scholarly journals Thiamine pyrophosphate riboswitches in Bacteroides species regulate transcription or translation of thiamine transport and biosynthesis genes

2019 ◽  
Author(s):  
Zachary A. Costliow ◽  
Patrick H. Degnan ◽  
Carin K. Vanderpool
Keyword(s):  
Gut Microbiome ◽  
Transcriptional Response ◽  
Thiamine Pyrophosphate ◽  
Individual Species ◽  
Vitamin B ◽  
Transcriptional Level ◽  
Thiamine Transport ◽  
Branched Chain ◽  
Species Specific ◽  
Thiamine Biosynthesis

AbstractThiamine (vitamin B1) and its phosphorylated precursors are necessary for decarboxylation reactions required in carbohydrate and branched chain amino acid metabolism. Due to its critical roles in central metabolism, thiamine is essential for human and animal hosts and their resident gut microbes. However, little is known about how thiamine availability shapes the composition of gut microbial communities and the physiology of individual species within those communities. Our previous work has implicated both thiamine biosynthesis and transport activities in the fitness of Bacteroides species. To better understand thiamine-dependent gene regulation in Bacteroides, we examined thiamine biosynthesis and transport genes in three representative species: Bacteroides thetaiotaomicron, Bacteroides uniformis, and Bacteroides vulgatus. All three species possess thiamine biosynthetic operons controlled by highly conserved cis-acting thiamine pyrophosphate (TPP) riboswitches. B. thetaiotaomicron and B. uniformis have additional TPP riboswitch-controlled operons encoding thiamine transport functions. Transcriptome analyses showed that each Bacteroides species had a distinct transcriptional response to exogenous thiamine. Analysis of transcript levels and translational fusions demonstrated that in B. thetaiotaomicron, the TPP riboswitch upstream of biosynthesis genes acts at the level of transcription, while TPP riboswitches upstream of transport operons work at the level of translation. In B. uniformis and B. vulgatus, TPP riboswitches work at the transcriptional level to control downstream operons. The varying responses to exogenous thiamine and use of varied regulatory mechanisms may play an important role in niche establishment by the Bacteroidetes in the complex and constantly shifting gut environment.ImportanceBacteroides species are important and abundant members of human gut microbiome communities. Their activities in the gut are influenced by constant changes in nutrient availability. In this study, we investigated the genetic basis of thiamine (Vitamin B1) uptake and biosynthesis in three representative Bacteroides species. We found species-specific differences in the response to exogenous thiamine, and distinct mechanisms for regulation of uptake and biosynthesis gene expression. Our work implies that gut Bacteroides have evolved distinct strategies for making or acquiring an essential nutrient. These mechanisms may play an important role in the success of Bacteroides in establishing a niche within complex gut microbiome communities.

scholarly journals A Novel Transcriptional Regulator Related to Thiamine Phosphate Synthase Controls Thiamine Metabolism Genes in Archaea

2016 ◽  
Vol 199 (4) ◽  
Author(s):  
Dmitry A. Rodionov ◽  
Semen A. Leyn ◽  
Xiaoqing Li ◽  
Irina A. Rodionova
Keyword(s):  
Comparative Genomics ◽  
Dna Binding ◽  
Transcriptional Control ◽  
Binding Domain ◽  
Thiamine Pyrophosphate ◽  
Vitamin B ◽  
Binding Assays ◽  
Content Type ◽  
Thiamine Metabolism ◽  
Thiamine Biosynthesis

