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1.
Mol Cell ; 81(15): 3145-3159.e7, 2021 08 05.
Artigo em Inglês | MEDLINE | ID: mdl-34214465

RESUMO

Hershey and Chase used bacteriophage T2 genome delivery inside Escherichia coli to demonstrate that DNA, not protein, is the genetic material. Seventy years later, our understanding of viral genome delivery in prokaryotes remains limited, especially for short-tailed phages of the Podoviridae family. These viruses expel mysterious ejection proteins found inside the capsid to form a DNA-ejectosome for genome delivery into bacteria. Here, we reconstitute the phage T7 DNA-ejectosome components gp14, gp15, and gp16 and solve the periplasmic tunnel structure at 2.7 Å resolution. We find that gp14 forms an outer membrane pore, gp15 assembles into a 210 Å hexameric DNA tube spanning the host periplasm, and gp16 extends into the host cytoplasm forming a ∼4,200 residue hub. Gp16 promotes gp15 oligomerization, coordinating peptidoglycan hydrolysis, DNA binding, and lipid insertion. The reconstituted gp15:gp16 complex lacks channel-forming activity, suggesting that the pore for DNA passage forms only transiently during genome ejection.


Assuntos
Bacteriófago T7/genética , DNA Viral/química , Periplasma/química , Proteínas do Core Viral/química , Biologia Computacional , Microscopia Crioeletrônica , Citoplasma/química , DNA Viral/metabolismo , Bicamadas Lipídicas/metabolismo , Periplasma/genética , Periplasma/metabolismo , Podoviridae/química , Podoviridae/genética , Proteínas do Core Viral/metabolismo
2.
Proc Natl Acad Sci U S A ; 118(4)2021 01 26.
Artigo em Inglês | MEDLINE | ID: mdl-33472976

RESUMO

The monotopic phosphoglycosyl transferase (monoPGT) superfamily comprises over 38,000 nonredundant sequences represented in bacterial and archaeal domains of life. Members of the superfamily catalyze the first membrane-committed step in en bloc oligosaccharide biosynthetic pathways, transferring a phosphosugar from a soluble nucleoside diphosphosugar to a membrane-resident polyprenol phosphate. The singularity of the monoPGT fold and its employment in the pivotal first membrane-committed step allows confident assignment of both protein and corresponding pathway. The diversity of the family is revealed by the generation and analysis of a sequence similarity network for the superfamily, with fusion of monoPGTs with other pathway members being the most frequent and extensive elaboration. Three common fusions were identified: sugar-modifying enzymes, glycosyl transferases, and regulatory domains. Additionally, unexpected fusions of the monoPGT with members of the polytopic PGT superfamily were discovered, implying a possible evolutionary link through the shared polyprenol phosphate substrate. Notably, a phylogenetic reconstruction of the monoPGT superfamily shows a radial burst of functionalization, with a minority of members comprising only the minimal PGT catalytic domain. The commonality and identity of the fusion partners in the monoPGT superfamily is consistent with advantageous colocalization of pathway members at membrane interfaces.


Assuntos
Proteínas de Bactérias/química , Glicoconjugados/química , Glicosiltransferases/química , Bactérias Gram-Negativas/enzimologia , Bactérias Gram-Positivas/enzimologia , Polissacarídeos/química , Sequência de Aminoácidos , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Citoplasma/enzimologia , Citoplasma/genética , Evolução Molecular , Expressão Gênica , Redes Reguladoras de Genes , Glicoconjugados/metabolismo , Glicosiltransferases/genética , Glicosiltransferases/metabolismo , Bactérias Gram-Negativas/classificação , Bactérias Gram-Negativas/genética , Bactérias Gram-Positivas/classificação , Bactérias Gram-Positivas/genética , Redes e Vias Metabólicas/genética , Modelos Moleculares , Periplasma/enzimologia , Periplasma/genética , Filogenia , Polissacarídeos/metabolismo , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Especificidade por Substrato
3.
Protein Expr Purif ; 210: 106310, 2023 10.
Artigo em Inglês | MEDLINE | ID: mdl-37211150

RESUMO

Escherichia coli has been widely employed as a host for heterologous protein expression. However, due to certain limitations, alternative hosts like Pseudomonas, Lactococcus and Bacillus are being explored. Pseudomonas bharatica CSV86T, a novel soil isolate, preferentially degrades wide range of aromatics over simple carbon sources like glucose and glycerol. Strain also possesses advantageous eco-physiological traits, making it an ideal host for engineering xenobiotic degradation pathways, which necessitates the development of heterologous expression systems. Based on the efficient growth, short lag-phase and rapid metabolism of naphthalene, Pnah and Psal promoters (regulated by NahR) were selected for expression. Pnah was found to be strong and leaky as compared to Psal, using 1-naphthol 2-hydroxylase (1NH, ∼66 kDa) as reporter gene in strain CSV86T. The Carbaryl hydrolase (CH, ∼72 kDa) from Pseudomonas sp. C5pp was expressed under Pnah in strain CSV86T and could successfully be translocated to the periplasm due to the presence of the Tmd + Sp sequence. The recombinant CH was purified from the periplasmic fraction and the kinetic characteristics were found to be similar to the native protein from strain C5pp. These results potentiate the suitability of P. bharatica CSV86T as a desirable host, while Pnah and the Tmd + Sp can be employed for overexpression and periplasmic localisation, respectively. Such tools find application in heterologous protein expression and metabolic engineering applications.


