BB0250 of Borrelia burgdorferi Is a Conserved and Essential Inner Membrane Protein Required for Cell Division

The gene bb0250 of Borrelia burgdorferi is a homolog of the dedA family, encoding integral inner membrane proteins that are present in nearly all species of bacteria. To date, no precise function has been attributed to any dedA gene. Unlike many bacterial species, such as Escherichia coli, which has eight dedA genes, B. burgdorferi possesses only one, annotated bb0250, providing a unique opportunity to investigate the functions of the dedA family. Here, we show that bb0250 is able to restore normal growth and cell division to a temperature-sensitive E. coli mutant with simultaneous deletions of two dedA genes, yqjA and yghB, and encodes a protein that localizes to the inner membrane of E. coli. The bb0250 gene could be deleted from B. burgdorferi only after introduction of a promoterless bb0250 under the control of an inducible lac promoter, indicating that it is an essential gene in this organism. Growth of the mutant in the absence of isopropyl-β-d-thiogalactopyranoside resulted in cell death, preceded by cell division defects characterized by elongated cells and membrane bulges, demonstrating that bb0250 is required for proper cell division and envelope integrity. Finally, we show that BB0250 depletion leads to imbalanced membrane phospholipid composition in borrelia. These results demonstrate a strong conservation of function of the dedA gene family across diverse species of Gram-negative bacteria and a requirement for this protein family for normal membrane lipid composition and cell division.The dedA family is a highly conserved bacterial gene family encoding inner membrane proteins of unknown function (35). There are more than 2,000 homologs currently found in the NCBI protein database (protein BLAST score versus Escherichia coli DedA of <0.02), and many species of bacteria have multiple homologs. This built-in redundancy has precluded easy genetic analysis. Each of the dedA homologs in E. coli (yqjA, yghB, yabI, yohD, dedA, ydjX, ydjZ, and yqaA) is individually nonessential as the single gene knockouts have been made and are available in the Keio collection (1). Our group has determined that simultaneous deletion of yghB and yqjA from E. coli results in a strain (named BC202; ΔyghB::Kan^r ΔyqjA::Tet^r) that has abnormal membrane phospholipid composition, does not complete cell division (forming chains of cells), and fails to grow at 42°C (35). YghB and YqjA are proteins of 219 and 220 amino acids, respectively, displaying 61% amino acid identity. The other six E. coli homologs display roughly 25 to 30% amino acid identity with each other and YghB/YqjA.The E. coli mutant BC202 referred to above displays several intriguing phenotypes that reflect important functions for the DedA family. The membrane and cell division defects of BC202 are present at both the permissive and nonpermissive growth temperatures. However, BC202 is not hypersensitive to antibiotics or detergents, likely signifying an intact outer membrane, under permissive growth conditions (35). We have demonstrated that the periplasmic amidases AmiA and AmiC are not exported to the periplasm in E. coli mutant BC202 (31). These amidases are normally exported across the inner membrane via the twin arginine transport (Tat) pathway in E. coli (6), a Sec-independent protein export pathway found in many bacteria and also present in archaea and plants (4, 5, 11, 26). AmiA and AmiC are required for normal cell division and envelope integrity (19). ΔTat mutants also display cell division defects due to loss of amidase export (6, 33). Overexpression of the components of the Tat pathway (TatABC) restores normal cell division and growth to BC202 (31). However, BC202 shares some, but not all, phenotypes with ΔTat and amidase mutants. In spite of this progress, a precise function for these genes remains to be determined.We are interested in determining if the functions of dedA family genes are conserved in diverse bacterial species. The spirochete Borrelia burgdorferi is a Gram-negative pathogen that is the cause of Lyme disease (3, 9, 34). B. burgdorferi has a complex enzootic life cycle where it cycles between tick and vertebrate hosts with unique patterns of gene expression to ensure survival in each host (20, 29). The B. burgdorferi genome has been sequenced and consists of one linear chromosome and 21 linear and circular plasmids (17). Notably, its genome possesses only one dedA family homolog, annotated bb0250, present on the linear chromosome. Since tools for the genetic manipulation of B. burgdorferi are available and because of the lack of genome redundancy of dedA genes in this organism, we sought to examine the function and essentiality of B. burgdorferi bb0250. Here, we show that cloned bb0250 can complement the mutant phenotypes of E. coli mutant BC202 and localizes to the inner membrane in E. coli. Furthermore, we have deleted bb0250 from B. burgdorferi, and we demonstrate that it is an essential gene in this organism. Loss of gene expression from an inducible plasmid results in cell division defects, morphological abnormalities, changes in membrane phospholipid composition, and growth arrest, implying a general role for DedA family membrane proteins in cell division and maintenance of proper membrane composition and function. Intriguingly, these phenotypes are independent of any role these proteins may play in the Tat protein export pathway since the B. burgdorferi genome does not encode homologs of TatABC or any proteins with predicted Tat-dependent signal peptides (12). These results demonstrate conserved and important functions for DedA family inner membrane proteins in bacterial cell physiology.     

