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1.
Int J Mol Sci ; 25(10)2024 May 16.
Artigo em Inglês | MEDLINE | ID: mdl-38791467

RESUMO

Yeast two-hybrid approaches, which are based on fusion proteins that must co-localise to the nucleus to reconstitute the transcriptional activity of GAL4, have greatly contributed to our understanding of the nitrogen interaction network of cyanobacteria, the main hubs of which are the trimeric PII and the monomeric PipX regulators. The bacterial two-hybrid system, based on the reconstitution in the E. coli cytoplasm of the adenylate cyclase of Bordetella pertussis, should provide a relatively faster and presumably more physiological assay for cyanobacterial proteins than the yeast system. Here, we used the bacterial two-hybrid system to gain additional insights into the cyanobacterial PipX interaction network while simultaneously assessing the advantages and limitations of the two most popular two-hybrid systems. A comprehensive mutational analysis of PipX and bacterial two-hybrid assays were performed to compare the outcomes between yeast and bacterial systems. We detected interactions that were previously recorded in the yeast two-hybrid system as negative, as well as a "false positive", the self-interaction of PipX, which is rather an indirect interaction that is dependent on PII homologues from the E. coli host, a result confirmed by Western blot analysis with relevant PipX variants. This is, to our knowledge, the first report of the molecular basis of a false positive in the bacterial two-hybrid system.


Assuntos
Proteínas de Bactérias , Cianobactérias , Proteínas PII Reguladoras de Nitrogênio , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/genética , Cianobactérias/metabolismo , Cianobactérias/genética , Escherichia coli/metabolismo , Escherichia coli/genética , Proteínas PII Reguladoras de Nitrogênio/metabolismo , Proteínas PII Reguladoras de Nitrogênio/genética , Ligação Proteica , Técnicas do Sistema de Duplo-Híbrido
2.
Plasmid ; 118: 102608, 2021 11.
Artigo em Inglês | MEDLINE | ID: mdl-34801582

RESUMO

We developed a simplified, highly efficient Gateway reaction that recombines target DNA to expression (destination) plasmids in vivo and subsequently conjugates the final vector into a recipient strain, all in a single step. This recipient strain does not need to contain any selective marker and can be freely chosen as long as it is sensitive to ccdB counterselection and can be targeted by the RP4α conjugation system. Our protocol is simple, robust, and cost effective. It works in 96-well plate format and performs across a range of temperatures. We designed modular, minimal destination vectors containing a modified Gateway insert to ease vector design by providing locations for insertion of tags, promoters, or conjugations. To demonstrate the utility of our system, we created destination vectors with split adenylate cyclase tags for bacterial two-hybrid (B2H) studies and screened a library of diguanylate cyclases for protein-protein interactions in a single step.


Assuntos
Escherichia coli , Vetores Genéticos , Clonagem Molecular , DNA , Escherichia coli/genética , Vetores Genéticos/genética , Plasmídeos/genética
3.
J Appl Microbiol ; 131(2): 658-670, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-33249680

RESUMO

AIMS: This study aimed to explore potential drug targets of Streptococcus suis at the system level. METHODS AND RESULTS: A homologous protein mapping method was used in the construction of a protein-protein interaction (PPI) network of S. suis, which presented 1147 non-redundant interaction pairs among 286 proteins. The parameters of PPI networks were calculated and showed scale-free network properties. In all, 41 possibly essential proteins identified from 47 highly connected proteins were selected as potential drug target candidates. Of these proteins, 30 were already regarded as drug targets in other bacterial species. Six transporters with high connections to other functional proteins were identified as probably not essential but important functional proteins. Afterward, the subnetwork centred with cell division protein FtsZ was used in confirming the PPI network through bacterial two-hybrid analysis. CONCLUSIONS: The predicted PPI network covers 13·04% of the proteome in S. suis. The selected 41 potential drug target candidates are conserved between S. suis and several model bacteria. SIGNIFICANCE AND IMPACT OF THE STUDY: The predictions included proteins known to be drug targets, and a verifying experiment confirmed the reliability of predicted interactions. This work is the first to present systematic computational PPI data for S. suis and provides potential drug targets, which are valuable in exploring novel anti-streptococcus drugs.