Assuntos
Periplasma , Pseudomonas , Pseudomonas/genética , Periplasma/genética , Periplasma/metabolismo , Carbaril/metabolismo , Hidrolases/metabolismo , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo
4.
Metab Eng ; 72: 68-81, 2022 07.
Artigo em Inglês | MEDLINE | ID: mdl-35257866

RESUMO

Escherichia coli, the most studied prokaryote, is an excellent host for producing valuable chemicals from renewable resources as it is easy to manipulate genetically. Since the periplasmic environment can be easily controlled externally, elucidating how the localization of specific proteins or small molecules in the periplasm affects metabolism may lead to bioproduction development using E. coli. We investigated metabolic changes and its mechanisms occurring when specific proteins are localized to the E. coli periplasm. We found that the periplasmic localization of ß-glucosidase promoted the shikimate pathway involved in the synthesis of aromatic chemicals. The periplasmic localization of other proteins with an affinity for glucose-6-phosphate (G6P), such as inactivated mutants of Pgi, Zwf, and PhoA, similarly accelerated the shikimate pathway. Our results indicate that G6P is transported from the cytoplasm to the periplasm by the glucose transporter protein EIICBGlc, and then captured by ß-glucosidase.


Assuntos
Celulases , Proteínas de Escherichia coli , Celulases/metabolismo , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Glucose-6-Fosfato/metabolismo , Periplasma/genética
5.
Nature ; 537(7622): 661-665, 2016 09 29.
Artigo em Inglês | MEDLINE | ID: mdl-27571282

RESUMO

The field of biocatalysis has advanced from harnessing natural enzymes to using directed evolution to obtain new biocatalysts with tailor-made functions. Several tools have recently been developed to expand the natural enzymatic repertoire with abiotic reactions. For example, artificial metalloenzymes, which combine the versatile reaction scope of transition metals with the beneficial catalytic features of enzymes, offer an attractive means to engineer new reactions. Three complementary strategies exist: repurposing natural metalloenzymes for abiotic transformations; in silico metalloenzyme (re-)design; and incorporation of abiotic cofactors into proteins. The third strategy offers the opportunity to design a wide variety of artificial metalloenzymes for non-natural reactions. However, many metal cofactors are inhibited by cellular components and therefore require purification of the scaffold protein. This limits the throughput of genetic optimization schemes applied to artificial metalloenzymes and their applicability in vivo to expand natural metabolism. Here we report the compartmentalization and in vivo evolution of an artificial metalloenzyme for olefin metathesis, which represents an archetypal organometallic reaction without equivalent in nature. Building on previous work on an artificial metallohydrolase, we exploit the periplasm of Escherichia coli as a reaction compartment for the 'metathase' because it offers an auspicious environment for artificial metalloenzymes, mainly owing to low concentrations of inhibitors such as glutathione, which has recently been identified as a major inhibitor. This strategy facilitated the assembly of a functional metathase in vivo and its directed evolution with substantially increased throughput compared to conventional approaches that rely on purified protein variants. The evolved metathase compares favourably with commercial catalysts, shows activity for different metathesis substrates and can be further evolved in different directions by adjusting the workflow. Our results represent the systematic implementation and evolution of an artificial metalloenzyme that catalyses an abiotic reaction in vivo, with potential applications in, for example, non-natural metabolism.


Assuntos
Alcenos/química , Alcenos/síntese química , Evolução Molecular Direcionada/métodos , Metaloproteínas/química , Metaloproteínas/metabolismo , Engenharia de Proteínas/métodos , Rutênio/metabolismo , Biocatálise , Escherichia coli/citologia , Escherichia coli/genética , Metaloproteínas/genética , Modelos Moleculares , Periplasma/enzimologia , Periplasma/genética , Especificidade por Substrato
6.
Proc Natl Acad Sci U S A ; 116(33): 16314-16319, 2019 08 13.
Artigo em Inglês | MEDLINE | ID: mdl-31363054

