Topological analysis of glucosyltransferase GtrV of Shigella flexneri by a dual reporter system and identification of a unique reentrant loop

Defining Membrane Protein Topology Using pho-lac Reporter Fusions

Experimental determination of membrane protein topology can be achieved using various techniques. Here, we present the pho-lac dual reporter system, a simple, convenient, and reliable tool to analyze the topology of membrane protein in vivo. The system is based on the use of two topological markers with complementary properties: The Escherichia coli β-galactosidase, LacZ, which is active in the cytoplasm, and the E. coli alkaline phosphatase, PhoA, which is active in the bacterial periplasm. Specifically, in this pho-lac gene system, the reporter molecule is a chimera composed of the mature PhoA that is in-frame with the β-galactosidase α-peptide (LacZα). Hence, when targeted to the periplasm, the PhoA-LacZα dual reporter displays high alkaline phosphatase activity but no β-galactosidase activity. Conversely, when located in the cytoplasm, PhoA-LacZα has no phosphatase activity but exhibits high β-galactosidase activity in E. coli cells expressing the α-fragment of LacZ, LacZα (via the α-complementation phenomenon). The dual nature of the PhoA-LacZα reporter allows a simple way to normalize both enzymatic activities to obtain readily interpretable information about the subcellular location of the fusion site between the membrane protein under study and the reporter. In addition, the PhoA-LacZα reporter permits the utilization of dual indicator agar plates to easily discriminate between colonies bearing cytoplasmic fusions, periplasmic fusions, or out-of-frame fusions. In total, the phoA-lacZα fusion reporter approach is a direct and rather inexpensive method to characterize the topology of membrane proteins in vivo.

Structure and genetics of Escherichia coli O antigens

Escherichia coli includes clonal groups of both commensal and pathogenic strains, with some of the latter causing serious infectious diseases. O antigen variation is current standard in defining strains for taxonomy and epidemiology, providing the basis for many serotyping schemes for Gram-negative bacteria. This review covers the diversity in E. coli O antigen structures and gene clusters, and the genetic basis for the structural diversity. Of the 187 formally defined O antigens, six (O31, O47, O67, O72, O94 and O122) have since been removed and three (O34, O89 and O144) strains do not produce any O antigen. Therefore, structures are presented for 176 of the 181 E. coli O antigens, some of which include subgroups. Most (93%) of these O antigens are synthesized via the Wzx/Wzy pathway, 11 via the ABC transporter pathway, with O20, O57 and O60 still uncharacterized due to failure to find their O antigen gene clusters. Biosynthetic pathways are given for 38 of the 49 sugars found in E. coli O antigens, and several pairs or groups of the E. coli antigens that have related structures show close relationships of the O antigen gene clusters within clades, thereby highlighting the genetic basis of the evolution of diversity.

Genetic Characterization of the O-Antigen and Development of a Molecular Serotyping Scheme for Enterobacter cloacae

Enterobacter cloacae is a well-characterized opportunistic pathogen that is closely associated with various nosocomial infections. The O-antigen, which is one of the most variable constituents on the cell surface, has been used widely and traditionally for serological classification of many gram-negative bacteria. E. cloacae is divided into 30 serotypes, based on its O-antigen diversity. In this study, by using genomic and comparative-genomic approaches, we analyzed the O-antigen gene clusters of 26 E. cloacae serotypes in depth. We also identified the sero-specific gene for each serotype and developed a multiplex polymerase chain reaction (PCR) method. The sensitivity of the assay was 0.1 ng for genomic DNA and 10³ colony forming units for pure cultures. The assay reliability was evaluated by double-blinded testing with 81 clinical strains. Furthermore, we established a valid, genome-based tool for in silico serotyping of E. cloacae. By screening 431 E. cloacae genomes deposited in GenBank, 304 were classified into current antigenic scheme, and 112 were allocated into 55 putative novel serotypes. Our results represent the first genetic basis of the O-antigen diversity and variation of E. cloacae, providing a rationale for studying the O-antigen associated evolution and pathogenesis of this bacterium. In addition, we extended the current serotyping system for E. cloacae, which is important for detection and epidemiological surveillance purposes for this important pathogen.