Inefficient Tat-Dependent Export of Periplasmic Amidases in an Escherichia coli Strain with Mutations in Two DedA Family Genes

The DedA family genes are found in most bacterial genomes. Two of these proteins are Escherichia coli YqjA and YghB, predicted inner membrane proteins of unknown function sharing 61% amino acid identity. The E. coli single deletion mutants are largely without phenotype, but the double mutant (BC202; ΔyqjA::Tet^r ΔyghB::Kan^r) is characterized by incomplete cell division, temperature sensitivity, and altered phospholipid levels (K. Thompkins et al., J. Bacteriol. 190:4489-4500, 2008). In this report, we have better characterized the cell division chaining defect of BC202. Fluorescence recovery after photobleaching indicates that 58% of the cells in chains are compartmentalized by at least a cytoplasmic membrane. Green fluorescent protein fusions to the cell division proteins FtsZ, ZipA, FtsI, FtsL, and FtsQ are correctly localized to new septation sites in BC202. Periplasmic amidases AmiC and AmiA, secreted by the twin arginine transport (Tat) pathway, are localized to the cytoplasm in BC202. Overexpression of AmiA, AmiC, or AmiB, a periplasmic amidase secreted via the general secretory pathway, restores normal cell division but does not suppress the temperature sensitivity of BC202, indicating that YghB and YqjA may play additional roles in cellular physiology. Strikingly, overexpression of the Tat export machinery (TatABC) results in normal cell division and growth at elevated temperatures. These data collectively suggest that the twin arginine pathway functions inefficiently in BC202, likely due to the altered levels of membrane phospholipids in this mutant. These results underscore the importance of membrane composition in the proper function of the Tat protein export pathway.Roughly 25 to 30% of the genes in sequenced genomes are predicted to encode integral membrane proteins (12). The functions of many of these genes, even in a well-studied organism such as Escherichia coli, remain unknown. We have reported on the functional redundancy of two highly conserved and related E. coli inner membrane proteins, YqjA and YghB (40). These proteins belong to a large family (commonly called the DedA family) found widespread in most sequenced genomes. yghB and yqjA encode predicted inner membrane proteins with multiple membrane-spanning domains and 61% amino acid identity. In addition, E. coli contains three other genes predicted to encode proteins with significant similarity to YqjA and YghB (YabI, YohD, and DedA; amino acid BLAST E value of <1 × 10⁻⁶) and two other proteins with lower degrees of similarity (YdjX and YdjZ). Currently, there are >1,000 genes in the NCBI protein database annotated as either belonging to this family or possessing significant amino acid identity to E. coli DedA/YghB/YqjA (protein BLAST E values of <0.02). No member of this family has a known function, nor is it known whether they possess common functions across phylogenetic groups.Individually, yghB and yqjA are nonessential genes, as each single deletion mutant grows normally (2). However, BC202, an E. coli strain with targeted deletions of both yqjA and yghB, does not grow above 42°C and displays a dramatic cell division phenotype by forming chains of cells when grown at the permissive temperature of 30°C. Phase-contrast and scanning electron microscopy analysis of BC202 suggests that mutants can begin septation but are blocked at a later step in constriction (40). The cause of this phenotype is unclear.BC202 also has alterations in membrane phospholipid composition (40). While BC202 is capable of synthesizing all classes of phospholipids at all growth temperatures, it is depleted of phosphatidylethanolamine (PE), with elevated levels of the acidic phospholipids phosphatidylglycerol (PG) and cardiolipin (CL). In some respects, BC202 resembles phosphatidylserine synthase deletion mutants, such as AD90 (pss93::Kan^r), which produces no membrane PE (14). Mutants deficient in PE are viable, but they require divalent cations for growth (14) and display cell division abnormalities (28, 33). Likewise, normal growth and cell division are restored to BC202 when LB growth medium is supplemented with millimolar concentrations of divalent cations (40). Unlike many mutants defective in cell wall synthesis, BC202 is not hypersensitive to detergents or antibiotics, indicating the presence of an intact outer membrane when grown at the permissive temperature.BC202, therefore, displays several phenotypes: a block at an apparent late stage of cell division, temperature sensitivity, and an imbalance in membrane phospholipid composition. To better understand the functions of YghB and YqjA, we have hypothesized two roles for these genes that are not mutually exclusive to explain the phenotypes of BC202. First, YqjA/YghB may play direct roles in cell division. The phospholipid phenotype may be a consequence secondary to the primary cell division defect in this scenario. Second, YqjA/YghB may play a direct role in efficient PE synthesis or controlling membrane phospholipid composition. The cell division phenotype may be a secondary consequence of the lipid imbalance. Here, we have better characterized the cell division phenotype of BC202 by using green fluorescent protein (GFP) fusions of cell division proteins and fluorescence recovery after photobleaching (FRAP) analysis. We find that while most of the cell division proteins are correctly localized to new septal rings, the periplasmic amidase AmiC is not localized to the septal ring as was reported previously (5), and this may be responsible for the observed cell division phenotype of BC202. AmiC is found mostly in the cytoplasmic compartment in BC202, as is AmiA, both of which are exported to the periplasm by the twin arginine pathway (5). The cell division defect of BC202 can be corrected by overexpression of periplasmic amidases or the TatABC operon, collectively suggesting that the Tat pathway functions inefficiently in BC202.     