Assuntos
Proteínas de Bactérias/metabolismo , Mapeamento de Interação de Proteínas , Streptococcus suis/metabolismo , Antibacterianos/farmacologia , Proteínas de Bactérias/antagonistas & inibidores , Proteínas de Membrana Transportadoras/metabolismo , Proteoma/metabolismo , Streptococcus suis/efeitos dos fármacos
4.
J Bacteriol ; 202(12)2020 05 27.
Artigo em Inglês | MEDLINE | ID: mdl-32253340

RESUMO

Listeria monocytogenes is a model facultative intracellular pathogen. Tight regulation of virulence proteins is essential for a successful infection, and the gene encoding the annotated thioredoxin YjbH was identified in two forward genetic screens as required for virulence factor production. Accordingly, an L. monocytogenes strain lacking yjbH is attenuated in a murine model of infection. However, the function of YjbH in L. monocytogenes has not been investigated. Here, we provide evidence that L. monocytogenes YjbH is involved in the nitrosative stress response, likely through its interaction with the redox-responsive transcriptional regulator SpxA1. YjbH physically interacted with SpxA1, and our data support a model in which YjbH is a protease adaptor that regulates SpxA1 protein abundance. Whole-cell proteomics identified eight additional proteins whose abundance was altered by YjbH, and we demonstrated that YjbH physically interacted with each in bacterial two-hybrid assays. Thioredoxin proteins canonically require active motif cysteines for function, but thioredoxin activity has not been tested for L. monocytogenes YjbH. We demonstrated that cysteine residues of the YjbH thioredoxin domain active motif are essential for L. monocytogenes sensitivity to nitrosative stress, cell-to-cell spread in a tissue culture model of infection, and several protein-protein interactions. Together, these results demonstrated that the function of YjbH in L. monocytogenes requires its thioredoxin active motif and that YjbH has a role in the posttranslational regulation of several proteins, including SpxA1.IMPORTANCE The annotated thioredoxin YjbH in Listeria monocytogenes has been implicated in virulence, but its function in the cell is unknown. In other bacterial species, YjbH is a protease adaptor that mediates degradation of the transcriptional regulator Spx. Here, we investigated the function of L. monocytogenes YjbH and demonstrated its role in the nitrosative stress response and posttranslational regulation of several proteins with which YjbH physically interacts, including SpxA1. Furthermore, we demonstrated that the cysteine residues of the YjbH thioredoxin active motif are required for the nitrosative stress response, cell-to-cell spread, and some protein-protein interactions. YjbH is widely conserved among Firmicutes, and this work reveals its unique requirement of the thioredoxin-active motif in L. monocytogenes.


Assuntos
Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Listeria monocytogenes/metabolismo , Tiorredoxinas/química , Tiorredoxinas/metabolismo , Motivos de Aminoácidos , Sequência de Aminoácidos , Bacillus subtilis/química , Bacillus subtilis/genética , Bacillus subtilis/metabolismo , Proteínas de Bactérias/genética , Regulação Bacteriana da Expressão Gênica , Humanos , Listeria monocytogenes/química , Listeria monocytogenes/genética , Listeriose/microbiologia , Ligação Proteica , Alinhamento de Sequência , Tiorredoxinas/genética
5.
Microbiology (Reading) ; 166(9): 826-836, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32749956

RESUMO

Bacterial cell division is mediated by a protein complex known as the divisome. Many protein-protein interactions in the divisome have been characterized. In this report, we analyse the role of the PASTA (Penicillin-binding protein And Serine Threonine kinase Associated) domains of Bacillus subtilis PBP2B. PBP2B itself is essential and cannot be deleted, but removing the PBP2B PASTA domains results in impaired cell division and a heat-sensitive phenotype. This resembles the deletion of divIB, a known interaction partner of PBP2B. Bacterial two-hybrid and co-immunoprecipitation analyses show that the interaction between PBP2B and DivIB is weakened when the PBP2B PASTA domains are removed. Combined, our results show that the PBP2B PASTA domains are required to strengthen the interaction between PBP2B and DivIB.


Assuntos
Bacillus subtilis/metabolismo , Proteínas de Bactérias/metabolismo , Proteínas de Membrana/metabolismo , Proteínas de Ligação às Penicilinas/química , Proteínas de Ligação às Penicilinas/metabolismo , Bacillus subtilis/genética , Bacillus subtilis/crescimento & desenvolvimento , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Peptidil Transferases/química , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Estabilidade Proteica , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/metabolismo , Temperatura
6.
Int J Med Microbiol ; 308(4): 425-437, 2018 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-29572102