RESUMO

Critical for diverse biological processes, proteases represent one of the largest families of pharmaceutical targets. To inhibit pathogenic proteases with desired selectivity, monoclonal antibodies (mAbs) hold great promise as research tools and therapeutic agents. However, identification of mAbs with inhibitory functions is challenging because current antibody discovery methods rely on binding rather than inhibition. This study developed a highly efficient selection method for protease inhibitory mAbs by coexpressing 3 recombinant proteins in the periplasmic space of Escherichia coli-an antibody clone, a protease of interest, and a ß-lactamase modified by insertion of a protease cleavable peptide sequence. During functional selection, inhibitory antibodies prevent the protease from cleaving the modified ß-lactamase, thereby allowing the cell to survive in the presence of ampicillin. Using this method to select from synthetic human antibody libraries, we isolated panels of mAbs inhibiting 5 targets of 4 main protease classes: matrix metalloproteinases (MMP-14, a predominant target in metastasis; MMP-9, in neuropathic pain), ß-secretase 1 (BACE-1, an aspartic protease in Alzheimer's disease), cathepsin B (a cysteine protease in cancer), and Alp2 (a serine protease in aspergillosis). Notably, 37 of 41 identified binders were inhibitory. Isolated mAb inhibitors exhibited nanomolar potency, exclusive selectivity, excellent proteolytic stability, and desired biological functions. Particularly, anti-Alp2 Fab A4A1 had a binding affinity of 11 nM and inhibition potency of 14 nM, anti-BACE1 IgG B2B2 reduced amyloid beta (Aß40) production by 80% in cellular assays, and IgG L13 inhibited MMP-9 but not MMP-2/-12/-14 and significantly relieved neuropathic pain development in mice.


Assuntos
Anticorpos Monoclonais/imunologia , Peptídeo Hidrolases/genética , Inibidores de Proteases/imunologia , Proteínas Recombinantes/imunologia , Doença de Alzheimer/imunologia , Doença de Alzheimer/terapia , Sequência de Aminoácidos/genética , Secretases da Proteína Precursora do Amiloide/genética , Secretases da Proteína Precursora do Amiloide/imunologia , Peptídeos beta-Amiloides/antagonistas & inibidores , Peptídeos beta-Amiloides/genética , Peptídeos beta-Amiloides/imunologia , Animais , Anticorpos Monoclonais/biossíntese , Anticorpos Monoclonais/farmacologia , Ácido Aspártico Endopeptidases/genética , Ácido Aspártico Endopeptidases/imunologia , Aspergilose/imunologia , Aspergilose/terapia , Catepsina B/genética , Catepsina B/imunologia , Escherichia coli/genética , Humanos , Metaloproteinase 14 da Matriz/genética , Metaloproteinase 14 da Matriz/imunologia , Metaloproteinase 9 da Matriz/genética , Metaloproteinase 9 da Matriz/imunologia , Inibidores de Metaloproteinases de Matriz/imunologia , Inibidores de Metaloproteinases de Matriz/metabolismo , Camundongos , Neoplasias/imunologia , Neoplasias/terapia , Peptídeo Hidrolases/química , Peptídeo Hidrolases/imunologia , Periplasma/genética , Inibidores de Proteases/farmacologia , Proteólise/efeitos dos fármacos , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/genética , Proteínas Recombinantes/farmacologia , Serina Proteases/genética , Serina Proteases/imunologia
7.
Proteins ; 89(11): 1473-1488, 2021 11.
Artigo em Inglês | MEDLINE | ID: mdl-34196044

RESUMO

In Gram-negative bacteria, the maintenance of lipid asymmetry (Mla) system is involved in the transport of phospholipids between the inner (IM) and outer membrane. The Mla system utilizes a unique IM-associated periplasmic solute-binding protein, MlaD, which possesses a conserved domain, MlaD domain. While proteins carrying the MlaD domain are known to be primarily involved in the trafficking of hydrophobic molecules, not much is known about this domain itself. Thus, in this study, the characterization of the MlaD domain employing bioinformatics analysis is reported. The profiling of the MlaD domain of different architectures reveals the abundance of glycine and hydrophobic residues and the lack of cysteine residues. The domain possesses a conserved N-terminal region and a well-preserved glycine residue that constitutes a consensus motif across different architectures. Phylogenetic analysis shows that the MlaD domain archetypes are evolutionarily closer and marked by the conservation of a functionally crucial pore loop located at the C-terminal region. The study also establishes the critical role of the domain-associated permeases and the driving forces governing the transport of hydrophobic molecules. This sheds sufficient light on the structure-function-evolutionary relationship of MlaD domain. The hexameric interface analysis reveals that the MlaD domain itself is not a sole player in the oligomerization of the proteins. Further, an operonic and interactome map analysis reveals that the Mla and the Mce systems are dependent on the structural homologs of the nuclear transport factor 2 superfamily.


Assuntos
Arabidopsis/metabolismo , Membrana Celular/metabolismo , Proteínas de Escherichia coli/química , Escherichia coli/metabolismo , Proteínas de Membrana/química , Mycobacterium tuberculosis/metabolismo , Periplasma/metabolismo , Motivos de Aminoácidos , Arabidopsis/classificação , Arabidopsis/genética , Sítios de Ligação , Transporte Biológico , Membrana Celular/genética , Biologia Computacional/métodos , Sequência Conservada , Escherichia coli/classificação , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Expressão Gênica , Interações Hidrofóbicas e Hidrofílicas , Proteínas de Membrana/genética , Proteínas de Membrana/metabolismo , Modelos Moleculares , Mycobacterium tuberculosis/classificação , Mycobacterium tuberculosis/genética , Periplasma/genética , Fosfolipídeos/química , Fosfolipídeos/metabolismo , Filogenia , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos
8.
Microbiology (Reading) ; 167(3)2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33502310