Identification of Bacillus subtilis YidC Substrates Using a MifM-instructed Translation Arrest-based Reporter

YidC is a member of the YidC/Oxa1/Alb3 protein family that is crucial for membrane protein biogenesis in the bacterial plasma membrane. While YidC facilitates the folding and complex assembly of membrane proteins along with the Sec translocon, it also functions as a Sec-independent membrane protein insertase in the YidC-only pathway. However, little is known about how membrane proteins are recognized and sorted by these pathways, especially in Gram-positive bacteria, for which only a small number of YidC substrates have been identified to date. In this study, we aimed to identify Bacillus subtilis membrane proteins whose membrane insertion depends on SpoIIIJ, the primary YidC homolog in B. subtilis. We took advantage of the translation arrest sequence of MifM, which can monitor YidC-dependent membrane insertion. Our systematic screening identified eight membrane proteins as candidate SpoIIIJ substrates. Results of our genetic study also suggest that the conserved arginine in the hydrophilic groove of SpoIIIJ is crucial for the membrane insertion of the substrates identified here. However, in contrast to MifM, a previously identified YidC substrate, the importance of the negatively charged residue on the substrates for membrane insertion varied depending on the substrate. These results suggest that B. subtilis YidC uses substrate-specific interactions to facilitate membrane insertion.     

Phage Resistance of a Marine Bacterium, Roseobacter denitrificans OCh114, as Revealed by Comparative Proteomics

Roseobacter is a dominant lineage in the marine environment. This group of bacteria is diverse in terms of both their phylogenetic composition and their physiological potential. Roseobacter denitrificans OCh114 is one of the most studied bacteria of the Roseobacter lineage. Recently, a lytic phage (RDJLΦ1) that infects this bacterium was isolated and a mutant strain (M1) of OCh114 that is resistant to RDJLΦ1 was also obtained. Here, we investigate the mechanisms supporting phage resistance of M1. Our results excluded the possibilities of several phage resistance mechanisms, including abortive infection, lysogeny, and the clustered regularly interspaced short palindromic repeats (CRISPRs) related mechanism. Adsorption kinetics assays revealed that adsorption inhibition might be a potential cause for the phage resistance of M1. Comparative proteomic analysis of M1 and OCh114 revealed significant changes in the membrane protein compliment of these bacteria. Five membrane proteins with important biological functions were significantly down-regulated in the phage-resistant M1. Meanwhile, several outer membrane porins with different modifications and an OmpA family domain protein were markedly up-regulated. We hypothesize that the down-regulated membrane proteins in M1 may serve as the potential phage receptors, whose absence prevented the adsorption of phage RDJLΦ1 to host cells and subsequent infection.     