RESUMO

Highly virulent Helicobacter pylori strains contain the cag pathogenicity island (cagPAI). It codes for about 30 proteins forming a type IV secretion system (T4SS) which translocates the pro-inflammatory protein CagA into epithelial host cells. While CagA and various other Cag proteins have been extensively studied, several cagPAI proteins are poorly characterized or of unknown function. CagN (HP0538) is of unknown function but highly conserved in the cagPAI suggesting an important role. cagM (HP0537) is the first gene of the cagMN operon and its product is part of the CagT4SS core complex. Both proteins do not have detectable homologs in other type IV secretion systems. We have characterized the biochemical and structural properties of CagN and CagM and their interaction. We demonstrate by circular dichroism, Multi-Angle Light Scattering (MALS) and small angle X-ray scattering (SAXS) that CagN is a folded, predominantly monomeric protein with an elongated shape in solution. CagM is folded and forms predominantly dimers that are also elongated in solution. We found by various in vivo and in vitro methods that CagN and CagM directly interact with each other. CagM self-interacts stably with a low nanomolar KD and can form stable multimers. Finally, in vivo experiments show that deletion of CagM reduces the amounts of CagN and other outer CagPAI proteins in H. pylori cells.


Assuntos
Proteínas de Bactérias/química , Ilhas Genômicas , Helicobacter pylori/patogenicidade , Sistemas de Secreção Tipo IV/metabolismo , Fusão Gênica Artificial , Proteínas de Bactérias/análise , Proteínas de Bactérias/genética , Dicroísmo Circular , Humanos , Interações Hidrofóbicas e Hidrofílicas , Cinética , Mutação , Proteínas Recombinantes/análise , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Espalhamento a Baixo Ângulo , Termodinâmica , beta-Galactosidase/genética , beta-Galactosidase/metabolismo
7.
Arch Microbiol ; 200(7): 1075-1086, 2018 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-29737367

RESUMO

The ESAT-6-like secretion system (ESS) of Staphylococcus aureus plays a significant role in persistent infections. EssB is a highly conserved bitopic ESS protein comprising a cytosolic N-terminus, single transmembrane helix and a C-terminus located on the trans-side of the membrane. Six systematic truncations covering various domains of EssB were constructed, followed by bacterial two-hybrid screening of their interaction with EsaA, another conserved integral membrane component of the ESS pathway. Results show that the transmembrane domain of EssB is critical for heterodimerization with EsaA. In vivo crosslinking followed by Western blot analysis revealed high molecular weight species when wild-type EssB and EsaA were crosslinked, but this band was not detected in the absence of the transmembrane domain of EssB. Heterologous overproduction of EssB, EsaA and five other components of the ESS pathway in Escherichia coli BL21(DE3), followed by fractionation experiments led to a remarkable increase in the periplasmic protein content, suggesting the assembly of partially regulated secretion mechanism. These data identify the transmembrane domain of EssB as indispensable for interaction with EsaA, thereby facilitating protein secretion across bacterial membranes in a fashion that requires other components of the ESS pathway.


Assuntos
Proteínas de Bactérias/metabolismo , Proteínas de Membrana/metabolismo , Staphylococcus aureus/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Humanos , Proteínas de Membrana/química , Proteínas de Membrana/genética , Ligação Proteica , Domínios Proteicos , Transporte Proteico , Infecções Estafilocócicas/microbiologia , Staphylococcus aureus/química , Staphylococcus aureus/genética
8.
BMC Microbiol ; 17(1): 232, 2017 Dec 12.
Artigo em Inglês | MEDLINE | ID: mdl-29233095

RESUMO

BACKGROUND: Bacterial cell division is an essential process driven by the formation of a Z-ring structure, as a cytoskeletal scaffold at the mid-cell, followed by the recruitment of various proteins which form the divisome. The cell division interactome reflects the complement of different interactions between all divisome proteins. To date, only two cell division interactomes have been characterized, in Escherichia coli and in Streptococcus pneumoniae. The cell divison proteins encoded by Neisseria gonorrhoeae include FtsZ, FtsA, ZipA, FtsK, FtsQ, FtsI, FtsW, and FtsN. The purpose of the present study was to characterize the cell division interactome of N. gonorrhoeae using several different methods to identify protein-protein interactions. We also characterized the specific subdomains of FtsA implicated in interactions with FtsZ, FtsQ, FtsN and FtsW. RESULTS: Using a combination of bacterial two-hybrid (B2H), glutathione S-transferase (GST) pull-down assays, and surface plasmon resonance (SPR), nine interactions were observed among the eight gonococcal cell division proteins tested. ZipA did not interact with any other cell division proteins. Comparisons of the N. gonorrhoeae cell division interactome with the published interactomes from E. coli and S. pneumoniae indicated that FtsA-FtsZ and FtsZ-FtsK interactions were common to all three species. FtsA-FtsW and FtsK-FtsN interactions were only present in N. gonorrhoeae. The 2A and 2B subdomains of FtsANg were involved in interactions with FtsQ, FtsZ, and FtsN, and the 2A subdomain was involved in interaction with FtsW. CONCLUSIONS: Results from this research indicate that N. gonorrhoeae has a distinctive cell division interactome as compared with other microorganisms.


