The Transporter Classification Database (TCDB): 2021 update

Saier, Milton H.; Reddy, Vamsee S.; Moreno–Hagelsieb, Gabriel; Hendargo, Kevin J.; Zhang, Yichi; Iddamsetty, Vasu; Lam, Katie Jing Kay; Tian, Nuo; Russum, Steven; Wang, Jia‐Ning; Medrano-Soto, Arturo

doi:10.1093/nar/gkaa1004

Cited by 283 publications

(249 citation statements)

References 48 publications

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“…S12). ††Several structures of SiaP have been solved including orthologues from different organisms, complexes with different substrates, and also mutant proteins. The complete list includes: 2CEY, 2CEX, 3B50, 2V4C, 2WX9, 2WYP, 2WYK, 2XA5, 2XWV, 2XWO, 2XXK, 2XWI, 2XWK, 4MAG, 4MMP, 4MNP, 5LTC, 6H76, 6H75. ‡‡TCDB [100] lists, under other names, two further SiaT proteins: 2.A.21.3.7 (reported [29] but uncharacterized, from Aliivibrio fischeri ) and 2.A.21.3.20 (genetically characterized [48], from Lactobacillus sakei ). Both feature in our phylogenetic analysis (). §§The best-characterized SiaT orthologue from S. aureus comes from strain RF122 [22] (locus tag SAB0251c), which does not possess a UniProt entry.…”

Section: Resultsmentioning

confidence: 99%

Multiple evolutionary origins reflect the importance of sialic acid transporters in the colonization potential of bacterial pathogens and commensals

et al. 2021

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Located at the tip of cell surface glycoconjugates, sialic acids are at the forefront of host–microbe interactions and, being easily liberated by sialidase enzymes, are used as metabolites by numerous bacteria, particularly by pathogens and commensals living on or near diverse mucosal surfaces. These bacteria rely on specific transporters for the acquisition of host-derived sialic acids. Here, we present the first comprehensive genomic and phylogenetic analysis of bacterial sialic acid transporters, leading to the identification of multiple new families and subfamilies. Our phylogenetic analysis suggests that sialic acid-specific transport has evolved independently at least eight times during the evolution of bacteria, from within four of the major families/superfamilies of bacterial transporters, and we propose a robust classification scheme to bring together a myriad of different nomenclatures that exist to date. The new transporters discovered occur in diverse bacteria, including Spirochaetes , Bacteroidetes , Planctomycetes and Verrucomicrobia , many of which are species that have not been previously recognized to have sialometabolic capacities. Two subfamilies of transporters stand out in being fused to the sialic acid mutarotase enzyme, NanM, and these transporter fusions are enriched in bacteria present in gut microbial communities. Our analysis supports the increasing experimental evidence that competition for host-derived sialic acid is a key phenotype for successful colonization of complex mucosal microbiomes, such that a strong evolutionary selection has occurred for the emergence of sialic acid specificity within existing transporter architectures.

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Section: Resultsmentioning

confidence: 99%

Multiple evolutionary origins reflect the importance of sialic acid transporters in the colonization potential of bacterial pathogens and commensals

et al. 2021

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“…Individual ABCs can be grouped into nine families (named ABC-A through ABC-I) based on the sequence homology in their conserved NBD. Although there exists substantial variation within these subgroups, family members share some common allocrites and functions across a range of organisms [ 4 ]. Classification of genes into a particular ABC family can therefore be used as a starting point to investigate potentially interesting genes in non-model organisms.…”

Section: Introductionmentioning

confidence: 99%

“…Less is known about the ABC superfamily in arthropods compared to other taxonomic groups such as mammals or bacteria [ 4 ]. However, there has been an increasing effort to understand the molecular biology of arthropods for several reasons.…”

