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Dhar R, Bowman AM, Hatungimana B, Sg Slusky J. Evolutionary Engineering a Larger Porin Using a Loop-to-Hairpin Mechanism. J Mol Biol 2023; 435:168292. [PMID: 37769963 PMCID: PMC11215794 DOI: 10.1016/j.jmb.2023.168292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/03/2023]
Abstract
In protein evolution, diversification is generally driven by genetic duplication. The hallmarks of this mechanism are visible in the repeating topology of various proteins. In outer membrane β-barrels, duplication is visible with β-hairpins as the repeating unit of the barrel. In contrast to the overall use of duplication in diversification, a computational study hypothesized evolutionary mechanisms other than hairpin duplications leading to increases in the number of strands in outer membrane β-barrels. Specifically, the topology of some 16- and 18-stranded β-barrels appear to have evolved through a loop to β-hairpin transition. Here we test this novel evolutionary mechanism by creating a chimeric protein from an 18-stranded β-barrel and an evolutionarily related 16-stranded β-barrel. The chimeric combination of the two was created by replacing loop L3 of the 16-stranded barrel with the sequentially matched transmembrane β-hairpin region of the 18-stranded barrel. We find the resulting chimeric protein is stable and has characteristics of increased strand number. This study provides the first experimental evidence supporting the evolution through a loop to β-hairpin transition.
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Affiliation(s)
- Rik Dhar
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA. https://twitter.com/Rik_Skywalker
| | - Alexander M Bowman
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA
| | - Brunojoel Hatungimana
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA
| | - Joanna Sg Slusky
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA; Computational Biology Program, The University of Kansas, Lawrence, KS 66047, USA.
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2
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Chafale A, Das S, Kapley A. Valorization of oily sludge waste using biosurfactant-producing bacteria. World J Microbiol Biotechnol 2023; 39:316. [PMID: 37743461 DOI: 10.1007/s11274-023-03759-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/09/2023] [Indexed: 09/26/2023]
Abstract
Oily sludge generated by the petroleum industry is not only an environmental hazard, but since it contains crude oil too, it is a valuable resource as well. This study demonstrates a methodology for the valorization of the oily sludge that allows the recovery of oil fractions by the action of microbes producing surface-active metabolites. Two bacterial isolates were used in the study that were producing different biosurfactants, identified via FTIR analysis as well as through genomic mapping of the biosurfactant pathways using RAST, ANTISMASH 7.0, STRING databases. Serratia spp. AKBS12, produced a mono-rhamnolipid, while Acinetobacter spp. AKBS16, produced emulsan. Although recovery efficiency of both biosurfactants was similar, the recovery profile with respect to the class of hydrocarbons differed. The rhamnolipid produced by Serratia spp. AKBS12 extracted mono-chained paraffins and linear alkanes, while emulsan, produced by Acinetobacter spp. AKBS16 could extract heavier paraffins. The extraction procedure is simple and involves mixing the biosurfactant with oily sludge at a temperature of 30 °C with an incubation of 9 days. Sulphuric acid precipitation releases the oil trapped in the oily sludge. The study is the first step in developing user-friendly, innovative technologies that can be linked to the concept of a circular economy.
