The IUBMB-Endorsed Transporter Classification System

Busch, Wolfgang; Saier, Milton H.

doi:10.1385/1-59259-387-9:21

Cited by 19 publications

(14 citation statements)

References 12 publications

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“…A unique family of amino acid transporter (AAP) genes from members of the trypanosomatid family (25 in Leishmania , 17 in T. brucei and 19 in T. cruzi ) has been identified, based on the existence of amino acid permease pfam domains [81], [82]. This trypanosomatid-specific group of amino acid transporters corresponds to a distinct clade within the amino acid/auxin permease (AAAP) super family [83], [84]. The analysis of these gene families revealed 15 and 16 AAP genes in EM1 and HART1 respectively, fewer than in the mammalian trypanosomatid genomes (Table 2 and Figure S18, details in Table S3E and Text S1).…”

Section: Resultsmentioning

confidence: 99%

The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants

et al. 2014

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Members of the family Trypanosomatidae infect many organisms, including animals, plants and humans. Plant-infecting trypanosomes are grouped under the single genus Phytomonas, failing to reflect the wide biological and pathological diversity of these protists. While some Phytomonas spp. multiply in the latex of plants, or in fruit or seeds without apparent pathogenicity, others colonize the phloem sap and afflict plants of substantial economic value, including the coffee tree, coconut and oil palms. Plant trypanosomes have not been studied extensively at the genome level, a major gap in understanding and controlling pathogenesis. We describe the genome sequences of two plant trypanosomatids, one pathogenic isolate from a Guianan coconut and one non-symptomatic isolate from Euphorbia collected in France. Although these parasites have extremely distinct pathogenic impacts, very few genes are unique to either, with the vast majority of genes shared by both isolates. Significantly, both Phytomonas spp. genomes consist essentially of single copy genes for the bulk of their metabolic enzymes, whereas other trypanosomatids e.g. Leishmania and Trypanosoma possess multiple paralogous genes or families. Indeed, comparison with other trypanosomatid genomes revealed a highly streamlined genome, encoding for a minimized metabolic system while conserving the major pathways, and with retention of a full complement of endomembrane organelles, but with no evidence for functional complexity. Identification of the metabolic genes of Phytomonas provides opportunities for establishing in vitro culturing of these fastidious parasites and new tools for the control of agricultural plant disease.

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Section: Resultsmentioning

confidence: 99%

The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants

et al. 2014

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“…Secondary antibiotic/multiple drug resistance transporters can be divided into four families [1,2]: (i) major facilitator superfamily (MFS); (ii) small multidrug resistance family (SMR); (iii) multidrug and toxic compound extrusion family (MATE); and (iv) resistance nodulation cell division superfamily (RND, TC# 2.A.6). Members of the RND superfamily involved in the transport of antibiotics belong to the family of the (largely Gram‐negative bacterial) hydrophobe/amphiphile efflux‐1 (HAE1) family (TC# 2.A.6.2).…”

Section: Introductionmentioning

confidence: 99%

Crystallographic analysis of AcrB

et al. 2004

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A His-tagged derivative of the multidrug e¥ux pump AcrB could be crystallized in three di¡erent space groups (R3, R32 and P321). Experimental MAD-phasing maps from R32 AcrB His crystals were obtained to a resolution of 3.5 A î . Datasets of native and substrate soaked AcrB His crystals were collected at the Swiss Light Source X06SA beamline up to a resolution of 2.7 A î and re¢nement of these data provided good quality electron density maps, which allowed us to complement the published AcrB structure (PDB code 1iwg). Introduction of amino acids 860^865 and 868 lacking in the 1iwg structure and deletion of a highly disordered region (amino acids 669^678) improved R free and average B factors in the 2.7 A î model. We could not identify signi¢cant densities indicating speci¢c antibiotic binding sites in the AcrB R32 space group datasets under the soaking conditions tested. ß

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“…The E. coli outer membrane protein W (OmpW) (Jalajakumari and Manning 1990) belongs to a family of small outer membrane proteins responsible for transport of small molecules across the membrane (Bush and Saier 2003). A crystal structure of the 191-amino acid protein OmpW in a mixture of the LDAO (lauryl-dimethylamine-oxide) and OG ( n -octyl-β- D -glucoside) detergents at 2.7 Å resolution shows an 8-stranded β-barrel with height ≈ 50 Å and diameter ≈ 17 Å (Hong et al 2006).…”

mentioning

confidence: 99%

Micro-coil NMR to monitor optimization of the reconstitution conditions for the integral membrane protein OmpW in detergent micelles

et al. 2012

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Optimization of aqueous solutions of the integral membrane protein (IMP) OmpW for NMR structure determination has been monitored with micro-coil NMR, which enables the acquisition of NMR spectra using only micrograms of protein and detergent. The detergent 30-Fos (2-undecylphosphocholine) was found to yield the best 2D [15N,1H]-TROSY correlation NMR spectra of [2H,15N]-labeled OmpW. For the OmpW structure determination we then optimized the 30-Fos concentration, the sample temperature and long-time stability, and the deuteration level of the protein. Some emerging guidelines for reconstitution of β-barrel integral membrane proteins in structural biology are discussed.

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The IUBMB-Endorsed Transporter Classification System

Cited by 19 publications

References 12 publications

The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants

The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants

Crystallographic analysis of AcrB

Micro-coil NMR to monitor optimization of the reconstitution conditions for the integral membrane protein OmpW in detergent micelles

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