The Bacillus subtilis Nucleotidyltransferase Is a tRNA CCA-Adding Enzyme

There has been increased interest in bacterial polyadenylation with the recent demonstration that 3′ poly(A) tails are involved in RNA degradation. Poly(A) polymerase I (PAP I) of Escherichia coli is a member of the nucleotidyltransferase (Ntr) family that includes the functionally related tRNA CCA-adding enzymes. Thirty members of the Ntr family were detected in a search of the current database of eubacterial genomic sequences. Gram-negative organisms from the β and γ subdivisions of the purple bacteria have two genes encoding putative Ntr proteins, and it was possible to predict their activities as either PAP or CCA adding by sequence comparisons with the E. coli homologues. Prediction of the functions of proteins encoded by the genes from more distantly related bacteria was not reliable. The Bacillus subtilis papS gene encodes a protein that was predicted to have PAP activity. We have overexpressed and characterized this protein, demonstrating that it is a tRNA nucleotidyltransferase. We suggest that the papS gene should be renamed cca, following the notation for its E. coli counterpart. The available evidence indicates that cca is the only gene encoding an Ntr protein, despite previous suggestions that B. subtilis has a PAP similar to E. coli PAP I. Thus, the activity involved in RNA 3′ polyadenylation in the gram-positive bacteria apparently resides in an enzyme distinct from its counterpart in gram-negative bacteria.     

Identification and Characterization of a Novel Porin Family Highlights a Major Difference in the Outer Membrane of Chlamydial Symbionts and Pathogens

The Chlamydiae constitute an evolutionary well separated group of intracellular bacteria comprising important pathogens of humans as well as symbionts of protozoa. The amoeba symbiont Protochlamydia amoebophila lacks a homologue of the most abundant outer membrane protein of the Chlamydiaceae, the major outer membrane protein MOMP, highlighting a major difference between environmental chlamydiae and their pathogenic counterparts. We recently identified a novel family of putative porins encoded in the genome of P. amoebophila by in silico analysis. Two of these Protochlamydia outer membrane proteins, PomS (pc1489) and PomT (pc1077), are highly abundant in outer membrane preparations of this organism. Here we show that all four members of this putative porin family are toxic when expressed in the heterologous host Escherichia coli. Immunofluorescence analysis using antibodies against heterologously expressed PomT and PomS purified directly from elementary bodies, respectively, demonstrated the location of both proteins in the outer membrane of P. amoebophila. The location of the most abundant protein PomS was further confirmed by immuno-transmission electron microscopy. We could show that pomS is transcribed, and the corresponding protein is present in the outer membrane throughout the complete developmental cycle, suggesting an essential role for P. amoebophila. Lipid bilayer measurements demonstrated that PomS functions as a porin with anion-selectivity and a pore size similar to the Chlamydiaceae MOMP. Taken together, our results suggest that PomS, possibly in concert with PomT and other members of this porin family, is the functional equivalent of MOMP in P. amoebophila. This work contributes to our understanding of the adaptations of symbiotic and pathogenic chlamydiae to their different eukaryotic hosts.     

Functional and structural characterization of polysaccharide co-polymerase proteins required for polymer export in ATP-binding cassette transporter-dependent capsule biosynthesis pathways