RESUMO

Biofilm formation in the human intestinal pathogen Vibrio cholerae is in part regulated by norspermidine, spermidine and spermine. V. cholerae senses these polyamines through a signalling pathway consisting of the periplasmic protein, NspS, and the integral membrane c-di-GMP phosphodiesterase MbaA. NspS and MbaA belong to a proposed class of novel signalling systems composed of periplasmic ligand-binding proteins and membrane-bound c-di-GMP phosphodiesterases containing both GGDEF and EAL domains. In this signal transduction pathway, NspS is hypothesized to interact with MbaA in the periplasm to regulate its phosphodiesterase activity. Polyamine binding to NspS likely alters this interaction, leading to the activation or inhibition of biofilm formation depending on the polyamine. The purpose of this study was to determine the amino acids important for NspS function. We performed random mutagenesis of the nspS gene, identified mutant clones deficient in biofilm formation, determined their responsiveness to norspermidine and mapped the location of these residues onto NspS homology models. Single mutants clustered on two lobes of the NspS model, but the majority were found on a single lobe that appeared to be more mobile upon norspermidine binding. We also identified residues in the putative ligand-binding site that may be important for norspermidine binding and interactions with MbaA. Ultimately, our results provide new insights into this novel signalling pathway in V. cholerae and highlight differences between periplasmic binding proteins involved in transport versus signal transduction.


Assuntos
Proteínas de Bactérias/genética , Biofilmes , Vibrio cholerae/genética , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Regulação Bacteriana da Expressão Gênica , Mutagênese , Periplasma/genética , Periplasma/metabolismo , Domínios Proteicos , Alinhamento de Sequência , Transdução de Sinais , Vibrio cholerae/química , Vibrio cholerae/fisiologia
9.
Microbiology (Reading) ; 167(3)2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33620307

RESUMO

Rhodobacter sphaeroides can use C4-dicarboxylic acids to grow heterotrophically or photoheterotropically, and it was previously demonstrated in Rhodobacter capsulatus that the DctPQM transporter system is essential to support growth using these organic acids under heterotrophic but not under photoheterotrophic conditions. In this work we show that in R. sphaeroides this transporter system is essential for photoheterotrophic and heterotrophic growth, when C4-dicarboxylic acids are used as a carbon source. We also found that over-expression of dctPQM is detrimental for photoheterotrophic growth in the presence of succinic acid in the culture medium. In agreement with this, we observed a reduction of the dctPQM promoter activity in cells growing under these conditions, indicating that the amount of DctPQM needs to be reduced under photoheterotrophic growth. It has been reported that the two-component system DctS and DctR activates the expression of dctPQM. Our results demonstrate that in the absence of DctR, dctPQM is still expressed albeit at a low level. In this work, we have found that the periplasmic component of the transporter system, DctP, has a role in both transport and in signalling the DctS/DctR two-component system.


Assuntos
Proteínas de Bactérias/metabolismo , Proteínas de Membrana Transportadoras/metabolismo , Periplasma/metabolismo , Rhodobacter sphaeroides/metabolismo , Proteínas de Bactérias/genética , Transporte Biológico , Ácidos Dicarboxílicos/metabolismo , Regulação Bacteriana da Expressão Gênica/efeitos da radiação , Processos Heterotróficos , Luz , Proteínas de Membrana Transportadoras/genética , Periplasma/genética , Processos Fototróficos , Regiões Promotoras Genéticas , Rhodobacter sphaeroides/genética , Rhodobacter sphaeroides/crescimento & desenvolvimento , Rhodobacter sphaeroides/efeitos da radiação , Ácido Succínico/metabolismo
10.
Protein Expr Purif ; 185: 105906, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-33991675

RESUMO

Nanobodies are single-domain antibody constructs derived from the variable regions of heavy chain only (VHH) camelid IgGs. Their small size and single gene format make them amenable to various molecular biology applications that require a protein affinity-based approach. These features, in addition to their high solubility, allows their periplasmic expression, extraction and purification in E. coli systems with relative ease, using standardized protocols. However, some Nanobodies are recalcitrant to periplasmic expression, extraction and purification within E. coli systems. To improve their expression would require either a change in the expression host, vector or an increased scale of expression, all of which entail an increase in the complexity of their expression, and production cost. However, as shown here, specific changes in the existing standard E. coli culture protocol, aimed at reducing breakdown of selective antibiotic pressure, increasing the initial culture inoculum and improving transport to the periplasmic space, rescued the expression of several such refractory Nanobodies. The periplasmic extraction protocol was also changed to ensure efficient osmolysis, prevent both protein degradation and prevent downstream chelation of Ni2+ ions during IMAC purification. Adoption of this protocol will lead to an improvement of the expression of Nanobodies in general, and specifically, those that are recalcitrant.