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Affiliation(s)
- Ayushi Chafale
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sera Das
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Analytical Instruments Division, National Environmental Engineering Research Institute, Council of Scientific and Industrial Research, Nehru Marg, Nagpur, 440020, India
| | - Atya Kapley
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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3
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Dhar R, Bowman AM, Hatungimana B, Slusky JS. Evolutionary engineering a larger porin using a loop-to-hairpin mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544993. [PMID: 37398247 PMCID: PMC10312768 DOI: 10.1101/2023.06.14.544993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
In protein evolution, diversification is generally driven by genetic duplication. The hallmarks of this mechanism are visible in the repeating topology of various proteins. In outer membrane β-barrels, duplication is visible with β-hairpins as the repeating unit of the barrel. In contrast to the overall use of duplication in diversification, a computational study hypothesized evolutionary mechanisms other than hairpin duplications leading to increases in the number of strands in outer membrane β-barrels. Specifically, the topology of some 16- and 18-stranded β-barrels appear to have evolved through a loop to β-hairpin transition. Here we test this novel evolutionary mechanism by creating a chimeric protein from an 18-stranded β-barrel and an evolutionarily related 16-stranded β-barrel. The chimeric combination of the two was created by replacing loop L3 of the 16-stranded barrel with the sequentially matched transmembrane β-hairpin region of the 18-stranded barrel. We find the resulting chimeric protein is stable and has characteristics of increased strand number. This study provides the first experimental evidence supporting the evolution through a loop to β-hairpin transition. Highlights We find evidence supporting a novel diversification mechanism in membrane β-barrelsThe mechanism is the conversion of an extracellular loop to transmembrane β-hairpinA chimeric protein modeling this mechanism folds stably in the membraneThe chimera has more β-structure and a larger pore, consistent with a loop-to-hairpin transition.
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Affiliation(s)
- Rik Dhar
- Department of Molecular Biosciences, The University of Kansas, Lawrence KS 66045
| | - Alexander M Bowman
- Department of Molecular Biosciences, The University of Kansas, Lawrence KS 66045
| | | | - Joanna Sg Slusky
- Department of Molecular Biosciences, The University of Kansas, Lawrence KS 66045
- Computational Biology Program, The University of Kansas, Lawrence KS 66047
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4
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Mutanda I, Sun J, Jiang J, Zhu D. Bacterial membrane transporter systems for aromatic compounds: Regulation, engineering, and biotechnological applications. Biotechnol Adv 2022; 59:107952. [PMID: 35398204 DOI: 10.1016/j.biotechadv.2022.107952] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/20/2022] [Accepted: 04/02/2022] [Indexed: 12/13/2022]
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5
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Abstract
All currently known architectures of outer-membrane beta barrels (OMBBs) have only one barrel. While the vast majority function as oligomers, with barrels from different chains packing against each other in the membrane, it was assumed that these multiple chains are needed to form multibarrel structures. And yet, here we show that multibarrel chains exist. Using state-of-the-art sequence and structure analysis tools, we report the discovery of more than 30 multibarrel architectures from gram-negative bacteria. The discovery of these architectures reveals another interesting chapter in OMBB evolution and has implications for protein engineering. The evolutionary advantages of multibarrels are yet to be discovered. Outer-membrane beta barrels (OMBBs) are found in the outer membrane of gram-negative bacteria and eukaryotic organelles. OMBBs fold as antiparallel β-sheets that close onto themselves, forming pores that traverse the membrane. Currently known structures include only one barrel, of 8 to 36 strands, per chain. The lack of multi-OMBB chains is surprising, as most OMBBs form oligomers, and some function only in this state. Using a combination of sensitive sequence comparison methods and coevolutionary analysis tools, we identify many proteins combining multiple beta barrels within a single chain; combinations that include eight-stranded barrels prevail. These multibarrels seem to be the result of independent, lineage-specific fusion and amplification events. The absence of multibarrels that are universally conserved in bacteria with an outer membrane, coupled with their frequent de novo genesis, suggests that their functions are not essential but rather beneficial in specific environments. Adjacent barrels of complementary function within the same chain may allow for functions beyond those of the individual barrels.