ABSTRACT Thiamine (vitamin B1) is a precursor of thiamine pyrophosphate (TPP), an essential coenzyme in the central metabolism of all living organisms. Bacterial thiamine biosynthesis and salvage genes are controlled at the RNA level by TPP-responsive riboswitches. In Archaea, TPP riboswitches are restricted to the Thermoplasmatales order. Mechanisms of transcriptional control of thiamine genes in other archaeal lineages remain unknown. Using the comparative genomics approach, we identified a novel family of transcriptional regulators (named ThiR) controlling thiamine biosynthesis and transport genes in diverse lineages in the Crenarchaeota phylum as well as in the Halobacteria and Thermococci classes of the Euryarchaeota. ThiR regulators are composed of an N-terminal DNA-binding domain and a C-terminal ligand-binding domain, which is similar to the archaeal thiamine phosphate synthase ThiN. By using comparative genomics, we predicted ThiR-binding DNA motifs and reconstructed ThiR regulons in 67 genomes representing all above-mentioned lineages. The predicted ThiR-binding motifs are characterized by palindromic symmetry with several distinct lineage-specific consensus sequences. In addition to thiamine biosynthesis genes, the reconstructed ThiR regulons include various transporters for thiamine and its precursors. Bioinformatics predictions were experimentally validated by in vitro DNA-binding assays with the recombinant ThiR protein from the hyperthermophilic archaeon Metallosphaera yellowstonensis MK1. Thiamine phosphate and, to some extent, TPP and hydroxyethylthiazole phosphate were required for the binding of ThiR to its DNA targets, suggesting that ThiR is derepressed by limitation of thiamine phosphates. The thiamine phosphate-binding residues previously identified in ThiN are highly conserved in ThiR regulators, suggesting a conserved mechanism for effector recognition. IMPORTANCE Thiamine pyrophosphate is a cofactor for many essential enzymes for glucose and energy metabolism. Thiamine or vitamin B1 biosynthesis and its transcriptional regulation in Archaea are poorly understood. We applied the comparative genomics approach to identify a novel family of regulators for the transcriptional control of thiamine metabolism genes in Archaea and reconstructed the respective regulons. The predicted ThiR regulons in archaeal genomes control the majority of thiamine biosynthesis genes. The reconstructed regulon content suggests that numerous uptake transporters for thiamine and/or its precursors are encoded in archaeal genomes. The ThiR regulon was experimentally validated by DNA-binding assays with Metallosphaera spp. These discoveries contribute to our understanding of metabolic and regulatory networks involved in vitamin homeostasis in diverse lineages of Archaea.

scholarly journals Thiamine Acquisition Strategies Impact Metabolism and Competition in the Gut Microbe Bacteroides thetaiotaomicron

mSystems ◽  
2017 ◽  
Vol 2 (5) ◽  
Author(s):  
Zachary A. Costliow ◽  
Patrick H. Degnan
Keyword(s):  
Indirect Effects ◽  
Water Soluble ◽  
Vitamin B ◽  
Direct And Indirect Effects ◽  
Content Type ◽  
Gut Microbes ◽  
Acquisition Strategies ◽  
Thiamine Transport ◽  
Gut Microbe ◽  
Thiamine Biosynthesis