Assuntos
Escherichia coli/metabolismo , Periplasma/metabolismo , Proteínas Recombinantes/isolamento & purificação , Anticorpos de Domínio Único/biossíntese , Sequência de Aminoácidos , Clonagem Molecular , Meios de Cultura/química , Meios de Cultura/farmacologia , Escherichia coli/genética , Expressão Gênica , Vetores Genéticos/química , Vetores Genéticos/metabolismo , Pressão Osmótica , Periplasma/genética , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/efeitos dos fármacos , Proteínas Recombinantes/genética , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Anticorpos de Domínio Único/genética , Anticorpos de Domínio Único/isolamento & purificação
11.
Protein Expr Purif ; 177: 105746, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-32916300

RESUMO

Periplasmic expression of recombinant proteins ensures the production of biologically active proteins in a correctly folded state with several key advantages. This research focused on the in-frame cloning of rhIL-15 in pET-20 (+) vector with pelB-leader sequence to direct the protein to the bacterial periplasm. The target construct periplasmic expression was evaluated in four strains, BL21 (DE3), BL21 (DE3) pLysS, Rosetta 2 (DE3) and Rosetta-gami 2 (DE3). Soluble periplasmic expression of IL-15 was highest in Rosetta-gami 2 (DE3) followed by Rossetta 2 (DE3) whereas negligible expression was observed with rest of two expression host. Best expression clone was selected for purification by dye ligand affinity chromatography. Purified rhIL-15 was characterized by SDS-PAGE, Western blotting and SEC-HPLC. This is the first report of functional recombinant human interleukin-15 being expressed and purified with yield of 120 mg/L in the periplasmic space of E. coli.


Assuntos
Clonagem Molecular/métodos , Interleucina-15/genética , Periplasma/genética , Animais , Linhagem Celular , Proliferação de Células/efeitos dos fármacos , Cromatografia de Afinidade/métodos , Eletroforese em Gel de Poliacrilamida , Escherichia coli/genética , Escherichia coli/metabolismo , Expressão Gênica , Vetores Genéticos/química , Vetores Genéticos/metabolismo , Humanos , Interleucina-15/biossíntese , Interleucina-15/farmacologia , Camundongos , Periplasma/metabolismo , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/genética , Proteínas Recombinantes/farmacologia , Solubilidade , Linfócitos T Citotóxicos/citologia , Linfócitos T Citotóxicos/efeitos dos fármacos , Linfócitos T Citotóxicos/imunologia
12.
Proc Natl Acad Sci U S A ; 115(26): 6840-6845, 2018 06 26.
Artigo em Inglês | MEDLINE | ID: mdl-29891657

RESUMO

Iron is an essential micronutrient for most bacteria and is obtained from iron-chelating siderophores or directly from iron-containing host proteins. For Gram-negative bacteria, classical iron transport systems consist of an outer membrane receptor, a periplasmic binding protein, and an inner membrane ABC transporter, which work in concert to deliver iron from the cell surface to the cytoplasm. We recently showed that Pectobacterium spp. are able to acquire iron from ferredoxin, a small and stable 2Fe-2S iron sulfur cluster containing protein and identified the ferredoxin receptor, FusA, a TonB-dependent receptor that binds ferredoxin on the cell surface. The genetic context of fusA suggests an atypical iron acquisition system, lacking a periplasmic binding protein, although the mechanism through which iron is extracted from the captured ferredoxin has remained unknown. Here we show that FusC, an M16 family protease, displays a highly targeted proteolytic activity against plant ferredoxin, and that growth enhancement of Pectobacterium due to iron acquisition from ferredoxin is FusC-dependent. The periplasmic location of FusC indicates a mechanism in which ferredoxin is imported into the periplasm via FusA before cleavage by FusC, as confirmed by the uptake and accumulation of ferredoxin in the periplasm in a strain lacking fusC The existence of homologous uptake systems in a range of pathogenic bacteria suggests that protein uptake for nutrient acquisition may be widespread in bacteria and shows that, similar to their endosymbiotic descendants mitochondria and chloroplasts, bacteria produce dedicated protein import systems.


Assuntos
Proteínas de Bactérias/metabolismo , Membrana Celular/metabolismo , Ferro/metabolismo , Proteínas de Membrana/metabolismo , Pectobacterium/metabolismo , Fator G para Elongação de Peptídeos/metabolismo , Proteólise , Proteínas de Bactérias/genética , Membrana Celular/genética , Proteínas de Membrana/genética , Pectobacterium/genética , Fator G para Elongação de Peptídeos/genética , Periplasma/genética , Periplasma/metabolismo
13.
Proc Natl Acad Sci U S A ; 115(29): E6855-E6862, 2018 07 17.
Artigo em Inglês | MEDLINE | ID: mdl-29967164

RESUMO

Cell division requires the assembly of a protein complex called the divisome. The divisome assembles in a hierarchical manner, with FtsA functioning as a hub to connect the Z-ring with the rest of the divisome and FtsN arriving last to activate the machine to synthesize peptidoglycan. FtsEX arrives as the Z-ring forms and acts on FtsA to initiate recruitment of the other divisome components. In the absence of FtsEX, recruitment is blocked; however, a multitude of conditions allow FtsEX to be bypassed. Here, we find that all such FtsEX bypass conditions, as well as the bypass of FtsK, depend upon the interaction of FtsN with FtsA, which promotes the back-recruitment of the late components of the divisome. Furthermore, our results suggest that these bypass conditions enhance the weak interaction of FtsN with FtsA and its periplasmic partners so that the divisome proteins are brought to the Z-ring when the normal hierarchical pathway is disrupted.