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6
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Russum S, Lam KJK, Wong NA, Iddamsetty V, Hendargo KJ, Wang J, Dubey A, Zhang Y, Medrano-Soto A, Saier MH. Comparative population genomic analyses of transporters within the Asgard archaeal superphylum. PLoS One 2021; 16:e0247806. [PMID: 33770091 PMCID: PMC7997004 DOI: 10.1371/journal.pone.0247806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/15/2021] [Indexed: 01/02/2023] Open
Abstract
Upon discovery of the first archaeal species in the 1970s, life has been subdivided into three domains: Eukarya, Archaea, and Bacteria. However, the organization of the three-domain tree of life has been challenged following the discovery of archaeal lineages such as the TACK and Asgard superphyla. The Asgard Superphylum has emerged as the closest archaeal ancestor to eukaryotes, potentially improving our understanding of the evolution of life forms. We characterized the transportomes and their substrates within four metagenome-assembled genomes (MAGs), that is, Odin-, Thor-, Heimdall- and Loki-archaeota as well as the fully sequenced genome of Candidatus Prometheoarchaeum syntrophicum strain MK-D1 that belongs to the Loki phylum. Using the Transporter Classification Database (TCDB) as reference, candidate transporters encoded within the proteomes were identified based on sequence similarity, alignment coverage, compatibility of hydropathy profiles, TMS topologies and shared domains. Identified transport systems were compared within the Asgard superphylum as well as within dissimilar eukaryotic, archaeal and bacterial organisms. From these analyses, we infer that Asgard organisms rely mostly on the transport of substrates driven by the proton motive force (pmf), the proton electrochemical gradient which then can be used for ATP production and to drive the activities of secondary carriers. The results indicate that Asgard archaea depend heavily on the uptake of organic molecules such as lipid precursors, amino acids and their derivatives, and sugars and their derivatives. Overall, the majority of the transporters identified are more similar to prokaryotic transporters than eukaryotic systems although several instances of the reverse were documented. Taken together, the results support the previous suggestions that the Asgard superphylum includes organisms that are largely mixotrophic and anaerobic but more clearly define their metabolic potential while providing evidence regarding their relatedness to eukaryotes.
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Affiliation(s)
- Steven Russum
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Katie Jing Kay Lam
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Nicholas Alan Wong
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Vasu Iddamsetty
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Kevin J. Hendargo
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Jianing Wang
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Aditi Dubey
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Yichi Zhang
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Arturo Medrano-Soto
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
- * E-mail: (MHS); (AMS)
| | - Milton H. Saier
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
- * E-mail: (MHS); (AMS)
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7
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Counihan NA, Modak JK, de Koning-Ward TF. How Malaria Parasites Acquire Nutrients From Their Host. Front Cell Dev Biol 2021; 9:649184. [PMID: 33842474 PMCID: PMC8027349 DOI: 10.3389/fcell.2021.649184] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/24/2021] [Indexed: 01/01/2023] Open
Abstract
Plasmodium parasites responsible for the disease malaria reside within erythrocytes. Inside this niche host cell, parasites internalize and digest host hemoglobin to source amino acids required for protein production. However, hemoglobin does not contain isoleucine, an amino acid essential for Plasmodium growth, and the parasite cannot synthesize it de novo. The parasite is also more metabolically active than its host cell, and the rate at which some nutrients are consumed exceeds the rate at which they can be taken up by erythrocyte transporters. To overcome these constraints, Plasmodium parasites increase the permeability of the erythrocyte membrane to isoleucine and other low-molecular-weight solutes it requires for growth by forming new permeation pathways (NPPs). In addition to the erythrocyte membrane, host nutrients also need to cross the encasing parasitophorous vacuole membrane (PVM) and the parasite plasma membrane to access the parasite. This review outlines recent advances that have been made in identifying the molecular constituents of the NPPs, the PVM nutrient channel, and the endocytic apparatus that transports host hemoglobin and identifies key knowledge gaps that remain. Importantly, blocking the ability of Plasmodium to source essential nutrients is lethal to the parasite, and thus, components of these key pathways represent potential antimalaria drug targets.
