The Transporter Classification Database: recent advances

Saier, Milton H.; Yen, Ming Ren; Noto, Keisuke; Tamang, Dorjee G.; Elkan, Charles

doi:10.1093/nar/gkn862

Cited by 395 publications

(381 citation statements)

References 21 publications

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“…This is curious in light of MAR-FISH-based studies clearly demonstrating the ability of acI to incorporate glucose (Buck et al, 2009;Salcher et al, 2013). However, most SAGs did contain ABC-type sugar transport components (for example, COG1653) ( Table 2 and Supplementary Table S5) and using the Transporter Classification Database (Saier et al, 2009), a periplasmic component with closest match to the glucose-binding protein in Thermus thermophilus (TC#3.A.1.1.24) was found in eight SAGs but was missing in AAA027-L06. Thus, we cannot confirm nor refute the ability of all acI members to take up glucose based on genomic evidence alone.…”

Section: Resultsmentioning

confidence: 99%

Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage

et al. 2014

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Members of the acI lineage of Actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. We obtained draft genome assemblies from 11 single cells representing three acI tribes (acI-A1, acI-A7, acI-B1) from four temperate lakes in the United States and Europe. Comparative analysis of acI SAGs and other available freshwater bacterial genomes showed that acI has more gene content directed toward carbohydrate acquisition as compared to Polynucleobacter and LD12 Alphaproteobacteria, which seem to specialize more on carboxylic acids. The acI genomes contain actinorhodopsin as well as some genes involved in anaplerotic carbon fixation indicating the capacity to supplement their known heterotrophic lifestyle. Genome-level differences between the acI-A and acI-B clades suggest specialization at the clade level for carbon substrate acquisition. Overall, the acI genomes appear to be highly streamlined versions of Actinobacteria that include some genes allowing it to take advantage of sunlight and N-rich organic compounds such as polyamines, di-and oligopeptides, branched-chain amino acids and cyanophycin. This work significantly expands the known metabolic potential of the cosmopolitan freshwater acI lineage and its ecological and genetic traits.

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Section: Resultsmentioning

confidence: 99%

Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage

et al. 2014

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“…FUR4 belongs to the Nucleobase:Cation Symporter1 (NCS1) family of transport proteins, also known as purine-related transporters (Saier et al, 2009;www.tcdb.org). The closest Arabidopsis homolog to this protein is encoded by At5g03555.…”

Section: Biochemical Characterization Of Pluto a Nucleobase Transpormentioning

confidence: 99%

De Novo Pyrimidine Nucleotide Synthesis Mainly Occurs outside of Plastids, but a Previously Undiscovered Nucleobase Importer Provides Substrates for the Essential Salvage Pathway in Arabidopsis

et al. 2012

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Nucleotide de novo synthesis is highly conserved among organisms and represents an essential biochemical pathway. In plants, the two initial enzymatic reactions of de novo pyrimidine synthesis occur in the plastids. By use of green fluorescent protein fusions, clear support is provided for a localization of the remaining reactions in the cytosol and mitochondria. This implies that carbamoyl aspartate, an intermediate of this pathway, must be exported and precursors of pyrimidine salvage (i.e., nucleobases or nucleosides) are imported into plastids. A corresponding uracil transport activity could be measured in intact plastids isolated from cauliflower (Brassica oleracea) buds. PLUTO (for plastidic nucleobase transporter) was identified as a member of the Nucleobase:Cation-Symporter1 protein family from Arabidopsis thaliana, capable of transporting purine and pyrimidine nucleobases. A PLUTO green fluorescent protein fusion was shown to reside in the plastid envelope after expression in Arabidopsis protoplasts. Heterologous expression of PLUTO in an Escherichia coli mutant lacking the bacterial uracil permease uraA allowed a detailed biochemical characterization. PLUTO transports uracil, adenine, and guanine with apparent affinities of 16.4, 0.4, and 6.3 mM, respectively. Transport was markedly inhibited by low concentrations of a proton uncoupler, indicating that PLUTO functions as a proton-substrate symporter. Thus, a protein for the absolutely required import of pyrimidine nucleobases into plastids was identified.

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“…2.A.3.10). They differ with respect to substrate specificity, kinetic properties and regulation patterns (De Hertogh et al, 2002;Saier et al, 2009). In complex environments, these monomeric molecules are often the end products of the degradation of large polymers (lignocellulosic compounds, proteins or nucleic acids) by extracellular hydrolytic enzymes.…”

Section: Introductionmentioning

confidence: 99%

A novel fungal family of oligopeptide transporters identified by functional metatranscriptomics of soil eukaryotes

et al. 2011

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Functional environmental genomics has the potential to identify novel biological functions that the systematic sequencing of microbial genomes or environmental DNA may fail to uncover. We targeted the functions expressed by soil eukaryotes using a metatranscriptomic approach based on the use of soil-extracted polyadenylated messenger RNA to construct environmental complementary DNA expression libraries. Functional complementation of a yeast mutant defective in di/tripeptide uptake identified a novel family of oligopeptide transporters expressed by fungi. This family has a patchy distribution in the Basidiomycota and Ascomycota and is present in the genome of a Saccharomyces cerevisiae wine strain. High throughput phenotyping of yeast mutants expressing two environmental transporters showed that they both displayed broad substrate specificity and could transport more than 60-80 dipeptides. When expressed in Xenopus oocytes one environmental transporter induced currents upon dipeptide addition, suggesting protoncoupled co-transport of dipeptides. This transporter was also able to transport specifically cysteine. Deletion of the two copies of the corresponding gene family members in the genome of the wine yeast strain severely reduced the number of dipeptides that it could assimilate. These results demonstrate that these genes are functional and can be used by fungi to efficiently scavenge the numerous, low concentration, oligopeptides continuously generated in soils by proteolysis.

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The Transporter Classification Database: recent advances

Cited by 395 publications

References 21 publications

Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage

Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage

De Novo Pyrimidine Nucleotide Synthesis Mainly Occurs outside of Plastids, but a Previously Undiscovered Nucleobase Importer Provides Substrates for the Essential Salvage Pathway in Arabidopsis

A novel fungal family of oligopeptide transporters identified by functional metatranscriptomics of soil eukaryotes

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