Assuntos
Proteínas de Bactérias/metabolismo , Divisão Celular/fisiologia , Neisseria gonorrhoeae/citologia , Neisseria gonorrhoeae/metabolismo , Proteínas de Bactérias/química , Complexos Multiproteicos/química , Complexos Multiproteicos/metabolismo , Domínios e Motivos de Interação entre Proteínas , Ressonância de Plasmônio de Superfície , Técnicas do Sistema de Duplo-Híbrido
9.
J Biol Chem ; 290(44): 26856-65, 2015 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-26359492

RESUMO

Many bacterial pathogens, including Pseudomonas aeruginosa, use type IVa pili (T4aP) for attachment and twitching motility. T4aP are composed primarily of major pilin subunits, which are repeatedly assembled and disassembled to mediate function. A group of pilin-like proteins, the minor pilins FimU and PilVWXE, prime pilus assembly and are incorporated into the pilus. We showed previously that minor pilin PilE depends on the putative priming subcomplex PilVWX and the non-pilin protein PilY1 for incorporation into pili, and that with FimU, PilE may couple the priming subcomplex to the major pilin PilA, allowing for efficient pilus assembly. Here we provide further support for this model, showing interaction of PilE with other minor pilins and the major pilin. A 1.25 Å crystal structure of PilEΔ1-28 shows a typical type IV pilin fold, demonstrating how it may be incorporated into the pilus. Despite limited sequence identity, PilE is structurally similar to Neisseria meningitidis minor pilins PilXNm and PilVNm, recently suggested via characterization of mCherry fusions to modulate pilus assembly from within the periplasm. A P. aeruginosa PilE-mCherry fusion failed to complement twitching motility or piliation of a pilE mutant. However, in a retraction-deficient strain where surface piliation depends solely on PilE, the fusion construct restored some surface piliation. PilE-mCherry was present in sheared surface fractions, suggesting that it was incorporated into pili. Together, these data provide evidence that PilE, the sole P. aeruginosa equivalent of PilXNm and PilVNm, likely connects a priming subcomplex to the major pilin, promoting efficient assembly of T4aP.


Assuntos
Proteínas de Fímbrias/química , Fímbrias Bacterianas/química , Isoformas de Proteínas/química , Subunidades Proteicas/química , Pseudomonas aeruginosa/química , Proteínas Recombinantes de Fusão/química , Sequência de Aminoácidos , Sítios de Ligação , Cristalografia por Raios X , Proteínas de Fímbrias/genética , Proteínas de Fímbrias/metabolismo , Expressão Gênica , Genes Reporter , Teste de Complementação Genética , Proteínas Luminescentes/genética , Proteínas Luminescentes/metabolismo , Modelos Moleculares , Dados de Sequência Molecular , Neisseria meningitidis/química , Neisseria meningitidis/genética , Neisseria meningitidis/metabolismo , Ligação Proteica , Dobramento de Proteína , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Multimerização Proteica , Subunidades Proteicas/genética , Subunidades Proteicas/metabolismo , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/metabolismo , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Alinhamento de Sequência , Homologia Estrutural de Proteína , Proteína Vermelha Fluorescente
10.
Biochem Biophys Res Commun ; 478(1): 25-32, 2016 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-27470582

RESUMO

Bacteria utilize small-molecule iron chelators called siderophores to support growth in low-iron environments. The Escherichia coli catecholate siderophore enterobactin is synthesized in the cytoplasm upon iron starvation. Seven enzymes are required for enterobactin biosynthesis: EntA-F, H. Given that EntB-EntE and EntA-EntE interactions have been reported, we investigated a possible EntA-EntB-EntE interaction in E. coli cells. We subcloned the E. coli entA and entB genes into bacterial adenylate cylase two-hybrid (BACTH) vectors allowing for co-expression of EntA and EntB with N-terminal fusions to the adenylate cyclase fragments T18 or T25. BACTH constructs were functionally validated using the CAS assay and growth studies. Co-transformants expressing T18/T25-EntA and T25/T18-EntB exhibited positive two-hybrid signals indicative of an intracellular EntA-EntB interaction. To gain further insights into the interaction interface, we performed computational docking in which an experimentally validated EntA-EntE model was docked to the EntB crystal structure. The resulting model of the EntA-EntB-EntE ternary complex predicted that the IC domain of EntB forms direct contacts with both EntA and EntE. BACTH constructs that expressed the isolated EntB IC domain fused to T18/T25 were prepared in order to investigate interactions with T25/T18-EntA and T25/T18-EntE. CAS assays and growth studies demonstrated that T25-IC co-expressed with the EntB ArCP domain could complement the E. coli entB(-) phenotype. In agreement with the ternary complex model, BACTH assays demonstrated that the EntB IC domain interacts with both EntA and EntE.