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Affiliation(s)
| | - Joyanta K Modak
- School of Medicine, Deakin University, Waurn Ponds, VIC, Australia
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8
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Saier MH, Reddy VS, Moreno-Hagelsieb G, Hendargo KJ, Zhang Y, Iddamsetty V, Lam KJK, Tian N, Russum S, Wang J, Medrano-Soto A. The Transporter Classification Database (TCDB): 2021 update. Nucleic Acids Res 2021; 49:D461-D467. [PMID: 33170213 PMCID: PMC7778945 DOI: 10.1093/nar/gkaa1004] [Citation(s) in RCA: 166] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 12/20/2022] Open
Abstract
The Transporter Classification Database (TCDB; tcdb.org) is a freely accessible reference resource, which provides functional, structural, mechanistic, medical and biotechnological information about transporters from organisms of all types. TCDB is the only transport protein classification database adopted by the International Union of Biochemistry and Molecular Biology (IUBMB) and now (October 1, 2020) consists of 20 653 proteins classified in 15 528 non-redundant transport systems with 1567 tabulated 3D structures, 18 336 reference citations describing 1536 transporter families, of which 26% are members of 82 recognized superfamilies. Overall, this is an increase of over 50% since the last published update of the database in 2016. This comprehensive update of the database contents and features include (i) adoption of a chemical ontology for substrates of transporters, (ii) inclusion of new superfamilies, (iii) a domain-based characterization of transporter families for the identification of new members as well as functional and evolutionary relationships between families, (iv) development of novel software to facilitate curation and use of the database, (v) addition of new subclasses of transport systems including 11 novel types of channels and 3 types of group translocators and (vi) the inclusion of many man-made (artificial) transmembrane pores/channels and carriers.
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Affiliation(s)
- Milton H Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Vamsee S Reddy
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | | | - Kevin J Hendargo
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Yichi Zhang
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Vasu Iddamsetty
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Katie Jing Kay Lam
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Nuo Tian
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Steven Russum
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Jianing Wang
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Arturo Medrano-Soto
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
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9
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Outer membrane protein evolution. Curr Opin Struct Biol 2021; 68:122-128. [PMID: 33493965 DOI: 10.1016/j.sbi.2021.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/16/2020] [Accepted: 01/02/2021] [Indexed: 01/31/2023]
Abstract
Outer membrane proteins have remarkably homogeneous structure. They are all up down β-barrels. Up down barrels themselves are composed of repeated sets of β-hairpins. The consistency of the usage of the β-hairpin throughout the outer membrane milieu allows for interrogation of the evolution of these repetitive structures. Here we describe recent investigations of outer membrane protein evolution and how evolutionary precepts have been used for novel outer membrane protein design.
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10
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Cerón-Romero MA, Maurer-Alcalá XX, Grattepanche JD, Yan Y, Fonseca MM, Katz LA. PhyloToL: A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes. Mol Biol Evol 2020; 36:1831-1842. [PMID: 31062861 PMCID: PMC6657734 DOI: 10.1093/molbev/msz103] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Estimating multiple sequence alignments (MSAs) and inferring phylogenies are essential for many aspects of comparative biology. Yet, many bioinformatics tools for such analyses have focused on specific clades, with greatest attention paid to plants, animals, and fungi. The rapid increase in high-throughput sequencing (HTS) data from diverse lineages now provides opportunities to estimate evolutionary relationships and gene family evolution across the eukaryotic tree of life. At the same time, these types of data are known to be error-prone (e.g., substitutions, contamination). To address these opportunities and challenges, we have refined a phylogenomic pipeline, now named PhyloToL, to allow easy incorporation of data from HTS studies, to automate production of both MSAs and gene trees, and to identify and remove contaminants. PhyloToL is designed for phylogenomic analyses of diverse lineages across the tree of life (i.e., at scales of >100 My). We demonstrate the power of PhyloToL by assessing stop codon usage in Ciliophora, identifying contamination in a taxon- and gene-rich database and exploring the evolutionary history of chromosomes in the kinetoplastid parasite Trypanosoma brucei, the causative agent of African sleeping sickness. Benchmarking PhyloToL’s homology assessment against that of OrthoMCL and a published paper on superfamilies of bacterial and eukaryotic organellar outer membrane pore-forming proteins demonstrates the power of our approach for determining gene family membership and inferring gene trees. PhyloToL is highly flexible and allows users to easily explore HTS data, test hypotheses about phylogeny and gene family evolution and combine outputs with third-party tools (e.g., PhyloChromoMap, iGTP).
