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Tonb-Dependent Transporters in Sphingomonads: Unraveling Their Distribution and Function in Environmental Adaptation

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Tonb-Dependent Transporters in Sphingomonads: Unraveling Their Distribution and Function in Environmental Adaptation microorganisms Review TonB-Dependent Transporters in Sphingomonads: Unraveling Their Distribution and Function in Environmental Adaptation Devyani Samantarrai y, Annapoorni Lakshman Sagar y, Ramurthy Gudla and Dayananda Siddavattam * Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India; [email protected] (D.S.); [email protected] (A.L.S.); [email protected] (R.G.) * Correspondence: [email protected]; Tel.: +91-040-66794578 These authors contributed equally to this work. y Received: 30 November 2019; Accepted: 7 January 2020; Published: 3 March 2020 Abstract: TonB-dependent transport system plays a critical role in the transport of nutrients across the energy-deprived outer membrane of Gram-negative bacteria. It contains a specialized outer membrane TonB-dependent transporter (TBDT) and energy generating (ExbB/ExbD) and transducing (TonB) inner membrane multi-protein complex, called TonB complex. Very few TonB complex protein-coding sequences exist in the genomes of Gram-negative bacteria. Interestingly, the TBDT coding alleles are phenomenally high, especially in the genomes of bacteria surviving in complex and stressful environments. Sphingomonads are known to survive in highly polluted environments using rare, recalcitrant, and toxic substances as their sole source of carbon. Naturally, they also contain a huge number of TBDTs in the outer membrane. Out of them, only a few align with the well-characterized TBDTs. The functions of the remaining TBDTs are not known. Predictions made based on genome context and expression pattern suggest their involvement in the transport of xenobiotic compounds across the outer membrane. Keywords: TonB-dependent transporter (TBDT); sphingomonads; xenobiotics 1. Introduction The outer membrane of Gram-negative bacteria performs several important functions. It acts as a barrier to prevent the entry of antibiotics and other toxic chemicals and protects the cell wall by denying access to cell wall degrading enzymes. However, existence of an energy-deprived outer membrane is a hurdle for the uptake of nutrients in Gram-negative bacteria [1]. A majority of nutrients gains entry into periplasmic space by diffusing through the outer membrane via a pore-like structure formed in outer membrane-associated β-barrel containing proteins, otherwise known as porins [2]. However, certain scarcely available nutrients depend on active transport to cross the energy-deprived outer membrane. The active transport mechanism of the outer membrane is known as TonB-dependent transport system. The system contains two components, the inner membrane-associated TonB complex and an outer membrane-associated TonB-dependent transporter (TBDT). The TonB complex contains proton motif force (PMF) components, ExbB/ExbD, and energy transducer TonB in a ratio of 7:2:1 [3]. The TonB complex has unique role in outer membrane transport. The PMF components ExbB/ExbD generate energy by pumping protons across the inner membrane, while TonB transduces this energy to the outer membrane-localized TBDT. The TonB protein contains three domains: the N-terminal transmembrane helix, C-terminal domain, and a proline-rich rigid central domain. The N-terminal region is embedded in the inner membrane and is associated with one of the transmembrane domains of ExbB [4]. Microorganisms 2020, 8, 359; doi:10.3390/microorganisms8030359 www.mdpi.com/journal/microorganisms Microorganisms 2019, 7, x FOR PEER REVIEW 2 of 14 Microorganisms 2020, 8, 359 2 of 14 proline-rich rigid central domain. The N-terminal region is embedded in the inner membrane and is associated with one of the transmembrane domains of ExbB [4]. The longer C-terminal region extends Theinto longer periplasmic C-terminal space region andextends specifically into periplasmicinteracts with space TonB-box and specifically of the outer interacts membrane-localized with TonB-box of theTBDT. outer These membrane-localized interactions of TBDT.TonB Theseand TBDT interactions facilitate of TonB the andtransduction TBDT facilitate of energy the transduction required to oftransport energy requiredscarcely toavailable transport nutrients scarcely across available the nutrients outer membrane. across the outerThe TBDT membrane. possesses The unique TBDT possessesstructural unique features structural and exhibits features a two-domain and exhibits structure. a two-domain The C-terminal structure. domain The C-terminal embedded domain in the embeddedouter membrane in the outer contains membrane one of containsthe largest one 22-stranded of the largest β-barrel 22-stranded with extracellularβ-barrel with