Assuntos
Enterobactina/metabolismo , Proteínas de Escherichia coli/metabolismo , Escherichia coli/metabolismo , Hidrolases/metabolismo , Ligases/metabolismo , Oxirredutases atuantes sobre Doadores de Grupo CH-CH/metabolismo , Mapas de Interação de Proteínas , Escherichia coli/química , Escherichia coli/citologia , Proteínas de Escherichia coli/análise , Hidrolases/análise , Ligases/análise , Simulação de Acoplamento Molecular , Oxirredutases atuantes sobre Doadores de Grupo CH-CH/análise , Domínios e Motivos de Interação entre Proteínas
11.
BMC Biotechnol ; 16(1): 68, 2016 09 13.
Artigo em Inglês | MEDLINE | ID: mdl-27619907

RESUMO

BACKGROUND: In the presence of sufficient iron, the Escherichia coli protein Fur (Ferric Uptake Regulator) represses genes controlled by the Fur box, a consensus sequence near or within promoters of target genes. De-repression of Fur-controlled genes occurs upon iron deprivation. In the E. coli chromosome, there is a bidirectional intercistronic promoter region with two non-overlapping Fur boxes. This region controls Fur-regulated expression of entCEBAH in the clockwise direction and fepB in the anticlockwise direction. RESULTS: We cloned the E. coli bidirectional fepB/entC promoter region into low-copy-number plasmid backbones (pACYC184 and pBR322) along with downstream sequences encoding epitope tags and a multiple cloning site (MCS) compatible with the bacterial adenylate cyclase two-hybrid (BACTH) system. The vector pFCF1 allows for iron-controlled expression of FLAG-tagged proteins, whereas the pFBH1 vector allows for iron-controlled expression of HA-tagged proteins. We showed that E. coli knockout strains transformed with pFCF1-entA, pFCF1-entE and pFBH1-entB express corresponding proteins with appropriate epitope tags when grown under iron restriction. Furthermore, transformants exhibited positive chrome azurol S (CAS) assay signals under iron deprivation, indicating that the transformants were functional for siderophore biosynthesis. Western blotting and growth studies in rich and iron-depleted media demonstrated that protein expression from these plasmids was under iron control. Finally, we produced the vector pFCF2, a pFCF1 derivative in which a kanamycin resistance (KanR) gene was engineered in the direction opposite of the MCS. The entA ORF was then subcloned into the pFCF2 MCS. Bidirectional protein expression in an iron-deprived pFCF2-entA transformant was confirmed using antibiotic selection, CAS assays and growth studies. CONCLUSIONS: The vectors pFCF1, pFCF2, and pFBH1 have been shown to use the fepB/entC promoter region to control bidirectional in trans expression of epitope-tagged proteins in iron-depleted transformants. In the presence of intracellular iron, protein expression from these constructs was abrogated due to Fur repression. The compatibility of the pFCF1 and pFBH1 backbones allows for iron-controlled expression of multiple epitope-tagged proteins from a single co-transformant.


Assuntos
Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Escherichia coli/fisiologia , Regulação Bacteriana da Expressão Gênica/genética , Vetores Genéticos/genética , Ferro/metabolismo , Proteínas Repressoras/genética , Proteínas Repressoras/metabolismo , Engenharia Metabólica/métodos , Regiões Promotoras Genéticas/genética , Proteínas Recombinantes/metabolismo
12.
Biochim Biophys Acta ; 1828(9): 2015-25, 2013 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-23735543

RESUMO

Bacteria use type IV secretion systems to transfer genetic material and proteins from donor to recipient cells, using proteins encoded by conjugative plasmids. Among those proteins the so-called Type IV Coupling Protein plays a central role in the process. One of the best studied members of this family is TrwB, the conjugative coupling protein of R388 plasmid. Previous studies indicated that the transmembrane domain of TrwB plays a role beyond the mere anchoring of the protein to the membrane. TrwB has also been shown to interact with other conjugative proteins, such as the VirB10-like protein of R388 TrwE. The goal of this study is to elucidate the role of the different domains of TrwB and TrwE in their biological function, and in both self- and TrwB-TrwE interactions. To this aim, a series of TrwB and TrwE deletion mutant proteins were constructed. Conjugation and interaction studies revealed that the transmembrane domain of TrwB, and particularly its second transmembrane helix, is needed for TrwB self-interaction and for R388 conjugative transfer and that there are contacts between TrwB and TrwE in the membrane. On the contrary, the lack of the TMD of TrwE does not completely abolish R388 conjugation although the interaction between TrwE-TrwB is lost. These results identify protein-protein interactions inside the membrane needed for T4SS function.