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Affiliation(s)
- Mario A Cerón-Romero
- Department of Biological Sciences, Smith College, Northampton, MA.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, MA
| | - Xyrus X Maurer-Alcalá
- Department of Biological Sciences, Smith College, Northampton, MA.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, MA.,Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Jean-David Grattepanche
- Department of Biological Sciences, Smith College, Northampton, MA.,Biology Department, Temple University, Philadelphia, PA
| | - Ying Yan
- Department of Biological Sciences, Smith College, Northampton, MA
| | - Miguel M Fonseca
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - L A Katz
- Department of Biological Sciences, Smith College, Northampton, MA.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, MA
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11
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Buyuktimkin B, Zafar H, Saier MH. Comparative genomics of the transportome of Ten Treponema species. Microb Pathog 2019; 132:87-99. [PMID: 31029716 DOI: 10.1016/j.micpath.2019.04.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/02/2019] [Accepted: 04/23/2019] [Indexed: 02/08/2023]
Abstract
Treponema is a diverse bacterial genus, the species of which can be pathogenic, symbiotic, or free living. These treponemes can cause various diseases in humans and other animals, such as periodontal disease, bovine digital dermatitis and animal skin lesions. However, the most important and well-studied disease of treponemes that affects humans is 'syphilis'. This disease is caused by Treponema pallidum subspecie pallidum with 11-12 million new cases around the globe on an annual basis. In this study we analyze the transportome of ten Treponema species, with emphasis on the types of encoded transport proteins and their substrates. Of the ten species examined, two (T. primitia and T. azonutricium) reside as symbionts in the guts of termites; six (T. pallidum, T. paraluiscuniculi, T. pedis, T. denticola, T. putidum and T. brennaborense) are pathogens of either humans or animals, and T. caldarium and T. succinifaciens are avirulent species, the former being thermophilic. All ten species have a repertoire of transport proteins that assists them in residing in their respective ecological niches. For instance, oral pathogens use transport proteins that take up nutrients uniquely present in their ecosystem; they also encode multiple multidrug/macromolecule exporters that protect against antimicrobials and aid in biofilm formation. Proteins of termite gut symbionts convert cellulose into other sugars that can be metabolized by the host. As often observed for pathogens and symbionts, several of these treponemes have reduced genome sizes, and their small genomes correlate with their dependencies on the host. Overall, the transportomes of T. pallidum and other pathogens have a conglomerate of parasitic lifestyle-assisting proteins. For example, a T. pallidum repeat protein (TprK) mediates immune evasion; outer membrane proteins (OMPs) allow nutrient uptake and end product export, and several ABC transporters catalyze sugar uptake, considered pivotal to parasitic lifestyles. Taken together, the results of this study yield new information that may help open new avenues of treponeme research.
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Affiliation(s)
- Bora Buyuktimkin
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093-0116, USA
| | - Hassan Zafar
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093-0116, USA; Institute of Microbiology, University of Agriculture, Faisalabad, Punjab, Pakistan
| | - Milton H Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093-0116, USA.