Defining Membrane Protein Topology Using pho-lac Reporter Fusions

Experimental determination of membrane protein topology can be achieved using various techniques. Here we present the pho-lac dual reporter system, a simple, convenient, and reliable tool to analyze the topology of membrane proteins in vivo. The system is based on the use of two topological markers with complementary properties, the Escherichia coli β-galactosidase LacZ, which is active in the cytoplasm, and the E. coli alkaline phosphatase PhoA, which is active in the bacterial periplasm. Specifically, in this pho-lac gene system, the reporter molecule is a chimera composed of the mature PhoA that is in frame with the β-galactosidase α-peptide, LacZα. Hence, when targeted to the periplasm, the PhoA-LacZα dual reporter displays high alkaline phosphatase activity but no β-galactosidase activity. Conversely, when located in the cytoplasm, PhoA-LacZα has no phosphatase activity but exhibits high β-galactosidase activity in E. coli cells expressing the ω fragment of LacZ, LacZω (via the α-complementation phenomenon). The dual nature of the PhoA-LacZα reporter allows a simple way to normalize both enzymatic activities to obtain readily interpretable information about the subcellular location of the fusion site between the membrane protein under study and the reporter. In addition, the PhoA-LacZα reporter permits utilization of dual-indicator agar plates to easily discriminate between colonies bearing cytoplasmic fusions, periplasmic fusions, or out-of-frame fusions. In total, the phoA-lacZα fusion reporter approach is a straightforward and rather inexpensive method of characterizing the topology of membrane proteins in vivo.

pqiABC and yebST, Putative mce Operons of Escherichia coli, Encode Transport Pathways and Contribute to Membrane Integrity

The membranes of single-cell organisms are crucial as the first line of defense. The outer membrane of Gram-negative bacteria is an asymmetric bilayer in which lipopolysaccharides (LPSs) and phospholipids are localized in the outer and inner leaflet, respectively. This asymmetry is important for membrane integrity. In Escherichia coli, the Mla transport pathway maintains this asymmetry by removing phospholipids from the outer leaflet. The MlaD component of this system is a mammalian cell entry (MCE) domain protein, and E. coli has two other MCE domain proteins of unknown function (PqiB and YebT). Here, we show that these two proteins are components of novel transport pathways that contribute to membrane integrity. The pqiAB operon is regulated by SoxS and RpoS. The yebST operon contains pqiAB homologues. Here, we found a third member of the pqi operon, ymbA (pqiC). A PqiB-PqiC complex bridges the inner and the outer membrane, and in other bacteria, pqiBC genes are located in operons together with transporter proteins. We show here that simultaneous deletion of pqiABC and yebST operons in an Δmla background rendered cells more sensitive to SDS-EDTA, and the SDS-EDTA sensitivity of mla mutants was rescued by additional copies of pqiABC We also found that the yebST operon was induced by a defect in LPS molecules. In conclusion, PqiABC and YebST are novel transport pathways related to the Mla transport pathway and important for membrane integrity.

IMPORTANCE

Membranes of bacteria are crucial for stress resistance. The composition of the E. coli outer membrane is asymmetric, with asymmetry maintained by the Mla ABC transport pathway. We propose that the stress-inducible pqiABC operon and homologous yebST operon, both of previously unknown function, encode transport pathway proteins related to the Mla transport pathway. Deletion of these operons rendered cells more sensitive to membrane stress, and additional copies of pqiABC suppressed the SDS-EDTA sensitivity of mla mutant strains. We found that yebS'-'lacZ fusion was activated in mutant strains with defective LPS molecules.

A widespread three-component mechanism for the periplasmic modification of bacterial glycoconjugates

The diverse structures of bacterial glycoconjugates are generally established during the early stages of synthesis by the activities of nucleotide sugar-dependent glycosyltransferases active in the cytoplasm. However, in some cases, further modifications of varying complexity occur after the glycoconjugate is exported to the periplasm. These processes are distinguished by the involvement of polyprenyl monosphosphoryl donors and require glycosyltransferases possessing GT-C folds. Established prototypes are found in modifications of some bacterial lipopolysaccharides, where 4-amino-4-deoxy-l-arabinose is added to lipid A and glucose side branches are used to modify O-antigens. Here we review the current understanding of these systems and describe similarities to other periplasmic glycan modifications in bacteria and the N-glycosylation pathway for assembly of eukaryotic glycoproteins.