ABSTRACT Variation in the ability of gut microbes to transport, synthesize, and compete for vitamin B1 (thiamine) is expected to impact the structure and stability of the microbiota, and ultimately this variation may have both direct and indirect effects on human health. Our study identifies the diverse strategies employed by gut Bacteroidetes to acquire thiamine. We demonstrate how the presence or absence of thiamine biosynthesis or transport dramatically affects the abundance of B. thetaiotaomicron in a competitive environment. This study adds further evidence that altering the presence or concentrations of water-soluble vitamins such as thiamine may be an effective method for manipulating gut community composition. In turn, targeted thiamine delivery could be used therapeutically to alter dysbiotic communities linked to disease. Thiamine (vitamin B1) is an essential cofactor for all organisms. Humans primarily acquire thiamine through their diet, and thiamine deficiencies have adverse neurological effects. However, the role gut microbes play in modulating thiamine availability is poorly understood, and little is known about how thiamine impacts the stability of microbial gut communities. To investigate thiamine’s role in the gut, we utilized the model gut microbe Bacteroides thetaiotaomicron. Transcriptome sequencing (RNA-seq) revealed a global downregulation of thiamine and amino acid biosynthesis, glycolysis, and purine metabolism when thiamine was present. Using genetic mutants with thiamine biosynthesis and transport locus mutations, we determined both systems were critical for growth in thiamine-deficient medium. The defect in the double transport mutant suggests an uncharacterized feedback mechanism between thiamine transport and biosynthesis in B. thetaiotaomicron. Mutant phenotypes were recapitulated during pairwise competitions, reinforcing the importance of encoding versatile thiamine acquisition mechanisms when thiamine concentrations are variable. In addition, liquid chromatography-mass spectrometry (LC-MS) analyses corroborate that exogenous thiamine levels affect the internal thiamine pool of B. thetaiotaomicron. Furthermore, we computationally examined the ability of other gut microbes to acquire thiamine and identified lineage-specific differences in thiamine acquisition strategies. Among the Bacteroidetes, the capacities for both thiamine transport and biosynthesis are common. Together, these data show that thiamine acquisition mechanisms used by B. thetaiotaomicron not only are critical for its physiology and fitness but also provide the opportunity to model how other gut microbes may respond to the shifting availability of thiamine in the gut. IMPORTANCE Variation in the ability of gut microbes to transport, synthesize, and compete for vitamin B1 (thiamine) is expected to impact the structure and stability of the microbiota, and ultimately this variation may have both direct and indirect effects on human health. Our study identifies the diverse strategies employed by gut Bacteroidetes to acquire thiamine. We demonstrate how the presence or absence of thiamine biosynthesis or transport dramatically affects the abundance of B. thetaiotaomicron in a competitive environment. This study adds further evidence that altering the presence or concentrations of water-soluble vitamins such as thiamine may be an effective method for manipulating gut community composition. In turn, targeted thiamine delivery could be used therapeutically to alter dysbiotic communities linked to disease. Author Video: An author video summary of this article is available.

scholarly journals Signatures of conserved and unique molecular features in Afrotheria

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Arangasamy Yazhini ◽  
Narayanaswamy Srinivasan ◽  
Sankaran Sandhya
Keyword(s):  
Ribosomal Proteins ◽  
Individual Species ◽  
Functional Domain ◽  
Nucleic Acid Binding ◽  
Uncharacterized Protein ◽  
Homologous Proteins ◽  
Functional Roles ◽  
Molecular Features ◽  
Specific Proteins ◽  
Species Specific

AbstractAfrotheria is a clade of African-origin species with striking dissimilarities in appearance and habitat. In this study, we compared whole proteome sequences of six Afrotherian species to obtain a broad viewpoint of their underlying molecular make-up, to recognize potentially unique proteomic signatures. We find that 62% of the proteomes studied here, predominantly involved in metabolism, are orthologous, while the number of homologous proteins between individual species is as high as 99.5%. Further, we find that among Afrotheria, L. africana has several orphan proteins with 112 proteins showing < 30% sequence identity with their homologues. Rigorous sequence searches and complementary approaches were employed to annotate 156 uncharacterized protein sequences and 28 species-specific proteins. For 122 proteins we predicted potential functional roles, 43 of which we associated with protein- and nucleic-acid binding roles. Further, we analysed domain content and variations in their combinations within Afrotheria and identified 141 unique functional domain architectures, highlighting proteins with potential for specialized functions. Finally, we discuss the potential relevance of highly represented protein families such as MAGE-B2, olfactory receptor and ribosomal proteins in L. africana and E. edwardii, respectively. Taken together, our study reports the first comparative study of the Afrotherian proteomes and highlights salient molecular features.

scholarly journals PnuT uses a facilitated diffusion mechanism for thiamine uptake

2017 ◽  
Vol 150 (1) ◽  
pp. 41-50 ◽  
Author(s):  
Michael Jaehme ◽  
Rajkumar Singh ◽  
Alisa A. Garaeva ◽  
Ria H. Duurkens ◽  
Dirk-Jan Slotboom
Keyword(s):  
Substrate Binding ◽  
Diffusion Mechanism ◽  
Vitamin B1 ◽  
Pyridine Nucleotide ◽  
Thiamine Pyrophosphate ◽  
Facilitated Diffusion ◽  
Nicotinamide Riboside ◽  
Thiamine Transport ◽  
Shewanella Woodyi ◽  
Thiamine Analogues