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12
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Zafar H, Saier MH. Comparative genomics of transport proteins in seven Bacteroides species. PLoS One 2018; 13:e0208151. [PMID: 30517169 PMCID: PMC6281302 DOI: 10.1371/journal.pone.0208151] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/12/2018] [Indexed: 01/29/2023] Open
Abstract
The communities of beneficial bacteria that live in our intestines, the gut microbiome, are important for the development and function of the immune system. Bacteroides species make up a significant fraction of the human gut microbiome, and can be probiotic and pathogenic, depending upon various genetic and environmental factors. These can cause disease conditions such as intra-abdominal sepsis, appendicitis, bacteremia, endocarditis, pericarditis, skin infections, brain abscesses and meningitis. In this study, we identify the transport systems and predict their substrates within seven Bacteroides species, all shown to be probiotic; however, four of them (B. thetaiotaomicron, B. vulgatus, B. ovatus, B. fragilis) can be pathogenic (probiotic and pathogenic; PAP), while B. cellulosilyticus, B. salanitronis and B. dorei are believed to play only probiotic roles (only probiotic; OP). The transport system characteristics of the four PAP and three OP strains were identified and tabulated, and results were compared among the seven strains, and with E. coli and Salmonella strains. The Bacteroides strains studied contain similarities and differences in the numbers and types of transport proteins tabulated, but both OP and PAP strains contain similar outer membrane carbohydrate receptors, pore-forming toxins and protein secretion systems, the similarities were noteworthy, but these Bacteroides strains showed striking differences with probiotic and pathogenic enteric bacteria, particularly with respect to their high affinity outer membrane receptors and auxiliary proteins involved in complex carbohydrate utilization. The results reveal striking similarities between the PAP and OP species of Bacteroides, and suggest that OP species may possess currently unrecognized pathogenic potential.
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Affiliation(s)
- Hassan Zafar
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, United States of America
- Institute of Microbiology, University of Agriculture, Faisalabad, Punjab, Pakistan
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, United States of America
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13
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Franklin MW, Nepomnyachyi S, Feehan R, Ben-Tal N, Kolodny R, Slusky JS. Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins. eLife 2018; 7:40308. [PMID: 30489257 PMCID: PMC6340704 DOI: 10.7554/elife.40308] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/28/2018] [Indexed: 11/13/2022] Open
Abstract
Outer membrane proteins (OMPs) are the proteins in the surface of Gram-negative bacteria. These proteins have diverse functions but a single topology: the β-barrel. Sequence analysis has suggested that this common fold is a β-hairpin repeat protein, and that amplification of the β-hairpin has resulted in 8-26-stranded barrels. Using an integrated approach that combines sequence and structural analyses, we find events in which non-amplification diversification also increases barrel strand number. Our network-based analysis reveals strand-number-based evolutionary pathways, including one that progresses from a primordial 8-stranded barrel to 16-strands and further, to 18-strands. Among these pathways are mechanisms of strand number accretion without domain duplication, like a loop-to-hairpin transition. These mechanisms illustrate perpetuation of repeat protein topology without genetic duplication, likely induced by the hydrophobic membrane. Finally, we find that the evolutionary trace is particularly prominent in the C-terminal half of OMPs, implicating this region in the nucleation of OMP folding.
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Affiliation(s)
| | - Sergey Nepomnyachyi
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel.,Department of Computer Science, University of Haifa, Haifa, Israel
| | - Ryan Feehan
- Center for Computational Biology, University of Kansas, Kansas, United States
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Rachel Kolodny
- Department of Computer Science, University of Haifa, Haifa, Israel
| | - Joanna Sg Slusky
- Center for Computational Biology, University of Kansas, Kansas, United States.,Department of Molecular Biosciences, University of Kansas, Kansas, United States
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Diep P, Mahadevan R, Yakunin AF. Heavy Metal Removal by Bioaccumulation Using Genetically Engineered Microorganisms. Front Bioeng Biotechnol 2018; 6:157. [PMID: 30420950 PMCID: PMC6215804 DOI: 10.3389/fbioe.2018.00157] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/09/2018] [Indexed: 11/25/2022] Open
Abstract
Wastewater effluents from mines and metal refineries are often contaminated with heavy metal ions, so they pose hazards to human and environmental health. Conventional technologies to remove heavy metal ions are well-established, but the most popular methods have drawbacks: chemical precipitation generates sludge waste, and activated carbon and ion exchange resins are made from unsustainable non-renewable resources. Using microbial biomass as the platform for heavy metal ion removal is an alternative method. Specifically, bioaccumulation is a natural biological phenomenon where microorganisms use proteins to uptake and sequester metal ions in the intracellular space to utilize in cellular processes (e.g., enzyme catalysis, signaling, stabilizing charges on biomolecules). Recombinant expression of these import-storage systems in genetically engineered microorganisms allows for enhanced uptake and sequestration of heavy metal ions. This has been studied for over two decades for bioremediative applications, but successful translation to industrial-scale processes is virtually non-existent. Meanwhile, demands for metal resources are increasing while discovery rates to supply primary grade ores are not. This review re-thinks how bioaccumulation can be used and proposes that it can be developed for bioextractive applications-the removal and recovery of heavy metal ions for downstream purification and refining, rather than disposal. This review consolidates previously tested import-storage systems into a biochemical framework and highlights efforts to overcome obstacles that limit industrial feasibility, thereby identifying gaps in knowledge and potential avenues of research in bioaccumulation.