Assuntos
Membrana Celular/química , Conjugação Genética/genética , Proteínas de Ligação a DNA/química , Proteínas de Escherichia coli/química , Escherichia coli/química , Membrana Celular/metabolismo , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Mutação , Plasmídeos , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Estrutura Secundária de Proteína , Transporte Proteico
13.
mSystems ; 8(1): e0089722, 2023 02 23.
Artigo em Inglês | MEDLINE | ID: mdl-36622157

RESUMO

The presence or absence of BlsA, a protein with a blue light-sensing flavin domain in the genomes of Acinetobacter species has aroused curiosity about its roles in the regulation of bacterial lifestyle under light. Genomic and transcriptomic analyses revealed the loss of BlsA in several multidrug-resistant (MDR) A. baumannii strains as well as the light-mediated induction of blsA, along with a possible BlsA-interacting partner BipA. Their direct in vivo interactions were verified using a bacterial two-hybrid system. The results demonstrated that the C-terminal region of BipA could bind to the C-terminal residues of BlsA under blue light at 23°C but not at 37°C. Genetic manipulations of blsA and bipA revealed that the coexistence of BlsA and BipA was required to induce the light-dependent expression of ompA in A. baumannii ATCC 17978 at 23°C. The same phenomenon occurred in the BlsA-deficient MDR strain in our functional complementation assay; however, the underlying molecular mechanism remains poorly understood. BlsA-modulated amounts of OmpA, the most abundant porin, in the outer membrane affected the membrane integrity and permeability of small molecules. Dark conditions or the deletion of ompA made the membrane more permeable to lipophilic ethidium bromide (EtBr) but not to meropenem. Interestingly, light illumination and low temperature conditions made the cells more sensitive to meropenem; however, this bactericidal effect was not noted in the blsA mutant or in the BlsA-deficient MDR strains. Light-mediated cell death and the reduction of biofilm formation at 23°C were abolished in the blsA mutant strain, suggesting multifaceted roles of BlsA in A. baumannii strains. IMPORTANCE Little is known about the functional roles of BlsA and its interacting partners in Acinetobacter species. Intriguingly, no BlsA homolog was found in several clinical isolates, suggesting that BlsA was not required inside the host because of the lack of blue light and the warm temperature conditions. As many chromophore-harboring proteins interact with various partners to control light-dependent cellular behaviors, the maintenance of blsA in the genomes of many Acinetobacter species during their evolution may be beneficial when fluctuations occur in two important environmental factors: light and temperature. Our study is the first to report the novel protein partner of BlsA, namely, BipA, and its contribution to multiple phenotypic changes, including meropenem resistance and biofilm formation. Rapid physiological acclimation to changing light or temperature conditions may be possible in the presence of the light-sensing BlsA protein, which may have more interacting partners than expected.


Assuntos
Acinetobacter baumannii , Acinetobacter baumannii/genética , Meropeném/farmacologia , Luz , Biofilmes
14.
FEBS J ; 290(12): 3165-3184, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-36748301

RESUMO

In human cells, de novo purine nucleotide biosynthesis is known to be regulated through the formation of a metabolon called purinosome. Here, we employed a bacterial two-hybrid approach to characterize the protein-protein interactions network among the corresponding enzymes of Escherichia coli. Our study revealed a dense network of binary interactions that connect most purine nucleotide biosynthesis enzymes. Notably, PurK, an exclusive prokaryotic enzyme, appears as one of the central hubs of this network. We further showed that modifications in PurK, which disrupted several interactions in the network, affected the purine nucleotide pools and altered the bacterial fitness. Our data suggest that the bacterial de novo purine nucleotide biosynthesis enzymes can assemble in a supramolecular complex and that proper interactions among the components of this complex can contribute to bacterial fitness.