Neisseria meningitidis serogroup B and Escherichia coli K1 bacteria produce a capsular polysaccharide (CPS) that is composed of α2,8-linked polysialic acid (PSA). Biosynthesis of PSA in these bacteria occurs via an ABC (ATP-binding cassette) transporter-dependent pathway. In N. meningitidis, export of PSA to the surface of the bacterium requires two proteins that form an ABC transporter (CtrC and CtrD) and two additional proteins, CtrA and CtrB, that are proposed to form a cell envelope-spanning export complex. CtrA is a member of the outer membrane polysaccharide export (OPX) family of proteins, which are proposed to form a pore to mediate export of CPSs across the outer membrane. CtrB is an inner membrane protein belonging to the polysaccharide co-polymerase (PCP) family. PCP proteins involved in other bacterial polysaccharide assembly systems form structures that extend into the periplasm from the inner membrane. There is currently no structural information available for PCP or OPX proteins involved in an ABC transporter-dependent CPS biosynthesis pathway to support their proposed roles in polysaccharide export. Here, we report cryo-EM images of purified CtrB reconstituted into lipid bilayers. These images contained molecular top and side views of CtrB and showed that it formed a conical oligomer that extended ∼125 Å from the membrane. This structure is consistent with CtrB functioning as a component of an envelope-spanning complex. Cross-complementation of CtrA and CtrB in E. coli mutants with defects in genes encoding the corresponding PCP and OPX proteins show that PCP-OPX pairs require interactions with their cognate partners to export polysaccharide. These experiments add further support for the model of an ABC transporter-PCP-OPX multiprotein complex that functions to export CPS across the cell envelope.     

The ER membrane complex (EMC) can functionally replace the Oxa1 insertase in mitochondria

Two multisubunit protein complexes for membrane protein insertion were recently identified in the endoplasmic reticulum (ER): the guided entry of tail anchor proteins (GET) complex and ER membrane complex (EMC). The structures of both of their hydrophobic core subunits, which are required for the insertion reaction, revealed an overall similarity to the YidC/Oxa1/Alb3 family members found in bacteria, mitochondria, and chloroplasts. This suggests that these membrane insertion machineries all share a common ancestry. To test whether these ER proteins can functionally replace Oxa1 in yeast mitochondria, we generated strains that express mitochondria-targeted Get2–Get1 and Emc6–Emc3 fusion proteins in Oxa1 deletion mutants. Interestingly, the Emc6–Emc3 fusion was able to complement an Δoxa1 mutant and restored its respiratory competence. The Emc6–Emc3 fusion promoted the insertion of the mitochondrially encoded protein Cox2, as well as of nuclear encoded inner membrane proteins, although was not able to facilitate the assembly of the Atp9 ring. Our observations indicate that protein insertion into the ER is functionally conserved to the insertion mechanism in bacteria and mitochondria and adheres to similar topological principles.

Redirecting the core subunits of the protein membrane insertion complex EMC into mitochondria rescues cells deficient for the mitochondrial Oxa1 system; this supports the hypothesis that the machinery for protein insertion into the ER membrane is functionally analogous to the YidC/Oxa1/Alb3 family of bacteria, mitochondria and chloroplasts.     

The α-barrel tip region of Escherichia coli TolC homologs of Vibrio vulnificus interacts with the MacA protein to form the functional macrolide-specific efflux pump MacAB-TolC

TolC and its homologous family of proteins are outer membrane factors that are essential for exporting small molecules and toxins across the outer membrane in Gram-negative bacteria. Two open reading frames in the Vibrio vulnificus genome that encode proteins homologous to Escherichia coli TolC, designated TolCV1 and TolCV2, have 51.3% and 29.6% amino acid identity to TolC, respectively. In this study, we show that TolCV1 and TolCV2 functionally and physically interacted with the membrane fusion protein, MacA, a component of the macrolide-specific MacAB-TolC pump of E. coli. We further show that the conserved residues located at the aperture tip region of the α-hairpin of TolCV1 and TolCV2 played an essential role in the formation of the functional MacAB-TolC pump using site-directed mutational analyses. Our findings suggest that these outer membrane factors have conserved tip-to-tip interaction with the MacA membrane fusion protein for action of the drug efflux pump in Gramnegative bacteria.     