Section: Introductionmentioning

confidence: 99%

Comparative and functional genomics of the ABC transporter superfamily across arthropods

et al. 2021

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Background The ATP-binding cassette (ABC) transporter superfamily is comprised predominantly of proteins which directly utilize energy from ATP to move molecules across the plasma membrane. Although they have been the subject of frequent investigation across many taxa, arthropod ABCs have been less well studied. While the manual annotation of ABC transporters has been performed in many arthropods, there has so far been no systematic comparison of the superfamily within this order using the increasing number of sequenced genomes. Furthermore, functional work on these genes is limited. Results Here, we developed a standardized pipeline to annotate ABCs from predicted proteomes and used it to perform comparative genomics on ABC families across arthropod lineages. Using Kruskal-Wallis tests and the Computational Analysis of gene Family Evolution (CAFE), we were able to observe significant expansions of the ABC-B full transporters (P-glycoproteins) in Lepidoptera and the ABC-H transporters in Hemiptera. RNA-sequencing of epithelia tissues in the Lepidoptera Helicoverpa armigera showed that the 7 P-glycoprotein paralogues differ substantially in their tissue distribution, suggesting a spatial division of labor. It also seems that functional redundancy is a feature of these transporters as RNAi knockdown showed that most transporters are dispensable with the exception of the highly conserved gene Snu, which is probably due to its role in cuticular formation. Conclusions We have performed an annotation of the ABC superfamily across > 150 arthropod species for which good quality protein annotations exist. Our findings highlight specific expansions of ABC transporter families which suggest evolutionary adaptation. Future work will be able to use this analysis as a resource to provide a better understanding of the ABC superfamily in arthropods.

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“…Phylogenetic analysis of bicarbonate transporter sequences from N. inconspicua (Supplementary Figure S7 ) reveals two loci belonging to a metazoan-type clade orthologous to plasma membrane-localized and low CO 2 -sensitive bicarbonate transporters from P. tricornutum, as well as a single transporter ortholog predicted to be localized to the P. tricornutum chloroplast. Additional bicarbonate transporter family proteins detected using HMM pattern PF00955 belong to a more distant clade, along with other diatom sequences annotated as boron transporters (TC 2.A.31.3, 49 ), leading to uncertainty about a potential role in the CCM. Excluding these, N. inconspicua has slightly fewer (n = 3 per genome) bicarbonate transporters overall than diatoms on average (n = 4 per genome) suggesting there has been little need to expand bicarbonate acquisition capabilities through genetic diversification in this species.…”

Section: Resultsmentioning

confidence: 99%

Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom

Oliver

Podell

Pinowska

et al. 2021

Sci Rep

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A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia inconspicua. The 50 Mbp haploid size of the nuclear genome is nearly double that of model diatom Phaeodactylum tricornutum, but 30% smaller than closer relative Fragilariopsis cylindrus. Diploid assembly, which was facilitated by low levels of allelic heterozygosity (2.7%), included 14 candidate chromosome pairs composed of long, syntenic contigs, covering 93% of the total assembly. Telomeric ends were capped with an unusual 12-mer, G-rich, degenerate repeat sequence. Predicted proteins were highly enriched in strain-specific marker domains associated with cell-surface adhesion, biofilm formation, and raphe system gliding motility. Expanded species-specific families of carbonic anhydrases suggest potential enhancement of carbon concentration efficiency, and duplicated glycolysis and fatty acid synthesis pathways across cytosolic and organellar compartments may enhance peak metabolic output, contributing to competitive success over other organisms in mixed cultures. The N. inconspicua genome delivers a robust new reference for future functional and transcriptomic studies to illuminate the physiology of benthic pennate diatoms and harness their unique adaptations to support commercial algae biomass and bioproduct production.

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The Transporter Classification Database (TCDB): 2021 update

Cited by 283 publications

References 48 publications

Multiple evolutionary origins reflect the importance of sialic acid transporters in the colonization potential of bacterial pathogens and commensals

Multiple evolutionary origins reflect the importance of sialic acid transporters in the colonization potential of bacterial pathogens and commensals

Comparative and functional genomics of the ABC transporter superfamily across arthropods

Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom

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