Assuntos
Divisão Celular/fisiologia , Proteínas de Escherichia coli/metabolismo , Escherichia coli/metabolismo , Proteínas de Membrana/metabolismo , Periplasma/metabolismo , Transportadores de Cassetes de Ligação de ATP/genética , Transportadores de Cassetes de Ligação de ATP/metabolismo , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Regulador de Condutância Transmembrana em Fibrose Cística/genética , Regulador de Condutância Transmembrana em Fibrose Cística/metabolismo , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Proteínas de Membrana/genética , Periplasma/genética
14.
Trends Biochem Sci ; 41(10): 872-882, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27450425

RESUMO

Outer membrane proteins (OMPs) play a central role in the integrity of the outer membrane of Gram-negative bacteria. Unfolded OMPs (uOMPs) transit across the periplasm, and subsequent folding and assembly are crucial for biogenesis. Chaperones and the essential ß-barrel assembly machinery (BAM) complex facilitate these processes. In vitro studies suggest that some chaperones sequester uOMPs in internal cavities during their periplasmic transit to prevent deleterious aggregation. Upon reaching the outer membrane, the BAM complex acts catalytically to accelerate uOMP folding. Complementary in vivo experiments have revealed the localization and activity of the BAM complex in living cells. Completing an understanding of OMP biogenesis will require a holistic view of the interplay among the individual components discussed here.


Assuntos
Proteínas da Membrana Bacteriana Externa/química , Proteínas de Escherichia coli/química , Escherichia coli/metabolismo , Chaperonas Moleculares/química , Periplasma/metabolismo , Proteínas da Membrana Bacteriana Externa/genética , Proteínas da Membrana Bacteriana Externa/metabolismo , Sítios de Ligação , Escherichia coli/genética , Escherichia coli/ultraestrutura , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Expressão Gênica , Chaperonas Moleculares/genética , Chaperonas Moleculares/metabolismo , Simulação de Dinâmica Molecular , Periplasma/genética , Periplasma/ultraestrutura , Ligação Proteica , Conformação Proteica em Folha beta , Dobramento de Proteína , Domínios e Motivos de Interação entre Proteínas , Transporte Proteico , Desdobramento de Proteína , Termodinâmica
15.
J Bacteriol ; 202(8)2020 03 26.
Artigo em Inglês | MEDLINE | ID: mdl-32041800

RESUMO

The Gram-negative pathogen Neisseria gonorrhoeae (gonococcus [Gc]) colonizes lysozyme-rich mucosal surfaces. Lysozyme hydrolyzes peptidoglycan, leading to bacterial lysis. Gc expresses two proteins, SliC and NgACP, that bind and inhibit the enzymatic activity of lysozyme. SliC is a surface-exposed lipoprotein, while NgACP is found in the periplasm and also released extracellularly. Purified SliC and NgACP similarly inhibit lysozyme. However, whereas mutation of ngACP increases Gc susceptibility to lysozyme, the sliC mutant is only susceptible to lysozyme when ngACP is inactivated. In this work, we examined how lipidation contributes to SliC expression, cellular localization, and resistance of Gc to killing by lysozyme. To do so, we mutated the conserved cysteine residue (C18) in the N-terminal lipobox motif of SliC, the site for lipid anchor attachment, to alanine. SliC(C18A) localized to soluble rather than membrane fractions in Gc and was not displayed on the bacterial surface. Less SliC(C18A) was detected in Gc lysates compared to the wild-type protein. This was due in part to some release of the C18A mutant, but not wild-type, protein into the extracellular space. Surprisingly, Gc expressing SliC(C18A) survived better than SliC (wild type)-expressing Gc after exposure to lysozyme. We conclude that lipidation is not required for the ability of SliC to inhibit lysozyme, even though the lipidated cysteine is 100% conserved in Gc SliC alleles. These findings shed light on how members of the growing family of lysozyme inhibitors with distinct subcellular localizations contribute to bacterial defense against lysozyme.IMPORTANCENeisseria gonorrhoeae is one of many bacterial species that express multiple lysozyme inhibitors. It is unclear how inhibitors that differ in their subcellular localization contribute to defense from lysozyme. We investigated how lipidation of SliC, an MliC (membrane-bound lysozyme inhibitor of c-type lysozyme)-type inhibitor, contributes to its localization and lysozyme inhibitory activity. We found that lipidation was required for surface exposure of SliC and yet was dispensable for protecting the gonococcus from killing by lysozyme. To our knowledge, this is the first time the role of lipid anchoring of a lysozyme inhibitor has been investigated. These results help us understand how different lysozyme inhibitors are localized in bacteria and how this impacts resistance to lysozyme.