Interaction of Streptococcus mutans YidC1 and YidC2 with Translating and Nontranslating Ribosomes

The YidC/OxaI/Alb3 family of membrane proteins is involved in the biogenesis of integral membrane proteins in bacteria, mitochondria, and chloroplasts. Gram-positive bacteria often contain multiple YidC paralogs that can be subdivided into two major classes, namely, YidC1 and YidC2. The Streptococcus mutans YidC1 and YidC2 proteins possess C-terminal tails that differ in charges (+9 and + 14) and lengths (33 and 61 amino acids). The longer YidC2 C terminus bears a resemblance to the C-terminal ribosome-binding domain of the mitochondrial OxaI protein and, in contrast to the shorter YidC1 C terminus, can mediate the interaction with mitochondrial ribosomes. These observations have led to the suggestion that YidC1 and YidC2 differ in their abilities to interact with ribosomes. However, the interaction with bacterial translating ribosomes has never been addressed. Here we demonstrate that Escherichia coli ribosomes are able to interact with both YidC1 and YidC2. The interaction is stimulated by the presence of a nascent membrane protein substrate and abolished upon deletion of the C-terminal tail, which also abrogates the YidC-dependent membrane insertion of subunit c of the F₁F₀-ATPase into the membrane. It is concluded that both YidC1 and YidC2 interact with ribosomes, suggesting that the modes of membrane insertion by these membrane insertases are similar.     

Split-Doa10: A Naturally Split Polytopic Eukaryotic Membrane Protein Generated by Fission of a Nuclear Gene

Large polytopic membrane proteins often derive from duplication and fusion of genes for smaller proteins. The reverse process, splitting of a membrane protein by gene fission, is rare and has been studied mainly with artificially split proteins. Fragments of a split membrane protein may associate and reconstitute the function of the larger protein. Most examples of naturally split membrane proteins are from bacteria or eukaryotic organelles, and their exact history is usually poorly understood. Here, we describe a nuclear-encoded split membrane protein, split-Doa10, in the yeast Kluyveromyces lactis. In most species, Doa10 is encoded as a single polypeptide with 12–16 transmembrane helices (TMs), but split-KlDoa10 is encoded as two fragments, with the split occurring between TM2 and TM3. The two fragments assemble into an active ubiquitin-protein ligase. The K. lactis DOA10 locus has two ORFs separated by a 508-bp intervening sequence (IVS). A promoter within the IVS drives expression of the C-terminal KlDoa10 fragment. At least four additional Kluyveromyces species contain an IVS in the DOA10 locus, in contrast to even closely related genera, allowing dating of the fission event to the base of the genus. The upstream Kluyveromyces Doa10 fragment with its N-terminal RING-CH and two TMs resembles many metazoan MARCH (Membrane-Associated RING-CH) and related viral RING-CH proteins, suggesting that gene splitting may have contributed to MARCH enzyme diversification. Split-Doa10 is the first unequivocal case of a split membrane protein where fission occurred in a nuclear-encoded gene. Such a split may allow divergent functions for the individual protein segments.     

Bacterial-based membrane protein production

Escherichia coli is by far the most widely used bacterial host for the production of membrane proteins. Usually, different strains, culture conditions and production regimes are screened for to design the optimal production process. However, these E. coli-based screening approaches often do not result in satisfactory membrane protein production yields. Recently, it has been shown that (i) E. coli strains with strongly improved membrane protein production characteristics can be engineered or selected for, (ii) many membrane proteins can be efficiently produced in E. coli-based cell-free systems, (iii) bacteria other than E. coli can be used for the efficient production of membrane proteins, and, (iv) membrane protein variants that retain functionality but are produced at higher yields than the wild-type protein can be engineered or selected for. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.     

Functional assignment to JEV proteins using SVM

Identification of different protein functions facilitates a mechanistic understanding of Japanese encephalitis virus (JEV) infection and opens novel means for drug development. Support vector machines (SVM), useful for predicting the functional class of distantly related proteins, is employed to ascribe a possible functional class to Japanese encephalitis virus protein. Our study from SVMProt and available JE virus sequences suggests that structural and nonstructural proteins of JEV genome possibly belong to diverse protein functions, are expected to occur in the life cycle of JE virus. Protein functions common to both structural and non-structural proteins are iron-binding, metal-binding, lipid-binding, copper-binding, transmembrane, outer membrane, channels/Pores - Pore-forming toxins (proteins and peptides) group of proteins. Non-structural proteins perform functions like actin binding, zinc-binding, calcium-binding, hydrolases, Carbon-Oxygen Lyases, P-type ATPase, proteins belonging to major facilitator family (MFS), secreting main terminal branch (MTB) family, phosphotransfer-driven group translocators and ATP-binding cassette (ABC) family group of proteins. Whereas structural proteins besides belonging to same structural group of proteins (capsid, structural, envelope), they also perform functions like nuclear receptor, antibiotic resistance, RNA-binding, DNA-binding, magnesium-binding, isomerase (intra-molecular), oxidoreductase and participate in type II (general) secretory pathway (IISP).     

