scholarly journals AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Abhijeet Singh ◽  
Bettina Müller ◽  
Hans-Henrik Fuxelius ◽  
Anna Schnürer
Keyword(s):  
Carbon Fixation ◽  
Sequence Data ◽  
Gene Encoding ◽  
Formyltetrahydrofolate Synthetase ◽  
Protein Levels ◽  
Acetogenic Bacteria ◽  
Blast Database ◽  
Key Enzyme ◽  
Chemolithoautotrophic Bacteria ◽  
Taxonomic Studies

Abstract Acetogenic bacteria are imperative to environmental carbon cycling and diverse biotechnological applications, but their extensive physiological and taxonomical diversity is an impediment to systematic taxonomic studies. Acetogens are chemolithoautotrophic bacteria that perform reductive carbon fixation under anaerobic conditions through the Wood–Ljungdahl pathway (WLP)/acetyl-coenzyme A pathway. The gene-encoding formyltetrahydrofolate synthetase (FTHFS), a key enzyme of this pathway, is highly conserved and can be used as a molecular marker to probe acetogenic communities. However, there is a lack of systematic collection of FTHFS sequence data at nucleotide and protein levels. In an attempt to streamline investigations on acetogens, we developed AcetoBase - a repository and database for systematically collecting and organizing information related to FTHFS sequences. AcetoBase also provides an opportunity to submit data and obtain accession numbers, perform homology searches for sequence identification and access a customized blast database of submitted sequences. AcetoBase provides the prospect to identify potential acetogenic bacteria, based on metadata information related to genome content and the WLP, supplemented with FTHFS sequence accessions, and can be an important tool in the study of acetogenic communities. AcetoBase can be publicly accessed at https://acetobase.molbio.slu.se.

Investigation of the diversity of homoacetogenic bacteria in mesophilic and thermophilic anaerobic sludges using the formyltetrahydrofolate synthetase gene

2008 ◽  
Vol 57 (5) ◽  
pp. 675-680 ◽  
Author(s):  
P. Ryan ◽  
C. Forbes ◽  
E. Colleran
Keyword(s):  
Granular Sludge ◽  
Anaerobic Sludge ◽  
Heterotrophic Growth ◽  
Autotrophic Growth ◽  
Gene Encoding ◽  
Formyltetrahydrofolate Synthetase ◽  
Homoacetogenic Bacteria ◽  
Wide Range ◽  
Key Enzyme ◽  
Acetyl Coa Pathway

Homoacetogenic bacteria are strict anaerobes capable of autotrophic growth on H2/CO2 or CO, and of heterotrophic growth on a wide range of sugars, alcohols, methoxylated aromatic compounds and one carbon compounds, yielding acetate as their sole metabolic end-product. Batch activity tests on anaerobic granular sludge, using H2/CO2 as a substrate and 2-bromoethanesulfonate (BES) as a specific methanogenic inhibitor revealed that H2/CO2 conversion and concomitant acetate production commenced only after a lag period of 60–100 h. This finding suggests that the homoacetogenic population of digester sludge could be maintained by heterotrophic growth on sugars or other organic compounds, rather than by autotrophic growth on H2/CO2. In the present study, two upflow anaerobic sludge bed (UASB) reactors were operated at 37°C and 55°C for two distinct trial periods, each characterised by the application of influents designed to enrich for homoacetogenic bacteria. Specific primers designed for the amplification of the functional gene encoding formyltetrahydrofolate synthetase (FTHFS), a key enzyme in the acetyl-CoA pathway of acetogenesis, were used as a specific probe for acetogenic bacteria. The diversity of acetogens in the granular sludge cultivated in each reactor was revealed by application of FTHFS targeted PCR. Results show that biomass acetogenic composition was dependent upon the operational temperature of the reactor and the substrate supplied as influent.

scholarly journals Remodeling of intermediate metabolism in the diatom Phaeodactylum tricornutum under nitrogen stress

2014 ◽  
Vol 112 (2) ◽  
pp. 412-417 ◽  
Author(s):  
Orly Levitan ◽  
Jorge Dinamarca ◽  
Ehud Zelzion ◽  
Desmond S. Lun ◽  
L. Tiago Guerra ◽  
...  
Keyword(s):  
Phaeodactylum Tricornutum ◽  
Nitrogen Assimilation ◽  
Nitrogen Availability ◽  
Carbon Fixation ◽  
De Novo ◽  
Nitrogen Stress ◽  
Gene Encoding ◽  
Storage Lipids ◽  
Intermediate Metabolism ◽  
Key Enzyme

