helices on one side and two helices on the other. The smaller domain is composed of an open faced beta-sandwich represented by three antiparallel beta-strands, S5, S6, and S7, flanked by two oppositely oriented alpha-helices, H3 and H4. The topology of the large domain is conserved; however, structural variation is observed in the smaller domain among the different functional classes of the haloacid dehalogenase superfamily. Enzymatic assays on TA0175 revealed that this enzyme catalyzed the dephosphorylation of phosphoglycolate in vitro with similar kinetic properties seen for eukaryotic phosphoglycolate phosphatase. Activation by divalent cations, especially Mg2+, and competitive inhibition behavior with Cl- ions are similar between TA0175 and phosphoglycolate phosphatase. The experimental evidence presented for TA0175 is indicative of phosphoglycolate phosphatase.

Role of 2-phosphoglycolate phosphatase of Escherichia coli in metabolism of the 2-phosphoglycolate formed in DNA repair

The enzyme 2-phosphoglycolate phosphatase from Escherichia coli, encoded by the gph gene, was purified and characterized. The enzyme was highly specific for 2-phosphoglycolate and showed good catalytic efficiency (k(cat)/K(m)), which enabled the conversion of this substrate even at low intracellular concentrations. A comparison of the structural and functional features of this enzyme with those of 2-phosphoglycolate phosphatases of different origins showed a high similarity of the sequences, implying the use of the same catalytic mechanism. Western blot analysis revealed constitutive expression of the gph gene, regardless of the carbon source used, growth stage, or oxidative stress conditions. We showed that this housekeeping enzyme is involved in the dissimilation of the intracellular 2-phosphoglycolate formed in the DNA repair of 3'-phosphoglycolate ends. DNA strand breaks of this kind are caused by agents such as the radiomimetic compound bleomycin. The differential response between a 2-phosphoglycolate phosphatase-deficient mutant and its parental strain after treatment with bleomycin allowed us to connect the intracellular formation of 2-phosphoglycolate with the production of glycolate, which is subsequently incorporated into general metabolism. We thus provide evidence for a salvage function of 2-phosphoglycolate phosphatase in the metabolism of a two-carbon compound generated by the cellular DNA repair machinery.