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Affiliation(s)
| | | | - Alexander F. Yakunin
- BioZone - Centre for Applied Biosciences and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
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15
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Franklin MW, Nepomnyachiy S, Feehan R, Ben-Tal N, Kolodny R, Slusky JSG. Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold. Structure 2018; 26:1266-1274.e2. [PMID: 30057025 PMCID: PMC6125174 DOI: 10.1016/j.str.2018.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/17/2018] [Accepted: 06/20/2018] [Indexed: 11/22/2022]
Abstract
There are around 100 varieties of outer membrane proteins in each Gram-negative bacteria. All of these proteins have the same fold-an up-down β-barrel. It has been suggested that all membrane β-barrels excluding lysins are homologous. Here we suggest that β-barrels of efflux pumps have converged on this fold as well. By grouping structurally solved outer membrane β-barrels (OMBBs) by sequence we find that the membrane environment may have led to convergent evolution of the barrel fold. Specifically, the lack of sequence linkage to other barrels coupled with distinctive structural differences, such as differences in strand tilt and barrel radius, suggest that the outer membrane factor of efflux pumps evolutionarily converged on the barrel. Rather than being related to other OMBBs, sequence and structural similarity in the periplasmic region of the outer membrane factor of efflux pumps suggests an evolutionary link to the periplasmic subunit of the same pump complex.
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Affiliation(s)
| | - Sergey Nepomnyachiy
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel; Department of Computer Science, University of Haifa, Mount Carmel, Haifa 3498838, Israel
| | - Ryan Feehan
- Center for Computational Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Rachel Kolodny
- Department of Computer Science, University of Haifa, Mount Carmel, Haifa 3498838, Israel
| | - Joanna S G Slusky
- Center for Computational Biology, University of Kansas, Lawrence, KS 66045, USA; Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.
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16
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Heidari Tajabadi F, Medrano-Soto A, Ahmadzadeh M, Salehi Jouzani G, Saier MH. Comparative Analyses of Transport Proteins Encoded within the Genomes of Bdellovibrio bacteriovorus HD100 and Bdellovibrio exovorus JSS. J Mol Microbiol Biotechnol 2017; 27:332-349. [PMID: 29212086 DOI: 10.1159/000484563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/17/2017] [Indexed: 12/21/2022] Open
Abstract
Bdellovibrio, δ-proteobacteria, including B. bacteriovorus (Bba) and B. exovorus (Bex), are obligate predators of other Gram-negative bacteria. While Bba grows in the periplasm of the prey cell, Bex grows externally. We have analyzed and compared the transport proteins of these 2 organisms based on the current contents of the Transporter Classification Database (TCDB; www.tcdb.org). Bba has 103 transporters more than Bex, 50% more secondary carriers, and 3 times as many MFS carriers. Bba has far more metabolite transporters than Bex as expected from its larger genome, but there are 2 times more carbohydrate uptake and drug efflux systems, and 3 times more lipid transporters. Bba also has polyamine and carboxylate transporters lacking in Bex. Bba has more than twice as many members of the Mot-Exb family of energizers, but both may have energizers for gliding motility. They use entirely different types of systems for iron acquisition. Both contain unexpectedly large numbers of pseudogenes and incomplete systems, suggesting that they are undergoing genome size reduction. Interestingly, all 5 outer-membrane receptors in Bba are lacking in Bex. The 2 organisms have similar numbers and types of peptide and amino acid uptake systems as well as protein and carbohydrate secretion systems. The differences observed correlate with and may account, in part, for the different lifestyles of these 2 bacterial predators.