Assuntos
Escherichia coli , Nucleotídeos , Humanos , Escherichia coli/genética , Purinas , Nucleotídeos de Purina
15.
Methods Enzymol ; 679: 1-32, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36682859

RESUMO

Bacterial pathogens such as Pseudomonas aeruginosa use complex regulatory networks to tailor gene expression patterns to meet complex environmental challenges. P. aeruginosa is capable of causing both acute and chronic persistent infections, each type being characterized by distinct symptoms brought about by distinct sets of virulence mechanisms. The GacS/GacA phosphorelay system sits at the heart of a complex regulatory network that reciprocally governs the expression of virulence factors associated with either acute or chronic infections. A second non-enzymatic signaling cascade involving four proteins, ExsA, ExsC, ExsD, and ExsE is a key player in regulating the expression of the type three secretion system, an essential facilitator of acute infections. Both signaling pathways involve a remarkable array of non-canonical interactions that we sought to characterize. In the following section, we will outline several strategies, we adapted to map protein-protein interfaces and quantify the strength of biomolecular interactions by pairing complex mutational analyses with FRET binding assays and Bacterial-Two-Hybrid assays with appropriate functional assays. In the process, protocols were developed for disrupting large hydrophobic interfaces, deleting entire domains within a protein, and for mapping protein-protein interfaces formed primarily through backbone interactions.


Assuntos
Sistemas de Secreção Bacterianos , Transativadores , Transativadores/química , Sistemas de Secreção Bacterianos/metabolismo , Proteínas Repressoras/química , Proteínas de Bactérias/metabolismo , Pseudomonas aeruginosa/genética , Regulação Bacteriana da Expressão Gênica
16.
Biochimie ; 202: 159-165, 2022 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-35952947

RESUMO

Siderophores are high-affinity small-molecule chelators employed by bacteria to acquire iron from the extracellular environment. The Gram-negative bacterium Escherichia coli synthesizes and secretes enterobactin, a tris-catechol siderophore. Enterobactin is synthesized by six cytoplasmic enzyme activities: EntC, EntB (isochorismatase (IC) domain), EntA, EntE, EntB (aryl carrier protein (ArCP) domain), and EntF. While various pairwise protein-protein interactions have been reported between EntB, EntA, EntE, and EntF, evidence for an interaction between EntC and EntB has remained elusive. We have employed bacterial two-hybrid assays and in vivo crosslinking to demonstrate an intracellular EntC-EntB interaction. A T18-EntC/T25-EntB co-transformant exhibited a positive two-hybrid signal compared to a control T18-EntC/T25 co-transformant. In vivo formaldehyde crosslinking of E. coli cells co-expressing HA-tagged EntB and H6-tagged EntC resulted in an observable ∼80 kDa band on Western blots that cross-reacted with anti-HA and anti-H6, corresponding to one HA-EntB monomer (33 kDa) crosslinked with one H6-EntC monomer (45 kDa). This band disappeared upon sample boiling, confirming it to be a formaldehyde-crosslinked species. Bands of molecular masses greater than 80 kDa that cross-reacted with both antibodies were also observed. Automated docking of the crystal structures of monomeric EntC and dimeric EntB resulted in a top-ranked candidate docked ensemble in which the active sites of EntC and EntB were oriented in apposition and connected by an electropositive surface potentially capable of channeling negatively charged isochorismate. These research outcomes provide the first reported evidence of an EntC-EntB interaction, as well as the first experimental evidence of higher-order complexes containing EntC and EntB.


Assuntos
Enterobactina , Escherichia coli , Eletricidade Estática , Transporte Biológico , Formaldeído
17.
Methods Mol Biol ; 2548: 145-167, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36151497

RESUMO

The bacterial adenylate cyclase-based two-hybrid (BACTH) system is a robust and simple genetic assay used to monitor protein-protein interactions in vivo. This system is based on functional complementation between two fragments from the catalytic domain of Bordetella pertussis adenylate cyclase (AC) to reconstitute a cyclic AMP (cAMP)-signaling cascade in Escherichia coli. Interactions between two chimeric proteins result in the synthesis of cAMP, which activates the transcription of various catabolite operons, leading to selectable phenotypes. One advantageous feature of this signaling cascade is that the physical association between the two interacting hybrid proteins is spatially separated from the transcriptional activation readout. Consequently, the BACTH system can detect protein-protein interactions occurring at various subcellular localizations. The system has been used to characterize interactions between soluble or membrane proteins of prokaryotic, eukaryotic, or viral origin. The BACTH assay can be used to uncover the region(s), domain(s), or amino acid residue(s) of a protein involved in an interaction with a specific partner. The BACTH system can also be adapted for the high-throughput screening of small molecules able to interfere with protein-protein interactions.