loops. extracellular The N- loops.terminal The globular N-terminal domain, globular through domain, its unique through structural its unique features, structural establishes features, cross-talk establishes with cross-talk the inner withmembrane-localized the inner membrane-localized TonB complex. TonB An energy complex. coupling An energy consensus coupling pentapeptide consensus motif pentapeptide (ETVIV) motifdesignated (ETVIV) as designated“TonB-box” as physically “TonB-box” interacts physically with interacts the C-terminal with the domain C-terminal of inner domain membrane- of inner membrane-localized,localized, periplasmically periplasmically exposed exposedTonB [5]. TonB The [5TBDT]. The undergoes TBDT undergoes conformational conformational changes changes upon uponsubstrate substrate binding. binding. This Thisconformational conformational change change induces induces structural structural transition transition from from a state a state of oforder order to todisorder disorder in in the the TonB-box TonB-box motif motif [6]. [6]. This This disordered disordered state state of of TonB-box TonB-box of TBDT is recognized byby TonB.TonB. TheThe TBDT TBDT and and TonB TonB interactions interactions are are transient, transient, the the disordered disordered state state of of TonB-box TonB-box returns returns to to an an ordered ordered statestate after after completion completion of substrateof substrate transport transport [7]. TonB[7]. TonB plays aplays critical a rolecritical in supplyingrole in supplying energy required energy forrequired the structural for the transitionstructural oftransition TBDT. TonB of TBDT. harvests TonB energy harvests generated energy by generated PMF components by PMF components ExbB/ExbD andExbB/ExbD transduces and it transduces to TBDT (Figure it to TBDT1). (Figure 1). FigureFigure 1. 1.( A(A)) Schematic Schematic diagram diagram of of TonB-dependent TonB-dependent transport transport system. system. (B )(B Typical) Typical structural structural features features of anof outeran outer membrane membrane transporter transporter (TBDT), (TBDT), 22 β-barrel 22 β structure,-barrel structure, N-terminal N-term pluginal domain, plug and domain, substrate and bindingsubstrate motif binding are indicated motif are with indicated arrows. with arrows. TheThe TonB TonB complex complex of of TBDT TBDT is is highly highly conserved conserved among among Gram-negative Gram-negative bacteria. bacteria. The The genome genome sequencessequences of of Gram-negative Gram-negative bacteriabacteria containcontain aa limitedlimited numbernumber ofofalleles alleles totocode codefor for TonB TonB complex complex proteins,proteins, TonB TonB and and ExbB ExbB/ExbD./ExbD. Though Though the the overall overall structural structural features features of of TBDT TBDT are are conserved, conserved, there there existexist substantial substantial di differencesfferences in in the the residues residues of of ligand ligand binding binding sites. sites. Such Such diversity diversity in in the the residues residues of of ligandligand binding binding sites sites suggests suggests the the existence existence of of specialized specialized TBDTs TBDTs for for transport transport of of a a variety variety of of scarcely scarcely availableavailable nutrientsnutrients inin the the environment. environment. TheThe copycopy numbernumber ofof TBDTsTBDTsshows showsa a very very unique unique pattern pattern amongamong Gram-negative Gram-negative bacteria. bacteria. Genomes Genomes isolated isolated from from the the cells cells grown grown in in less less stressful stressful environments environments showshow existence existence of of a a smaller smaller number number of of TBDT TBDT coding coding alleles. alleles. Their Their numbers numbers in in such such strains strains does does not not exceedexceedfour four toto fivefive allelesalleles per genome. However, However, the the number number of of alleles alleles coding coding TBDTs TBDTs ie iemore more in the in thegenomes genomes of ofcells cells isolated isolated from from harsh harsh environments environments [8]. [8]. The The gut microbiomemicrobiome sequencessequences showshow anan unusuallyunusually high high number number of of TBDT TBDT coding coding sequences sequences [ 9[9].]. Similarly,Similarly, in in the the genomes genomes ofof sphingomonads,sphingomonads, namelynamelySphingobium Sphingobium japonicum japonicum, Sphingobium, Sphingobium indicum indicum, Sphingobium, Sphingobium fuliginis fuliginis,, which livewhich in harsh live climates,in harsh aclimates, very high a numbervery high of number TBDT coding of TBDT alleles coding are identified.alleles are Inidentified. fact, the numberIn fact, the of TBDTsnumber appears of TBDTs to proportionatelyappears to proportionately increase with theincrease complexity with the of the comp environmentlexity of the [9]. environment
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