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17
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Do J, Zafar H, Saier MH. Comparative genomics of transport proteins in probiotic and pathogenic Escherichia coli and Salmonella enterica strains. Microb Pathog 2017; 107:106-115. [PMID: 28344124 PMCID: PMC5591646 DOI: 10.1016/j.micpath.2017.03.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 12/13/2016] [Accepted: 03/21/2017] [Indexed: 12/11/2022]
Abstract
Escherichia coli is a genetically diverse species that can be pathogenic, probiotic, commensal, or a harmless laboratory strain. Pathogenic strains of E. coli cause urinary tract infections, diarrhea, hemorrhagic colitis, and pyelonephritis, while the two known probiotic E. coli strains combat inflammatory bowel disease and play a role in immunomodulation. Salmonella enterica, a close relative of E. coli, includes two important pathogenic serovars, Typhi and Typhimurium, causing typhoid fever and enterocolitis in humans, respectively, with the latter strain also causing a lethal typhoid fever-like disease in mice. In this study, we identify the transport systems and their substrates within seven E. coli strains: two probiotic strains, two extracellular pathogens, two intracellular pathogens, and K-12, as well as the two intracellular pathogenic S. enterica strains noted above. Transport systems characteristic of each probiotic or pathogenic species were thus identified, and the tabulated results obtained with all of these strains were compared. We found that the probiotic and pathogenic strains generally contain more iron-siderophore and sugar transporters than E. coli K-12. Pathogens have increased numbers of pore-forming toxins, protein secretion systems, decarboxylation-driven Na+ exporters, electron flow-driven monovalent cation exporters, and putative transporters of unknown function compared to the probiotic strains. Both pathogens and probiotic strains encode metabolite transporters that reflect their intracellular versus extracellular environments. The results indicate that the probiotic strains live extracellularly. It seems that relatively few virulence factors can convert a beneficial or commensal microorganism into a pathogen. Taken together, the results reveal the distinguishing features of these strains and provide a starting point for future engineering of beneficial enteric bacteria.
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Affiliation(s)
- Jimmy Do
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Hassan Zafar
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Milton H Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA.
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18
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Transport protein evolution deduced from analysis of sequence, topology and structure. Curr Opin Struct Biol 2016; 38:9-17. [PMID: 27270239 DOI: 10.1016/j.sbi.2016.05.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 05/04/2016] [Accepted: 05/05/2016] [Indexed: 11/21/2022]
Abstract
The vast majority of well studied transmembrane channels, secondary carriers, primary active transporters and group translocators are believed to have arisen vis intragenic duplication events from simple channel-forming peptides with just 1-3 transmembrane α-helical segments, found ubiquitously in nature. Only a few established channel-forming proteins appear to have evolved via other pathways. The proposed pathway for the evolutionary appearance of the five types of transport proteins involved intragenic duplication of transmembrane pore-forming peptide-encoding genes, giving rise to channel proteins. These gave rise to single protein secondary carriers which upon superimposition of addition protein domains and proteins, including energy-coupling proteins and extracytoplasmic receptors, gave rise to multidomain, multicomponent carriers, primary active transporters and group translocators. Some of the largest and best characterized superfamilies of these transmembrane transport proteins are discussed from topological and evolutionary standpoints.
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