Assuntos
Adenilil Ciclases , AMP Cíclico , Adenilil Ciclases/metabolismo , Aminoácidos/metabolismo , Bordetella pertussis/genética , AMP Cíclico/metabolismo , Descoberta de Drogas , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Membrana/metabolismo , Proteínas Recombinantes de Fusão/metabolismo
18.
ACS Synth Biol ; 11(9): 3015-3027, 2022 09 16.
Artigo em Inglês | MEDLINE | ID: mdl-35984356

RESUMO

Terpenoids, the largest and most structurally diverse group of natural products, include a striking variety of biologically active compounds, from flavors to medicines. Despite their well-documented biochemical versatility, the evolutionary processes that generate new functional terpenoids are poorly understood and difficult to recapitulate in engineered systems. This study uses a synthetic biochemical objective─a transcriptional system that links the inhibition of protein tyrosine phosphatase 1B (PTP1B), a human drug target, to the expression of a gene for antibiotic resistance in Escherichia coli (E. coli)─to evolve a terpene synthase to produce enzyme inhibitors. Site saturation mutagenesis of poorly conserved residues on γ-humulene synthase (GHS), a promicuous enzyme, yielded mutants that improved fitness (i.e., the antibiotic resistance of E. coli) by reducing GHS toxicity and/or by increasing inhibitor production. Intriguingly, a combination of two mutations enhanced the titer of a minority product─a terpene alcohol that inhibits PTP1B─by over 50-fold, and a comparison of similar mutants enabled the identification of a site where mutations permit efficient hydroxylation. Findings suggest that the plasticity of terpene synthases enables an efficient sampling of structurally distinct starting points for building new functional molecules and provide an experimental framework for exploiting this plasticity in activity-guided screens.


Assuntos
Alquil e Aril Transferases , Produtos Biológicos , Alquil e Aril Transferases/genética , Escherichia coli/genética , Humanos , Proteína Tirosina Fosfatase não Receptora Tipo 1 , Terpenos
19.
Bio Protoc ; 12(17)2022 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-36213104

RESUMO

Protein-protein interactions and protein modifications play central roles in all living organisms. Of the more than 200 types of post-translational modifications, ubiquitylation is the most abundant, and it profoundly regulates the functionality of the eukaryotic proteome. Various in vitro and in vivo methodologies to study protein interactions and modifications have been developed, each presenting distinctive benefits and caveats. Here, we present a comprehensive protocol for applying a split-Chloramphenicol Acetyl-Transferase (split-CAT) based system, to study protein-protein interactions and ubiquitylation in E. coli . Functional assembly of bait and prey proteins tethered to the split-CAT fragments result in antibiotic resistance and growth on selective media. We demonstrate assays for protein interactions, protein ubiquitylation, and the system response to small compound modulators. To facilitate data collection, we provide an updated Scanner Acquisition Manager Program for Laboratory Experiments (SAMPLE; https://github.com/PragLab/SAMPLE ) that can be employed to monitor the growth of various microorganisms, including E. coli and S. cerevisiae . The advantage posed by this system lies in its sensitivity to a wide range of chloramphenicol concentrations, which allows the detection of a large spectrum of protein-protein interactions, without the need for their purification. The tight linkage between binding or ubiquitylation and growth enables the estimation of apparent relative affinity, and represents the system's quantitative characteristics. Graphical abstract.

20.
Protein Sci ; 31(10): e4411, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-36173161

RESUMO

Many tyrosine kinases cannot be expressed readily in Escherichia coli, limiting facile production of these proteins for biochemical experiments. We used ancestral sequence reconstruction to generate a spleen tyrosine kinase (Syk) variant that can be expressed in bacteria and purified in soluble form, unlike the human members of this family (Syk and zeta-chain-associated protein kinase of 70 kDa [ZAP-70]). The catalytic activity, substrate specificity, and regulation by phosphorylation of this Syk variant are similar to the corresponding properties of human Syk and ZAP-70. Taking advantage of the ability to express this novel Syk-family kinase in bacteria, we developed a two-hybrid assay that couples the growth of E. coli in the presence of an antibiotic to successful phosphorylation of a bait peptide by the kinase. Using this assay, we screened a site-saturation mutagenesis library of the kinase domain of this reconstructed Syk-family kinase. Sites of loss-of-function mutations identified in the screen correlate well with residues established previously as critical to function and/or structure in protein kinases. We also identified activating mutations in the regulatory hydrophobic spine and activation loop, which are within key motifs involved in kinase regulation. Strikingly, one mutation in an ancestral Syk-family variant increases the soluble expression of the protein by 75-fold. Thus, through ancestral sequence reconstruction followed by deep mutational scanning, we have generated Syk-family kinase variants that can be expressed in bacteria with very high yield.


Assuntos
Escherichia coli , Peptídeos e Proteínas de Sinalização Intracelular , Antibacterianos , Precursores Enzimáticos/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Humanos , Peptídeos e Proteínas de Sinalização Intracelular/genética , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Mutagênese , Peptídeos/química , Fosforilação , Quinase Syk/genética , Quinase Syk/metabolismo , Tirosina/genética
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