Recent advances in recombinant protein expression by Corynebacterium, Brevibacterium, and Streptomyces: from transcription and translation regulation to secretion pathway selection

Gram-positive bacteria are widely used to produce recombinant proteins, amino acids, organic acids, higher alcohols, and polymers. Many proteins have been expressed in Gram-positive hosts such as Corynebacterium, Brevibacterium, and Streptomyces. The favorable and advantageous characteristics (e.g., high secretion capacity and efficient production of metabolic products) of these species have increased the biotechnological applications of bacteria. However, owing to multiplicity from genes encoding the proteins and expression hosts, the expression of recombinant proteins is limited in Gram-positive bacteria. Because there is a very recent review about protein expression in Bacillus subtilis, here we summarize recent strategies for efficient expression of recombinant proteins in the other three typical Gram-positive bacteria (Corynebacterium, Brevibacterium, and Streptomyces) and discuss future prospects. We hope that this review will contribute to the development of recombinant protein expression in Corynebacterium, Brevibacterium, and Streptomyces.     

Ail and PagC-Related Proteins in the Entomopathogenic Bacteria of Photorhabdus Genus

Among pathogenic Enterobacteriaceae, the proteins of the Ail/OmpX/PagC family form a steadily growing family of outer membrane proteins with diverse biological properties, potentially involved in virulence such as human serum resistance, adhesion and entry into eukaryotic culture cells. We studied the proteins Ail/OmpX/PagC in the bacterial Photorhabdus genus. The Photorhabdus bacteria form symbiotic complexes with nematodes of Heterorhabditis species, associations which are pathogenic to insect larvae. Our phylogenetic analysis indicated that in Photorhabdus asymbiotica and Photorhabdus luminescens only Ail and PagC proteins are encoded. The genomic analysis revealed that the Photorhabdus ail and pagC genes were present in a unique copy, except two ail paralogs from P. luminescens. These genes, referred to as ail1 _Pl and ail2 _Pl, probably resulted from a recent tandem duplication. Surprisingly, only ail1 _Pl expression was directly controlled by PhoPQ and low external Mg²⁺ conditions. In P. luminescens, the magnesium-sensing two-component regulatory system PhoPQ regulates the outer membrane barrier and is required for pathogenicity against insects. In order to characterize Ail functions in Photorhabdus, we showed that only ail2 _Pl and pagC _Pl had the ability, when expressed into Escherichia coli, to confer resistance to complement in human serum. However no effect in resistance to antimicrobial peptides was found. Thus, the role of Ail and PagC proteins in Photorhabdus life cycle is discussed.     

Thin Filament Proteins and Thin Filament-Linked Regulation of Vertebrate Muscle Contractio

Abstract

The 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 sugars in yeast (FPS1), and (7) transport of glycerol across bacterial cell membranes (GlpF). One other sequenced member of the MIP family (ORF1 of Lactococcus lactis) has no known physiological function. The biochemical functions of the eukaryotic proteins are not well established.

Computer analyses have revealed that the first and second halves of all MTP family proteins probably arose by a tandem, intragenic, duplication event. Thus, the primary structure of putative transmembrane helices 1 to 3 is similar to that of putative transmembrane helices 4 to 6 even though they are of opposite orientation in the membrane. Among the most conserved residues in these two repeated halves are a membrane-embedded glutamate (E) in helices 1 and 4, an asparagine-proline-alanine (NPA) sequence in the loops between helices 2 and 3 (cytoplasmically localized) and helices 5 and 6 (extracellularly localized), and a glycine within helices 3 and 6. Statistical analyses suggest that the two halves of these proteins have evolved to serve distinct functions: the first half is more important for the generalized or common functions of these proteins, while the second half of these proteins is more differentiated to provide specific or dissimilar functions of the proteins. The apparent origin of MIP family proteins by duplication of a three-spanner precursor protein suggests an evolutionary origin distinct from other transport proteins with six transmembrane spanners. Based on the phylogenetic tree for the 18 sequenced members of the MTP family, we propose that a single, primordial gene arose in prokaryotes shortly before the emergence of eukaryotes, mat this gene was vertically transmitted to the principal eukaryotic kingdoms, and that subsequent gene duplication and divergence events gave rise to kingdom-related subfamilies or clusters of the MIP family.     