Assuntos
Proteínas de Bactérias/metabolismo , Inibidores Enzimáticos/metabolismo , Gonorreia/microbiologia , Lipoproteínas/metabolismo , Muramidase/antagonistas & inibidores , Neisseria gonorrhoeae/metabolismo , Motivos de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Inibidores Enzimáticos/química , Gonorreia/enzimologia , Interações Hospedeiro-Patógeno , Humanos , Lipoproteínas/química , Lipoproteínas/genética , Muramidase/metabolismo , Neisseria gonorrhoeae/química , Neisseria gonorrhoeae/genética , Periplasma/genética , Periplasma/metabolismo , Transporte Proteico
16.
J Biomol NMR ; 74(6-7): 311-319, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32415582

RESUMO

Monoclonal antibody (mAb) drugs are clinically important for the treatment of various diseases. TTAC-0001 is under development as a new anti-cancer antibody drug targeting VEGFR-2. As the less severe toxicity of TTAC-0001 compared to Bevacizumab, likely due to the decreased in vivo half-life, seems to be related to its structural flexibility, it is important to map the exact flexible regions. Although the 13C/15N-labeled protein is required for NMR analyses, it is difficult to obtain antibody fragments (Fab and scFv) containing disulfide bonds through general cytosolic expression in Escherichia coli (E. coli). Here, we notably increased the periplasmic expression of the 13C/15N-labeled TTAC-0001-Fab (13C/15N-TTAC-Fab) through simple isopropyl ß-D-1-thiogalactopyranoside (IPTG)-induction at an increased optical density (1.5 OD600nm). Through NMR triple resonance experiments, two loop insertions (LI-1 between the VH and CH1; LI-2 between the VL and CL) were confirmed to be highly flexible. The additional LIs could be another way to engineer the antibody by changing the pharmacokinetic properties.


Assuntos
Anticorpos Monoclonais Humanizados/química , Anticorpos Monoclonais Humanizados/metabolismo , Ressonância Magnética Nuclear Biomolecular/métodos , Anticorpos Monoclonais Humanizados/genética , Isótopos de Carbono , Dissulfetos/química , Escherichia coli/genética , Fragmentos Fab das Imunoglobulinas/química , Fragmentos Fab das Imunoglobulinas/genética , Fragmentos Fab das Imunoglobulinas/metabolismo , Isopropiltiogalactosídeo , Marcação por Isótopo , Isótopos de Nitrogênio , Periplasma/genética , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Reprodutibilidade dos Testes , Receptor 2 de Fatores de Crescimento do Endotélio Vascular/metabolismo
17.
Annu Rev Genet ; 46: 209-31, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22934645

RESUMO

Colicins are protein toxins produced by Escherichia coli to kill related bacteria. They must cross the target cell outer membrane (OM), and some must also cross the inner membrane (IM). To accomplish cellular import, colicins have parasitized E. coli nutrient transporters as well as IM and periplasmic proteins normally used to maintain cell wall integrity or provide energy for nutrient uptake through transporters. Colicins have evolved to use both transporters and other membrane proteins through mechanisms different from those employed in physiological substrate uptake. Extended receptor-binding domains allow some colicins to search by lateral diffusion for binding sites on their OM translocators while bound to their primary OM receptor. Transport across the OM is initiated by entry of the unstructured N-terminal translocation domain into the translocator. Periplasmic and IM networks subsequently accomplish insertion of the colicin cytotoxic domain into or across the IM.


Assuntos
Proteínas da Membrana Bacteriana Externa/metabolismo , Membrana Celular/metabolismo , Colicinas/metabolismo , Proteínas de Escherichia coli/metabolismo , Escherichia coli/metabolismo , Proteínas de Membrana Transportadoras/metabolismo , Proteínas da Membrana Bacteriana Externa/genética , Sítios de Ligação , Metabolismo Energético , Escherichia coli/enzimologia , Proteínas de Escherichia coli/genética , Proteínas de Membrana/metabolismo , Proteínas de Membrana Transportadoras/genética , Periplasma/genética , Periplasma/metabolismo , Porinas/metabolismo , Mapeamento de Interação de Proteínas , Estrutura Terciária de Proteína , Transporte Proteico
18.
Biotechnol Bioeng ; 117(1): 39-48, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31544961

RESUMO

Carbonic anhydrase (CA) is a diffusion-limited enzyme that rapidly catalyzes the hydration of carbon dioxide (CO2 ). CA has been proposed as an eco-friendly yet powerful catalyst for CO2 capture and utilization. A bacterial whole-cell biocatalyst equipped with periplasmic CA provides an option for a cost-effective CO2 -capturing system. However, further utilization of the previously constructed periplasmic system has been limited by its relatively low activity and stability. Herein, we engineered three genetic components of the periplasmic system for the construction of a highly efficient whole-cell catalyst: a CA-coding gene, a signal sequence, and a ribosome-binding site (RBS). A stable and halotolerant CA (hmCA) from the marine bacterium Hydrogenovibrio marinus was employed to improve both the activity and stability of the system. The improved secretion and folding of hmCA and increased membrane permeability were achieved by translocation via the Sec-dependent pathway. The engineering of RBS strength further enhanced whole-cell activity by improving both the secretion and folding of hmCA. The newly engineered biocatalyst displayed 5.7-fold higher activity and 780-fold higher stability at 60°C compared with those of the previously constructed periplasmic system, providing new opportunities for applications in CO2 capture and utilization.


