Aiala Reizer

Two novel families of bacterial membrane proteins concerned with nodulation, cell division and transport.

Homology has been established for members of two families of functionally related bacterial membrane proteins. The first family (the resistance/nodulation/cell division (RND) family) Includes (i) two metal‐resistance efflux pumps in Alcaligenes eutrophus (CzcA and CnrA), (ii) three proteins which function together in nodulation of alfalfa roots by Rhizobium meliloti (NoIGHI), and (iii) a cell division protein in Escherichia coli (EnvD). The second family (the putative membrane fusion protein (MFP) family) includes a nodulation protein (NoIF), a cell division protein (EnvC), and a multidrug resistance transport protein (EmrA). We propose that an MFP functions co‐operatively with an RND protein to transport large or hydrophobic molecules across the two membranes of the Gram‐negative bacterial cell envelope.

The MIP Family of Integral Membrane Channel Proteins: Sequence Comparisons, Evolutionary Relationships, Reconstructed Pathway of Evolution, and Proposed Functional Differentiation of the Two Repeated Halves of the Proteins

AbstractThe major intrinsic protein (MIP) of the bovine lens fiber cell membrane was the first member of the MIP family of proteins to be sequenced and characterized. It is probably a homotetramer with transmembrane channel activity that plays a role in lens biogenesis or maintenance. The polypeptide chain of each subunit may span the membrane six times, and both the N- and C-termini face the cell cytoplasm. Eighteen sequenced or partially sequenced proteins from bacteria, yeast, plants, and animals have now been shown to be members of the MIP family. These proteins appear to function in (1) metazoan development and neurogenesis (MIP and BIB), (2) water transport across the human erythrocyte membrane (ChIP), (3) communication between host plant cells and symbiotic nitrogen-fixing bacteria (NOD), (4) transport across the tonoplast membrane during plant seed development (α-TIP), (5) water stress-induced resistance to desiccation in plants (Wsi-TIP), (6) suppression of a genetic growth defect on fermentable ...

A functional superfamily of sodium/solute symporters

Eleven families of sodium/solute symporters are defined based on their degrees of sequence similarities, and the protein members of these families are characterized in terms of their solute and cation specificities, their sizes, their topological features, their evolutionary relationships, and their relative degrees and regions of sequence conservation. In some cases, particularly where site-specific mutagenesis analyses have provided functional information about specific proteins, multiple alignments of members of the relevant families are presented, and the degrees of conservation of the mutated residues are evaluated. Signature sequences for several of the eleven families are presented to facilitate identification of new members of these families as they become sequenced. Phylogenetic tree construction reveals the evolutionary relationships between members of each family. One of these families is shown to belong to the previously defined major facilitator superfamily. The other ten families do not show sufficient sequence similarity with each other or with other identified transport protein families to establish homology between them. This study serves to clarify structural, functional and evolutionary relationships among eleven distinct families of functionally related transport proteins.

Evolutionary relationships between sugar kinases and transcriptional repressors in bacteria

We have characterized a new family of proteins (the ROK family) which includes six transcriptional repressors for sugar catabolic operons, three sugar kinases, and three unidentified open reading frames. Analysis of the aligned sequences and phylogenetic tree construction allow predictions regarding the functional nature of conserved domains and residues within these proteins as well as the pathway of evolutionary divergence that gave rise to the family.

Novel phosphotransferase system genes revealed by genome analysis - the complete complement of PTS proteins encoded within the genome of Bacillus subtilis

Bacillus subtilis can utilize several sugars as single sources of carbon and energy. Many of these sugars are transported and concomitantly phosphorylated by the phosphoenolpyruvate:sugar phosphotransferase system (PTS). In addition to its role in sugar uptake, the PTS is one of the major signal transduction systems in B. subtilis. In this study, an analysis of the complete set of PTS proteins encoded within the B. subtilis genome is presented. Fifteen sugar-specific PTS permeases were found to be present and the functions of novel PTS permeases were studied based on homology to previously characterized permeases, analysis of the structure of the gene clusters in which the permease encoding genes are located and biochemical analysis of relevant mutants. Members of the glucose, sucrose, lactose, mannose and fructose/mannitol families of PTS permeases were identified. Interestingly, nine pairs of IIB and IIC domains belonging to the glucose and sucrose permease families are present in B. subtilis; by contrast only five Enzyme IIA(Glc)-like proteins or domains are encoded within the B. subtilis genome. Consequently, some of the EIIA(Glc)-like proteins must function in phosphoryl transfer to more than one IIB domain of the glucose and sucrose families. In addition, 13 PTS-associated proteins are encoded within the B. subtilis genome. These proteins include metabolic enzymes, a bifunctional protein kinase/phosphatase, a transcriptional cofactor and transcriptional regulators that are involved in PTS-dependent signal transduction. The PTS proteins and the auxiliary PTS proteins represent a highly integrated network that catalyses and simultaneously modulates carbohydrate utilization in this bacterium.

Novel phosphotransferase-encoding genes revealed by analysis of the Escherichia coli genome: a chimeric gene encoding an Enzyme I homologue that possesses a putative sensory transduction domain.

