Structure of wild-type and mutant repressors and of the control region of the rbt operon of Klebsiella aerogenes

Enterobacterhormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes

Background: The predominant species in clinical Enterobacter isolates is E. hormaechei. Many articles, clinicians, and GenBank submissions misname these strains as E. cloacae. The lack of sequenced type strains or named species/subspecies for some clades in the E. cloacae complex complicate the issue. Methods: The genomes of the type strains for Enterobacter hormaechei subsp.  oharae, E.  hormaechei subsp.  steigerwaltii, and E. xiangfangensis, and two strains from Hoffmann clusters III and IV of the E. cloacae complex were sequenced. These genomes, the E.  hormaechei subsp.  hormaechei type strain, and other available Enterobacter type strains were analysed in conjunction with all extant Enterobacter genomes in NCBI's RefSeq using Average Nucleotide Identity (ANI). Results: There were five recognizable subspecies of E. hormaechei: E. hormaechei subsp. hoffmannii subsp. nov., E. hormaechei subsp. xiangfangensis comb. nov., and the three previously known subspecies. One of the strains sequenced from the E. cloacae complex was not a novel E. hormaechei subspecies but rather a member of a clade of a novel species: E. roggenkampii sp. nov.. E. muelleri was determined to be a later heterotypic synonym of E. asburiae which should take precedence. Conclusion: The phylogeny of the Enterobacter genus, particularly the cloacae complex, was re-evaluated based on the type strain genome sequences and all other available Enterobacter genomes in RefSeq.

Comprehensive Genome Analysis of Carbapenemase-Producing Enterobacter spp.: New Insights into Phylogeny, Population Structure, and Resistance Mechanisms

Knowledge regarding the genomic structure of Enterobacter spp., the second most prevalent carbapenemase-producing Enterobacteriaceae, remains limited. Here we sequenced 97 clinical Enterobacter species isolates that were both carbapenem susceptible and resistant from various geographic regions to decipher the molecular origins of carbapenem resistance and to understand the changing phylogeny of these emerging and drug-resistant pathogens. Of the carbapenem-resistant isolates, 30 possessed bla_KPC-2, 40 had bla_KPC-3, 2 had bla_KPC-4, and 2 had bla_NDM-1. Twenty-three isolates were carbapenem susceptible. Six genomes were sequenced to completion, and their sizes ranged from 4.6 to 5.1 Mbp. Phylogenomic analysis placed 96 of these genomes, 351 additional Enterobacter genomes downloaded from NCBI GenBank, and six newly sequenced type strains into 19 phylogenomic groups—18 groups (A to R) in the Enterobacter cloacae complex and Enterobacter aerogenes. Diverse mechanisms underlying the molecular evolutionary trajectory of these drug-resistant Enterobacter spp. were revealed, including the acquisition of an antibiotic resistance plasmid, followed by clonal spread, horizontal transfer of bla_KPC-harboring plasmids between different phylogenomic groups, and repeated transposition of the bla_KPC gene among different plasmid backbones. Group A, which comprises multilocus sequence type 171 (ST171), was the most commonly identified (23% of isolates). Genomic analysis showed that ST171 isolates evolved from a common ancestor and formed two different major clusters; each acquiring unique bla_KPC-harboring plasmids, followed by clonal expansion. The data presented here represent the first comprehensive study of phylogenomic interrogation and the relationship between antibiotic resistance and plasmid discrimination among carbapenem-resistant Enterobacter spp., demonstrating the genetic diversity and complexity of the molecular mechanisms driving antibiotic resistance in this genus.

Enterobacter spp., especially carbapenemase-producing Enterobacter spp., have emerged as a clinically significant cause of nosocomial infections. However, only limited information is available on the distribution of carbapenem resistance across this genus. Augmenting this problem is an erroneous identification of Enterobacter strains because of ambiguous typing methods and imprecise taxonomy. In this study, we used a whole-genome-based comparative phylogenetic approach to (i) revisit and redefine the genus Enterobacter and (ii) unravel the emergence and evolution of the Klebsiella pneumoniae carbapenemase-harboring Enterobacter spp. Using genomic analysis of 447 sequenced strains, we developed an improved understanding of the species designations within this complex genus and identified the diverse mechanisms driving the molecular evolution of carbapenem resistance. The findings in this study provide a solid genomic framework that will serve as an important resource in the future development of molecular diagnostics and in supporting drug discovery programs.