Evolutionary origins of members of a superfamily of integral membrane cytochrome c biogenesis proteins

We have analyzed the relationships of homologues of the Escherichia coli CcmC protein for probable topological features and evolutionary relationships. We present bioinformatic evidence suggesting that the integral membrane proteins CcmC (E. coli; cytochrome c biogenesis System I), CcmF (E. coli; cytochrome c biogenesis System I) and ResC (Bacillus subtilis; cytochrome c biogenesis System II) are all related. Though the molecular functions of these proteins have not been fully described, they appear to be involved in the provision of heme to c-type cytochromes, and so we have named them the putative Heme Handling Protein (HHP) family (TC #9.B.14). Members of this family exhibit 6, 8, 10, 11, 13 or 15 putative transmembrane segments (TMSs). We show that intragenic triplication of a 2 TMS element gave rise to a protein with a 6 TMS topology, exemplified by CcmC. This basic 6 TMS unit then gave rise to two distinct types of proteins with 8 TMSs, exemplified by ResC and the archaeal CcmC, and these further underwent fusional or insertional events yielding proteins with 10, 11 and 13 TMSs (ResC homologues) as well as 15 TMSs (CcmF homologues). Specific evolutionary pathways taken are proposed. This work provides the first evidence for the pathway of appearance of distantly related proteins required for post-translational maturation of c-type cytochromes in bacteria, plants, protozoans and archaea.     

Atomistic Molecular-Dynamics Simulations Enable Prediction of the Arginine Permeation Pathway through OccD1/OprD from Pseudomonas?aeruginosa

Pseudomonas aeruginosa is a Gram-negative bacterium that does not contain large, nonspecific porins in its outer membrane. Consequently, the outer membrane is highly impermeable to polar solutes and serves as a barrier against the penetration of antimicrobial agents. This is one of the reasons why such bacteria are intrinsically resistant to antibiotics. Polar molecules that permeate across the outer membrane do so through substrate-specific channels proteins. To design antibiotics that target substrate-channel proteins, it is essential to first identify the permeation pathways of their natural substrates. In P. aeruginosa, the largest family of substrate-specific proteins is the OccD (previously reported under the name OprD) family. Here, we employ equilibrium and steered molecular-dynamics simulations to study OccD1/OprD, the archetypical member of the OccD family. We study the permeation of arginine, one of the natural substrates of OccD1, through the protein. The combination of simulation methods allows us to predict the pathway taken by the amino acid, which is enabled by conformational rearrangements of the extracellular loops of the protein. Furthermore, we show that arginine adopts a specific orientation to form the molecular interactions that facilitate its passage through part of the protein. We predict a three-stage permeation process for arginine.     

Atomistic Molecular-Dynamics Simulations Enable Prediction of the Arginine Permeation Pathway through OccD1/OprD from Pseudomonas aeruginosa

Pseudomonas aeruginosa is a Gram-negative bacterium that does not contain large, nonspecific porins in its outer membrane. Consequently, the outer membrane is highly impermeable to polar solutes and serves as a barrier against the penetration of antimicrobial agents. This is one of the reasons why such bacteria are intrinsically resistant to antibiotics. Polar molecules that permeate across the outer membrane do so through substrate-specific channels proteins. To design antibiotics that target substrate-channel proteins, it is essential to first identify the permeation pathways of their natural substrates. In P. aeruginosa, the largest family of substrate-specific proteins is the OccD (previously reported under the name OprD) family. Here, we employ equilibrium and steered molecular-dynamics simulations to study OccD1/OprD, the archetypical member of the OccD family. We study the permeation of arginine, one of the natural substrates of OccD1, through the protein. The combination of simulation methods allows us to predict the pathway taken by the amino acid, which is enabled by conformational rearrangements of the extracellular loops of the protein. Furthermore, we show that arginine adopts a specific orientation to form the molecular interactions that facilitate its passage through part of the protein. We predict a three-stage permeation process for arginine.