Assuntos
Dióxido de Carbono/metabolismo , Anidrases Carbônicas , Engenharia Celular/métodos , Piscirickettsiaceae , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sítios de Ligação/genética , Anidrases Carbônicas/genética , Anidrases Carbônicas/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Periplasma/genética , Periplasma/metabolismo , Piscirickettsiaceae/enzimologia , Piscirickettsiaceae/genética , Piscirickettsiaceae/metabolismo , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Ribossomos/metabolismo
19.
Biochem J ; 476(1): 115-135, 2019 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-30530842

RESUMO

Two-component systems (TCSs) are essential for bacteria to sense, respond, and adapt to changing environments, such as elevation of Cu(I)/Ag(I) ions in the periplasm. In Escherichia coli, the CusS-CusR TCS up-regulates the cusCFBA genes under increased periplasmic Cu(I)/Ag(I) concentrations to help maintain metal ion homeostasis. The CusS histidine kinase is a homodimeric integral membrane protein that binds to periplasmic Cu(I)/Ag(I) and transduces a signal to its cytoplasmic kinase domain. However, the mechanism of how metal binding in the periplasm activates autophosphorylation in the cytoplasm is unknown. Here, we report that only one of the two metal ion-binding sites in CusS enhances dimerization of the sensor domain. Utilizing nanodisc technology to study full-length CusS, we show that metal-induced dimerization in the sensor domain triggers kinase activity in the cytoplasmic domain. We also investigated autophosphorylation in the cytoplasmic domain of CusS and phosphotransfer between CusS and CusR. In vitro analyses show that CusS autophosphorylates its conserved H271 residue at the N1 position of the histidine imidazole. The phosphoryl group is removed by the response regulator CusR in a reaction that requires a conserved aspartate at position 51. Functional analyses in vivo of CusS and CusR variants with mutations in the autophosphorylation or phosphoacceptor residues suggest that the phosphotransfer event is essential for metal resistance in E. coli Biochemical analysis shows that the CusS dimer autophosphorylates using a cis mechanism. Our results support a signal transduction model in which rotation and bending movements in the cytoplasmic domain maintain the mode of autophosphorylation.


Assuntos
Cobre , Escherichia coli/enzimologia , Histidina Quinase , Periplasma/enzimologia , Transdução de Sinais , Prata , Cobre/química , Cobre/metabolismo , Dimerização , Escherichia coli/genética , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Histidina Quinase/química , Histidina Quinase/genética , Histidina Quinase/metabolismo , Periplasma/genética , Fosforilação , Domínios Proteicos , Estrutura Quaternária de Proteína , Prata/química , Prata/metabolismo , Transativadores/química , Transativadores/genética , Transativadores/metabolismo
20.
Proc Natl Acad Sci U S A ; 114(11): 2892-2897, 2017 03 14.
Artigo em Inglês | MEDLINE | ID: mdl-28242707

RESUMO

Secreted polysaccharides are important functional and structural components of bacterial biofilms. The opportunistic pathogen Pseudomonas aeruginosa produces the cationic exopolysaccharide Pel, which protects bacteria from aminoglycoside antibiotics and contributes to biofilm architecture through ionic interactions with extracellular DNA. A bioinformatics analysis of genome databases suggests that gene clusters for Pel biosynthesis are present in >125 bacterial species, yet little is known about how this biofilm exopolysaccharide is synthesized and exported from the cell. In this work, we characterize PelC, an outer membrane lipoprotein essential for Pel production. Crystal structures of PelC from Geobacter metallireducens and Paraburkholderia phytofirmans coupled with structure-guided disulfide cross-linking in P. aeruginosa suggest that PelC assembles into a 12- subunit ring-shaped oligomer. In this arrangement, an aromatic belt in proximity to its lipidation site positions the highly electronegative surface of PelC toward the periplasm. PelC is structurally similar to the Escherichia coli amyloid exporter CsgG; however, unlike CsgG, PelC does not possess membrane-spanning segments required for polymer export across the outer membrane. We show that the multidomain protein PelB with a predicted C-terminal ß-barrel porin localizes to the outer membrane, and propose that PelC functions as an electronegative funnel to guide the positively charged Pel polysaccharide toward an exit channel formed by PelB. Together, our findings provide insight into the unique molecular architecture and export mechanism of the Pel apparatus, a widespread exopolysaccharide secretion system found in environmental and pathogenic bacteria.


Assuntos
Biologia Computacional , Polissacarídeo-Liases/química , Polissacarídeos Bacterianos/química , Pseudomonas aeruginosa/química , Biofilmes/crescimento & desenvolvimento , Cristalografia por Raios X , Regulação Bacteriana da Expressão Gênica , Genoma Bacteriano , Lipoproteínas/química , Lipoproteínas/genética , Periplasma/química , Periplasma/genética , Periplasma/metabolismo , Polissacarídeo-Liases/genética , Polissacarídeos Bacterianos/genética , Pseudomonas aeruginosa/patogenicidade
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