Genes for D-arabinitol and ribitol catabolism from Klebsiella pneumoniae

The enzymes for catabolism of the pentitols D-arabinitol (Dal) and ribitol (Rbt) and the corresponding genes from Klebsiella pneumoniae (dal and rbt) and Escherichia coli (atl and rtl) have been used intensively in experimental evolutionary studies. Four dal and four rbt genes from the chromosome of K. pneumoniae 1033-5P14 were cloned and sequenced. These genes are clustered in two adjacent but divergently transcribed operons and separated by two convergently transcribed repressor genes, dalR and rbtR. Each operon encodes an NAD-dependent pentose dehydrogenase (dalD and rbtD), and ATP-dependent pentulose kinase (dalK and rbtK) and a pentose-specific ion symporter (dalT and rbtT). Although the biochemical reactions which they catalyse are highly similar, the enzymes showed interesting deviations. Thus, DalR (313 aa) and RbtR (270 aa) belong to different repressor families, and DalD (455 aa) and RbtD (248 aa), which are active as a monomer or as tetramers, respectively, belong to different dehydrogenase families. Of the two kinases (19.3% identity), DalK (487 aa) belongs to the subfamily of short D-xylulokinases and RbtK (D-ribulokinase; 535 aa) to the subfamily of long kinases. The repressor, dehydrogenase and kinase genes did not show extensive similarity beyond local motifs. This contrasts with the ion symporters (86.6% identity) and their genes (82.7% identity). Due to their unusually high similarity, parts of dalT and rbtT have previously been claimed erroneously to correspond to 'inverted repeats' and possible remnants of a 'metabolic transposon' comprising the dal and rbt genes. Other characteristic structures, e.g. a secondary att lambda site and chi-like sites, as well as the conservation of this gene group in E. coli C are also discussed.

Substrate recognition domains as revealed by active hybrids between the D-arabinitol and ribitol transporters from Klebsiella pneumoniae

Two new genes, dalT and rbtT, have been cloned from the dal operon for D-arabinitol and the rbt operon for ribitol uptake and degradation, respectively, in Klebsiella pneumoniae 1033-5P14, derivative KAY2026. Each gene codes for a specific transporter which, based on sequence data, belongs to a large family of carbohydrate transporters which constitutes 12 transmembrane helices. DalT and RbtT show an unusually high similarity (86.2% identical residues for totals of 425 and 427 amino acids, respectively). This allowed the construction of DalT'-Rbt"T and RbtT'-Dal'T crossover hybrids by using a natural restriction site overlapping Met202. This site is located within the large cytoplasmic loop which connects the putative helices 6 and 7 and in particular the amino- and the carboxy-terminal halves of the transporters. Both hybrids have close to normal transport activities but essentially the substrate specificities and kinetic properties of the amino-terminal half. This result localizes essential substrate binding and recognition sites to the amino-terminal halves of the proteins in this important class of carbohydrate transporters.

Structural characterization and corepressor binding of the Escherichia coli purine repressor

The Escherichia coli purine repressor, PurR, binds to a 16-bp operator sequence and coregulates the genes for de novo synthesis of purine and pyrimidine nucleotides, formation of a one-carbon unit for biosynthesis, and deamination of cytosine. We have characterized the purified repressor. Chemical cross-linking indicates that PurR is dimeric. Each subunit has an N-terminal domain of 52 amino acids for DNA binding and a C-terminal 289-residue domain for corepressor binding. Each domain was isolated after cleavage by trypsin. Sites for dimer formation are present within the corepressor binding domain. The corepressors hypoxanthine and guanine bind cooperatively to distinct sites in each subunit. Competition experiments indicate that binding of one purine abolishes cooperativity and decreases the affinity and the binding of the second corepressor. Binding of each corepressor results in a conformation change in the corepressor binding domain that was detected by intrinsic fluorescence of three tryptophan residues. These experiments characterize PurR as a complex allosteric regulatory protein.

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.

MalI, a novel protein involved in regulation of the maltose system of Escherichia coli, is highly homologous to the repressor proteins GalR, CytR, and LacI

The maltose regulon of Escherichia coli comprises several operons that are under common regulatory control of the MalT activator protein. Five mal genes, organized in two divergent operons, code for a binding-protein-dependent transport system specific for maltose and maltodextrins. MalK, one of the subunits of this transport system, not only is essential for transport but also plays a role in regulation. Mutations abolishing MalK function not only result in inability to transport maltose but also cause constitutive expression of the maltose regulon. For this constitutivity to be exerted, the function of an additional gene product, MalI, is necessary. Using the constitutive expression of a malK-lacZ fusion as a signal, we cloned the malI gene, expressed it in minicells, and determined its DNA sequence. The sequence predicted a protein of 34,729 molecular weight, in agreement with the apparent molecular weight of the protein (35,000) when expressed in minicells and analyzed by polyacrylamide gel electrophoresis and autoradiography. MalI exhibited high homology to the repressor proteins GalR, CytR, and LacI. When the amino acid sequences were appropriately aligned, MalI showed 28% identity to GalR, 21% to CytR, and 24% to LacI. Including conservative amino acid exchanges, these numbers increased to 69, 56, and 58%, respectively. The regions of high homology were clustered in particular at the N-terminal portion of the protein that includes the helix-turn-helix motif thought to be involved in DNA binding. The protein contained a short stretch of 30 amino acids that was surprisingly homologous to a sequence in MalT. The amino-terminal half of the protein exhibited significant homology with MalK. The transcriptional start of malI was determined by reverse transcriptase and by S1 nuclease mapping. We found a possible binding site for cyclic AMP receptor protein in the promoter region of malI as well as two perfect direct repeats of 14 base pairs with twofold symmetry indicating their possible role as operator sites. Upstream to malI we observed a divergent open reading frame that extended to the end of the sequenced DNA.