Membrane transporters of the bacterial pyridine nucleotide uptake (Pnu) family mediate the uptake of various B-type vitamins. For example, the PnuT transporters have specificity for vitamin B1 (thiamine). It has been hypothesized that Pnu transporters are facilitators that allow passive transport of the vitamin substrate across the membrane. Metabolic trapping by phosphorylation would then lead to accumulation of the transported substrates in the cytoplasm. However, experimental evidence for such a transport mechanism is lacking. Here, to determine the mechanism of thiamine transport, we purify PnuTSw from Shewanella woodyi and reconstitute it in liposomes to determine substrate binding and transport properties. We show that the electrochemical gradient of thiamine solely determines the direction of transport, consistent with a facilitated diffusion mechanism. Further, PnuTSw can bind and transport thiamine as well as the thiamine analogues pyrithiamine and oxythiamine, but does not recognize the phosphorylated derivatives thiamine monophosphate and thiamine pyrophosphate as substrates, consistent with a metabolic trapping mechanism. Guided by the crystal structure of the homologous nicotinamide riboside transporter PnuC, we perform mutagenesis experiments, which reveal residues involved in substrate binding and gating. The facilitated diffusion mechanism of transport used by PnuTSw contrasts sharply with the active transport mechanisms used by other bacterial thiamine transporters.

scholarly journals Locally rare species influence grassland ecosystem multifunctionality

2016 ◽  
Vol 371 (1694) ◽  
pp. 20150269 ◽  
Author(s):  
Santiago Soliveres ◽  
Peter Manning ◽  
Daniel Prati ◽  
Martin M. Gossner ◽  
Fabian Alt ◽  
...  
Keyword(s):  
Land Use ◽  
Rare Species ◽  
Common Species ◽  
Ecosystem Functions ◽  
Individual Species ◽  
Conservation Priorities ◽  
Below Ground ◽  
Species Specific ◽  
The Relationship ◽  
Ecosystem Multifunctionality

Species diversity promotes the delivery of multiple ecosystem functions (multifunctionality). However, the relative functional importance of rare and common species in driving the biodiversity–multifunctionality relationship remains unknown. We studied the relationship between the diversity of rare and common species (according to their local abundances and across nine different trophic groups), and multifunctionality indices derived from 14 ecosystem functions on 150 grasslands across a land-use intensity (LUI) gradient. The diversity of above- and below-ground rare species had opposite effects, with rare above-ground species being associated with high levels of multifunctionality, probably because their effects on different functions did not trade off against each other. Conversely, common species were only related to average, not high, levels of multifunctionality, and their functional effects declined with LUI. Apart from the community-level effects of diversity, we found significant positive associations between the abundance of individual species and multifunctionality in 6% of the species tested. Species-specific functional effects were best predicted by their response to LUI: species that declined in abundance with land use intensification were those associated with higher levels of multifunctionality. Our results highlight the importance of rare species for ecosystem multifunctionality and help guiding future conservation priorities.

scholarly journals Biomass Equations for 24 Understory Species in Coniferous and Broadleaved Mixed Forests in Northeastern China

2016 ◽  
Author(s):  
Huaijiang He ◽  
Chunyu Zhang ◽  
Fengguo Du ◽  
Xiuhai Zhao ◽  
Song Yang ◽  
...  
Keyword(s):  
Forest Ecosystem ◽  
Northeastern China ◽  
Individual Species ◽  
Total Biomass ◽  
Basal Diameter ◽  
Understory Species ◽  
Crown Area ◽  
Understory Plants ◽  
Species Specific ◽  
Best Fit

Understory plants are important components of forest ecosystem productivity and diversity. Compared to biomass models of overstory canopy trees, few are available for understory saplings and shrubs and therefore their roles in estimation of forest carbon pools are often ignored. In this study, we harvested 24 understory species including 4 saplings, 9 tree-like shrubs and 11 typical shrubs in coniferous and broadleaved mixed forest in northeastern China and developed the best fit allometric equations of above- and below-ground and total biomass by species-specific or multispecies using morphological measurements of basal diameter, height and crown area as independent variables. The result showed that single basal diameter, height or crown area had good explanatory power for both species-specific and multispecies (p&lt;0.001). The best-fit models included only basal diameter in sapling and tree-like shrubs, and combinations of crown area, height, and basal diameter in typical shrubs. The logarithmic model was most desired among the 4 model forms of linear, quadratic, multiple linear and logarithmic, for species-specific and multispecies. The models we developed should help the estimation of forest ecosystem carbon stocks, especially for belowground component, and provide tools for quantification of individual species biomass of understory plants.