Two genes (ptsI and ptsA) that encode homologues of the energy coupling Enzyme I of the phosphoenolpyruvate-dependent sugar-transporting phosphotransferase system (PTS) have previously been identified on the Escherichia coli chromosome. We here report the presence of a third E. coli gene, designated ptsP, that encodes an Enzyme I homologue, here designated Enzyme INtr. Enzyme INtr possesses an N-terminal domain homologous to the N-terminal domains of NifA proteins [(127 amino acids (aa)] joined via two tandem flexible linkers to the C-terminal Enzyme I-like domain (578 aa). Structural features of the putative ptsP operon, including transcriptional regulatory signals, are characterized. We suggest that Enzyme INtr functions in transcriptional regulation of nitrogen-related operons together with previously described PTS proteins encoded within the rpoN operon. It may thereby provide a link between carbon and nitrogen assimilatory pathways.

Analysis of the gluconate (gnt) operon of Bacillus subtilis

The gluconate (gnt) operon of Bacillus subtilis includes the gntR, gntK, gntP, and gntZ genes, respectively encoding the transcriptional repressor of the operon, gluconate kinase, the gluconate permease, and an unidentified open reading frame (Fujita and Fujita, 1987). We have compared the proteins encoded by the gnt operon of B. subtilis with published sequences and showed that (i) the gluconate repressor is homologous to several putative regulatory proteins in Escherichia coli, (ii) the gluconate kinase of B. subtilis is homologous to xylulose kinase, glycerol kinase and fucose kinase in E. coli (20‐26% identity; 12‐59 S.D.), (iii) the gluconate permease exhibits a C‐terminal domain which is homologous to a hydrophobic protein encoded by an unidentified open reading frame (dsdAp) which precedes the dsdA gene of E. coli (39% identity; 19 S.D.), and (iv) the gntZ gene product is homologous to 6‐phosphogluconate dehydrogenases of other bacteria and of animals (48‐56%; 82‐178 S.D.), thereby suggesting that the B. subtilis gntZ encodes 6‐phosphogluconate dehydro‐genase. Several conserved regions of the sequenced 6‐phosphogluconate dehydrogenases can serve as signature patterns of this protein. Computer analyses have indicated that the previously reported sequences of the porcine and ovine 6‐phosphogluconate dehydrogenases, as well as the hypothetical DsdAp protein, are probably erroneous. The probable reasons for the errors are reported along with the proposed revised sequences.

Bacterial Adenylyl Cyclases

Publisher Summary This chapter describes the enzyme (adenylyl cyclase) that effect the synthesis of Adenosine 3’,5’-cyclic monophosphate (cAMP) in various bacterial species. The content will rather reflect current major interests. The adenylyl cyclase from Escherichia coli has been a major subject of research interest ever since it was identified as the probable point for physiological regulation of cAMP levels in that organism and therefore a prime candidate for a protein mediator of the catabolite repression response mechanism. cAMP functions as a cytoplasmic element mediating some reactions crucial for efficient cellular function. An activity that has been found only in eukaryotic cells is the CAMP-dependent protein kinase . This enzyme is a well-known target of the action of cAMP as a second messenger, in which action this ligand transmits a signal generated by an extracellular hormone. The manner in which cAMP acts on the cAMP-dependent protein kinase involves a release of the catalytic moiety of the enzyme from a complex in which its activity is inhibited as a result of binding to a regulatory subunit.

Novel phosphotransferase system genes revealed by bacterial genome analysis - a gene cluster encoding a unique Enzyme I and the proteins of a fructose-like permease system

Previous publications have demonstrated the presence of a cryptic gene encoding a novel Enzyme I of the phosphoenolpyruvate:sugar phosphotransferase system (PTS). Recent Escherichia coli genome sequencing revealed a gene (ptsA) encoding a new Enzyme I homologue in the 89.1-89.3 centisome region. We have analysed this region, and here describe and characterize open reading frames (ORFs) encoding (1) a fused PTS Enzyme I-IIAFru homologue, (2) a glycerol dehydrogenase, (3) a transaldolase homologue, (4) two PTS IIBFru homologues, (5) a PTS IICFru homologue, and (6) homologues of pyruvate formate-lyase and its activating enzyme. Binary comparison scores, multiple alignments and phylogenetic trees establish the families of proteins to which each of the relevant ORFs belong. Identification of the putative products of this gene cluster leads to the proposal that several of the proteins encoded in this region function in anaerobic carbon metabolism.

Sequence and evolution of the FruR protein of Salmonella typhimurium: a pleiotropic transcriptional regulatory protein possessing both activator and repressor functions which is homologous to the periplasmic ribose-binding protein.

The repressor of the fructose (fru) operon of Salmonella typhimurium (FruR) has been implicated in the transcriptional regulation of dozens of genes concerned with central metabolic pathways of carbon utilization. We here report the nucleotide sequence of the gene encoding FruR and analyse both its operator-promoter region and its deduced amino acyl sequence. The FruR protein was overexpressed and was shown to have a molecular weight of about 36 kDa in agreement with the molecular weight deduced from the gene sequence. Sequence analyses revealed that FruR is homologous to 9 distinct bacterial DNA-binding proteins, most of which recognize sugar inducers and all of which possess helix-turn-helix motifs within their N-terminal regions and exhibit sequence identity throughout most of their lengths. FruR is also homologous to the periplasmic ribose-binding protein which serves as a constituent of the ribose transport/chemoreception system. The ribose-binding protein is in turn homologous to binding proteins specific for arabinose and galactose. The periplasmic binding proteins, the structures of some of which have been elucidated in three dimensions, lack the N-terminal helix-turn-helix region, but instead possess N-terminal hydrophobic signal sequences which target them to the periplasm. A phylogenetic tree for the more closely related proteins of this superfamily was constructed, and a signature motif was identified which should facilitate future detection of additional transcriptional regulatory proteins belonging to this family.