Burkholderia cenocepacia and Salmonella enterica ArnT proteins that transfer 4-amino-4-deoxy-l-arabinose to lipopolysaccharide share membrane topology and functional amino acids

We recently demonstrated that incorporation of 4-amino-4-deoxy-l-arabinose (l-Ara4N) to the lipid A moiety of lipopolysaccharide (LPS) is required for transport of LPS to the outer membrane and viability of the Gram-negative bacterium Burkholderia cenocepacia. ArnT is a membrane protein catalyzing the transfer of l-Ara4N to the LPS molecule at the periplasmic face of the inner membrane, but its topology and mechanism of action are not well characterized. Here, we elucidate the topology of ArnT and identify key amino acids that likely contribute to its enzymatic function. PEGylation assays using a cysteineless version of ArnT support a model of 13 transmembrane helices and a large C-terminal region exposed to the periplasm. The same topological configuration is proposed for the Salmonella enterica serovar Typhimurium ArnT. Four highly conserved periplasmic residues in B. cenocepacia ArnT, tyrosine-43, lysine-69, arginine-254 and glutamic acid-493, were required for activity. Tyrosine-43 and lysine-69 span two highly conserved motifs, ⁴²RYA⁴⁴ and ⁶⁶YFEKP⁷⁰, that are found in ArnT homologues from other species. The same residues in S. enterica ArnT are also needed for function. We propose these aromatic and charged amino acids participate in either undecaprenyl phosphate-l-Ara4N substrate recognition or transfer of l-Ara4N to the LPS.

Topological investigation of glucosyltransferase V in Shigella flexneri using the substituted cysteine accessibility method

Modification of the lipopolysaccharide O-antigen of Shigella converts the serotype, which is significant as acquired immune responses are serotype specific. Glucosyltransferases (Gtrs) modify the O-antigen by the addition of glucosyl-groups; however the precise mechanism of O-antigen modification is not fully understood. This study aims to substantiate inferences made on the GtrV topological structure using the substituted cysteine accessibility method (SCAM). Twenty-one amino acid residues were tested to clarify three features of GtrV: the extramembrane regions, a proposed reentrant loop, and a membrane border region. Overall, the results agreed with a previous topology proposed for GtrV. The topology of GtrV consists of 11 extramembrane regions with a cytoplasmic N-terminus, periplasmic C-terminus and 9 transmembrane (TM) helices. The existence of a reentrant loop between TM helices IV and V was verified, and the cytoplasmic membrane border region of TM helix II was examined in depth.

Topological characterisation and identification of critical domains within glucosyltransferase IV (GtrIV) of Shigella flexneri

Background

The three bacteriophage genes gtrA, gtrB and gtr_(type) are responsible for O-antigen glucosylation in Shigella flexneri. Both gtrA and gtrB have been demonstrated to be highly conserved and interchangeable among serotypes while gtr_(type) was found to be specific to each serotype, leading to the hypothesis that the Gtr_(type) proteins are responsible for attaching glucosyl groups to the O-antigen in a site- and serotype- specific manner. Based on the confirmed topologies of GtrI, GtrII and GtrV, such interaction and attachment of the glucosyl groups to the O-antigen has been postulated to occur in the periplasm.

Results

In this study, the topology of GtrIV was experimentally determined by creating different fusions between GtrIV and a dual-reporter protein, PhoA/LacZ. This study shows that GtrIV consists of 8 transmembrane helices, 2 large periplasmic loops, 2 small cytoplasmic N- and C- terminal ends and a re-entrant loop that occurs between transmembrane helices III and IV. Though this topology differs from that of GtrI, GtrII, GtrV and GtrX, it is very similar to that of GtrIc. Furthermore, both the N-terminal periplasmic and the C-terminal periplasmic loops are important for GtrIV function as shown via a series of loop deletion experiments and the creation of chimeric proteins between GtrIV and its closest structural homologue, GtrIc.

Conclusion

The current study provides the basis for elucidating the structure and mechanism of action of this important O-antigen modifying glucosyltransferase.

Structural and functional divergence of the newly identified GtrIc from its Gtr family of conserved Shigella flexneri serotype-converting glucosyltransferases

Glucosyltransferases (Gtrs) and O-acetyltransferase (Oac) are integral membrane proteins embedded within the cytoplasmic membrane of Shigella flexneri. Gtrs and Oac are responsible for unidirectional host serotype conversion by altering the epitopic properties of the bacterial surface lipopolysaccharide (LPS) O-antigen. In this study, we present the membrane topology of a recently recognized Gtr, GtrIc, which is known to mediate S. flenxeri serotype switching from 1a to 1c. The GtrIc topology is shown to deviate from those typically seen in S. flexneri Gtrs. GtrIc has 11 hydrophilic loops, 10 transmembrane helices, a double intramembrane dipping loop 5, and a cytoplasmic N- and C-terminus. Along with a unique membrane topology, the identification of non-critical Gtr-conserved peptide motifs within large periplasmic loops (N-terminal D/ExD/E and C-terminal KK), which have previously been proven essential for the activity of other Gtrs, challenge current opinions of a similar mechanism for enzyme function between members of the S. flexneri Gtr family.