scholarly journals Estimation of above-ground phytomass and carbon in tree resources outside the forest (TROF): A geo-spatial approach

2015 ◽  
Vol 24 (1) ◽  
pp. 34-40 ◽  
Author(s):  
B. P. Heyojoo ◽  
S. Nandy
Keyword(s):  
Satellite Image ◽  
Uttar Pradesh ◽  
Individual Species ◽  
Individual Tree ◽  
Spatial Approach ◽  
Specific Standard ◽  
Vegetation Carbon ◽  
Carbon Project ◽  
The Individual ◽  
Species Specific

This study aims to estimate above-ground phytomass and carbon of TROF ecosystem in part of Bijnor district in Uttar Pradesh state of India using IRS P6 LISS-IV satellite image by geo-spatial approach coupled with field sampling. Chacko’s formula was referred to compute number of samples in each TROF types and the sample plot size in each stratum was adopted from Vegetation Carbon Project (VCP) under National Carbon Project (NCP). With the help of field data consisting mainly the height and girth information, volume of each individual tree per plot was obtained using site and tree species-specific standard volumetric equations. The phytomass was calculated by multiplying volume with Biomass Expansion Factor (BEF) then with regional specific gravity of the individual species and summed up in each plot to get total phytomass per plot. The total phytomass per plot was reported to be maximum 544.00 t/ha for linear TROF followed by 121.89 t/ha for block TROF. The carbon from phytomass was obtained by multiplying the total phytomass by a conversion factor that represents the average carbon content in phytomass. Spectral modeling for phytomass with different bands and indices were established and the best fit curve (R2 = 0.552) with red band was applied to generate phytomass and carbon distribution map of the study area.Banko Janakari, Vol. 24, No. 1, pp. 34-40

Effects of different attractants and human scent on mesocarnivore detection at camera traps

2020 ◽  
Vol 47 (4) ◽  
pp. 338
Author(s):  
Bracy W. Heinlein ◽  
Rachael E. Urbanek ◽  
Colleen Olfenbuttel ◽  
Casey G. Dukes
Keyword(s):  
Fatty Acid ◽  
Castor Oil ◽  
Camera Trap ◽  
Camera Traps ◽  
Individual Species ◽  
Detection Rates ◽  
Capture Success ◽  
Affect Detection ◽  
Species Specific

Abstract ContextCamera traps paired with baits and scented lures can be used to monitor mesocarnivore populations, but not all attractants are equally effective. Several studies have investigated the efficacy of different attractants on the success of luring mesocarnivores to camera traps; fewer studies have examined the effect of human scent at camera traps. AimsWe sought to determine the effects of human scent, four attractants and the interaction between attractants and human scent in luring mesocarnivores to camera traps. Methods We compared the success of synthetic fermented egg (SFE), fatty acid scent (FAS) tablets, castor oil, and sardines against a control of no attractant in luring mesocarnivores to camera traps. We deployed each attractant and the control with either no regard to masking human scent or attempting to restrict human scent for a total of 10 treatments, and replicated treatments eight to nine times in two different phases. We investigated whether: (1) any attractants increased the probability of capturing a mesocarnivore at a camera trap; (2) not masking human scent affected the probability of capturing a mesocarnivore at a camera trap; and (3) any attractants increased the probability of repeat detections at a given camera trap. We also analysed the behaviour (i.e. speed and distance to attractant) of each mesocarnivore in relation to the attractants. Key resultsSardines improved capture success compared with the control treatments, whereas SFE, castor oil, and FAS tablets had no effect when all mesocarnivores were included in the analyses. Masking human scent did not affect detection rates in the multispecies analyses. Individually, the detection of some species depended on the interactions between masking (or not masking) human scent and some attractants. ConclusionsSardines were the most effective as a broad-based attractant for mesocarnivores. Mesocarnivores approached traps baited with sardines at slower rates, which allows for a higher success of capturing an image of the animal. ImplicationsHuman scent may not need to be masked when deploying camera traps for multispecies mesocarnivore studies, but researchers should be aware that individual species respond differently to attractants and may have higher capture success with species-specific attractants.

scholarly journals Investigating host-bacterial interactions among enteric pathogens

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Tungadri Bose ◽  
K. V. Venkatesh ◽  
Sharmila S. Mande
Keyword(s):  
Gut Microbiome ◽  
Therapeutic Strategies ◽  
Enteric Pathogens ◽  
World Health ◽  
Core Set ◽  
Pathogen Protein ◽  
Health Organization ◽  
Species Specific ◽  
Novel Therapeutic Strategies ◽  
Gut Pathogens

Abstract Background In 2017, World Health Organization (WHO) published a catalogue of 12 families of antibiotic-resistant “priority pathogens” that are posing the greatest threats to human health. Six of these dreaded pathogens are known to infect the human gastrointestinal system. In addition to causing gastrointestinal and systemic infections, these pathogens can also affect the composition of other microbes constituting the healthy gut microbiome. Such aberrations in gut microbiome can significantly affect human physiology and immunity. Identifying the virulence mechanisms of these enteric pathogens are likely to help in developing newer therapeutic strategies to counter them. Results Using our previously published in silico approach, we have evaluated (and compared) Host-Pathogen Protein-Protein Interaction (HPI) profiles of four groups of enteric pathogens, namely, different species of Escherichia, Shigella, Salmonella and Vibrio. Results indicate that in spite of genus/ species specific variations, most enteric pathogens possess a common repertoire of HPIs. This core set of HPIs are probably responsible for the survival of these pathogen in the harsh nutrient-limiting environment within the gut. Certain genus/ species specific HPIs were also observed. Conslusions The identified bacterial proteins involved in the core set of HPIs are expected to be helpful in understanding the pathogenesis of these dreaded gut pathogens in greater detail. Possible role of genus/ species specific variations in the HPI profiles in the virulence of these pathogens are also discussed. The obtained results are likely to provide an opportunity for development of novel therapeutic strategies against the most dreaded gut pathogens.

scholarly journals ABC Transporter Subfamily D: Distinct Differences in Behavior between ABCD1–3 and ABCD4 in Subcellular Localization, Function, and Human Disease

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Kosuke Kawaguchi ◽  
Masashi Morita
Keyword(s):  
Abc Transporters ◽  
Critical Role ◽  
Vitamin B ◽  
Long Chain Fatty Acids ◽  
Substrate Specificities ◽  
Related Disease ◽  
Chain Acyl ◽  
Membrane Bound ◽  
Branched Chain ◽  
Long Chain

ATP-binding cassette (ABC) transporters are one of the largest families of membrane-bound proteins and transport a wide variety of substrates across both extra- and intracellular membranes. They play a critical role in maintaining cellular homeostasis. To date, four ABC transporters belonging to subfamily D have been identified. ABCD1–3 and ABCD4 are localized to peroxisomes and lysosomes, respectively. ABCD1 and ABCD2 are involved in the transport of long and very long chain fatty acids (VLCFA) or their CoA-derivatives into peroxisomes with different substrate specificities, while ABCD3 is involved in the transport of branched chain acyl-CoA into peroxisomes. On the other hand, ABCD4 is deduced to take part in the transport of vitamin B12from lysosomes into the cytosol. It is well known that the dysfunction of ABCD1 results in X-linked adrenoleukodystrophy, a severe neurodegenerative disease. Recently, it is reported that ABCD3 and ABCD4 are responsible for hepatosplenomegaly and vitamin B12deficiency, respectively. In this review, the targeting mechanism and physiological functions of the ABCD transporters are summarized along with the related disease.

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