Identification of active site residues in the Shigella flexneri glucosyltransferase GtrV

The serotype-specific glucosyltransferase, GtrV, is responsible for glucosylation of the O-antigen repeating unit of Shigella flexneri serotype 5a strains. GtrV is an integral inner membrane protein with two essential periplasmic loops: the large Loop 2 and the C-terminal Loop 10. In this study, the full length of the Loop 2 was shown to be necessary for GtrV function. Site-directed mutagenesis within this loop revealed that conserved aromatic and charged amino acids have a critical role in the formation of the active site. Sequential deletions of the C-terminal end indicated that this region may be essential for assembly of the protein in the cytoplasmic membrane. The highly conserved FWAED motif is thought to form the substrate-binding site and was found to be critical in GtrV and GtrX, a serotype-specific glucosyltransferase with homology to GtrV. The data presented constitutes a targeted analysis of the formation of the GtrV active site and highlights the essential role of the large periplasmic Loop 2 in its function.

Genomic analysis of bacteriophage epsilon 34 of Salmonella enterica serovar Anatum (15+)

Background

The presence of prophages has been an important variable in genetic exchange and divergence in most bacteria. This study reports the determination of the genomic sequence of Salmonella phage ε³⁴, a temperate bacteriophage that was important in the early study of prophages that modify their hosts' cell surface and is of a type (P22-like) that is common in Salmonella genomes.

Results

The sequence shows that ε³⁴ is a mosaically related member of the P22 branch of the lambdoid phages. Its sequence is compared with the known P22-like phages and several related but previously unanalyzed prophage sequences in reported bacterial genome sequences.

Conclusion

These comparisons indicate that there has been little if any genetic exchange within the procapsid assembly gene cluster with P22-like E. coli/Shigella phages that are have orthologous but divergent genes in this region. Presumably this observation reflects the fact that virion assembly proteins interact intimately and divergent proteins can no longer interact. On the other hand, non-assembly genes in the "ant moron" appear to be in a state of rapid flux, and regulatory genes outside the assembly gene cluster have clearly enjoyed numerous and recent horizontal exchanges with phages outside the P22-like group. The present analysis also shows that ε³⁴ harbors a gtrABC gene cluster which should encode the enzymatic machinery to chemically modify the host O antigen polysaccharide, thus explaining its ability to alter its host's serotype. A comprehensive comparative analysis of the known phage gtrABC gene clusters shows that they are highly mobile, having been exchanged even between phage types, and that most "bacterial" gtrABC genes lie in prophages that vary from being largely intact to highly degraded. Clearly, temperate phages are very major contributors to the O-antigen serotype of their Salmonella hosts.

Topology and identification of critical residues of the O-acetyltransferase of serotype-converting bacteriophage, SF6, of Shigella flexneri

The modification of the LPS O-antigen, seen in the diverse serotypes of Shigella flexneri is brought about by the glucosyltransferases (Gtr) and the O-acetyltransferase (Oac). In this study, we establish the membrane topology of Oac using the dual reporter PhoA-LacZalpha. We have determined that Oac is an integral membrane protein with 10 transmembrane regions. The hydrophilic N- and C-termini are oriented in the cytoplasm. Functionally important cytoplasmic and periplasmic loops have also been identified. Furthermore, cytoplasmic residues R73 and R75R76 were found to be critical to Oac function.

Identification of essential loops and residues of glucosyltransferase V (GtrV) of Shigella flexneri

Lipopolysaccharide (LPS), particularly the O-antigen component, is one of many virulence determinants necessary for Shigella flexneri pathogenesis. O-antigen modification is mediated by glucosyltransferase (gtr) genes encoded by temperate serotype-converting bacteriophages. The gtrV and gtrX genes encode the GtrV and GtrX glucosyltransferases, respectively. These are integral membrane proteins, which catalyze the transfer of a glucosyl residue via an alpha1,3 linkage to rhamnose II and rhamnose I of the O-antigen unit. This mediates conversion of S. flexneri serotype Y to serotype 5a and X, respectively. Essential regions in the topology of GtrV protein were identified by in vivo recombination and a PCR-mediated approach. A series of GtrX-GtrV and GtrV-GtrX chimeric proteins were constructed based on the fact that GtrV and GtrX share sequence similarity. Analysis of their respective serotype conversion abilities led to the identification of two important periplasmic loops: loops No 2 and No 10 located in the N- and C-termini, respectively. Within these two loops, three conserved motifs were identified; two in loop No 2 and one in loop No 10. These conserved motifs contain acidic residues which were shown to be critical for GtrV function.

Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes

Alongside the well-studied membrane spanning helices, alpha-helical transmembrane (TM) proteins contain several functionally and structurally important types of substructures. Here, existing 3D structures of transmembrane proteins have been used to define and study the concept of reentrant regions, i.e. membrane penetrating regions that enter and exit the membrane on the same side. We find that these regions can be divided into three distinct categories based on secondary structure motifs, namely long regions with a helix-coil-helix motif, regions of medium length with the structure helix-coil or coil-helix and regions of short to medium length consisting entirely of irregular secondary structure. The residues situated in reentrant regions are significantly smaller on average compared to other regions and reentrant regions can be detected in the inter-transmembrane loops with an accuracy of approximately 70% based on their amino acid composition. Using TOP-MOD, a novel method for predicting reentrant regions, we have scanned the genomes of Escherichia coli, Saccharomyces cerevisiae and Homo sapiens. The results suggest that more than 10% of transmembrane proteins contain reentrant regions and that the occurrence of reentrant regions increases linearly with the number of transmembrane regions. Reentrant regions seem to be most commonly found in channel proteins and least commonly in signal receptors.

Bacteriophage-encoded glucosyltransferase GtrII of Shigella flexneri: membrane topology and identification of critical residues

The Shigella flexneri serotypes differ in the nature of their O-antigens. The addition of glucosyl or O-acetyl groups to the common backbone repeat units gives rise to the different serotypes. GtrII glucosylates rhamnose III of the O-antigen repeat unit, thus converting serotype Y (which has no modifications to the basic O-antigen repeat unit) into serotype 2a, the most prevalent serotype. In the present study, the topology of GtrII has been determined. GtrII has nine transmembrane helices, a re-entrant loop and three large periplasmic regions. Four critical residues (Glu40, Phe414, Cys435 and Lys478) were identified in two of the periplasmic regions. Despite the lack of sequence similarity between GtrII and the Gtrs from other serotypes, three of the critical residues identified are conserved in the remaining Gtrs. This is consistent with some degree of mechanistic conservation in this functionally related group of proteins.

Topological analysis of GtrA and GtrB proteins encoded by the serotype-converting cassette of Shigella flexneri

Serotype conversion (O-antigen glucosylation) in Shigella flexneri is mediated by temperate bacteriophages, which encode a three-gene cluster that contains gtrA, gtrB, and gtr([type]). Sequence analysis has revealed that gtrA and gtrB are conserved and readily interchangeable between serotypes. The gtr([type]) is unique in each serotype and responsible for specifically mediating conversion by the addition of a glucosyl group to the O-antigen units. Analysis of the GtrA and GtrB amino acid sequence using computer prediction programs indicated that GtrA and GtrB have four and two transmembrane segments, respectively. The topology model of GtrA was analyzed by constructing consecutive sandwich fusions using a dual reporter PhoA/LacZ at predetermined positions targeting each of the 3 cytoplasmic and 2 periplasmic hypothetical loops. The topology of GtrB was determined by constructing C-terminal truncated fusions of GtrB to full-length PhoA and LacZ by a PCR-mediated method. These approaches revealed that GtrA consists of four transmembrane segments with both the N-terminal and C-terminal ends in the cytoplasm. Accordingly, GtrB consists of two transmembrane segments with both ends also in the cytoplasm. Furthermore, membrane anchorage of the extended N-terminal end of GtrB was found to be important in catalysis. This study completes the topology of all three proteins (GtrA, GtrB, and the gtr([type]): GtrV) involved in the glucosyltransferase activity that results in serotype conversion of S. flexneri. A model is proposed showing how both O-antigen synthesis and modification take place in S. flexneri.