Diatoms are unicellular algae that accumulate significant amounts of triacylglycerols as storage lipids when their growth is limited by nutrients. Using biochemical, physiological, bioinformatics, and reverse genetic approaches, we analyzed how the flux of carbon into lipids is influenced by nitrogen stress in a model diatom, Phaeodactylum tricornutum. Our results reveal that the accumulation of lipids is a consequence of remodeling of intermediate metabolism, especially reactions in the tricarboxylic acid and the urea cycles. Specifically, approximately one-half of the cellular proteins are cannibalized; whereas the nitrogen is scavenged by the urea and glutamine synthetase/glutamine 2-oxoglutarate aminotransferase pathways and redirected to the de novo synthesis of nitrogen assimilation machinery, simultaneously, the photobiological flux of carbon and reductants is used to synthesize lipids. To further examine how nitrogen stress triggers the remodeling process, we knocked down the gene encoding for nitrate reductase, a key enzyme required for the assimilation of nitrate. The strain exhibits 40–50% of the mRNA copy numbers, protein content, and enzymatic activity of the wild type, concomitant with a 43% increase in cellular lipid content. We suggest a negative feedback sensor that couples photosynthetic carbon fixation to lipid biosynthesis and is regulated by the nitrogen assimilation pathway. This metabolic feedback enables diatoms to rapidly respond to fluctuations in environmental nitrogen availability.

scholarly journals Insights into Autotrophic Activities and Carbon Flow in Iron-Rich Pelagic Aggregates (Iron Snow)

2021 ◽  
Vol 9 (7) ◽  
pp. 1368
Author(s):  
Qianqian Li ◽  
Rebecca E. Cooper ◽  
Carl-Eric Wegner ◽  
Martin Taubert ◽  
Nico Jehmlich ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Co2 Fixation ◽  
Carbon Fixation ◽  
Stable Isotope Probing ◽  
Acidic Lake ◽  
General Role ◽  
Polysaccharide Biosynthesis ◽  
Iron Oxidizers ◽  
Metabolic Activities ◽  
Chemolithoautotrophic Bacteria

Pelagic aggregates function as biological carbon pumps for transporting fixed organic carbon to sediments. In iron-rich (ferruginous) lakes, photoferrotrophic and chemolithoautotrophic bacteria contribute to CO2 fixation by oxidizing reduced iron, leading to the formation of iron-rich pelagic aggregates (iron snow). The significance of iron oxidizers in carbon fixation, their general role in iron snow functioning and the flow of carbon within iron snow is still unclear. Here, we combined a two-year metatranscriptome analysis of iron snow collected from an acidic lake with protein-based stable isotope probing to determine general metabolic activities and to trace 13CO2 incorporation in iron snow over time under oxic and anoxic conditions. mRNA-derived metatranscriptome of iron snow identified four key players (Leptospirillum, Ferrovum, Acidithrix, Acidiphilium) with relative abundances (59.6–85.7%) encoding ecologically relevant pathways, including carbon fixation and polysaccharide biosynthesis. No transcriptional activity for carbon fixation from archaea or eukaryotes was detected. 13CO2 incorporation studies identified active chemolithoautotroph Ferrovum under both conditions. Only 1.0–5.3% relative 13C abundances were found in heterotrophic Acidiphilium and Acidocella under oxic conditions. These data show that iron oxidizers play an important role in CO2 fixation, but the majority of fixed C will be directly transported to the sediment without feeding heterotrophs in the water column in acidic ferruginous lakes.

scholarly journals A Cotton-Fiber-Associated Cyclin-Dependent Kinase A Gene: Characterization and Chromosomal Location

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Weifan Gao ◽  
Sukumar Saha ◽  
Din-Pow Ma ◽  
Yufang Guo ◽  
Johnie N. Jenkins ◽  
...  
Keyword(s):  
Cotton Fiber ◽  
Sequence Data ◽  
Snp Markers ◽  
Pcr Analysis ◽  
Cyclin Dependent Kinase ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Gene Characterization ◽  
Protein Levels ◽  
Catalytic Domains

A cotton fiber cDNA and its genomic sequences encoding an A-type cyclin-dependent kinase (GhCDKA) were cloned and characterized. The encoded GhCDKA protein contains the conserved cyclin-binding, ATP binding, and catalytic domains. Northern blot and RT-PCR analysis revealed that the GhCDKA transcript was high in 5–10 DPA fibers, moderate in 15 and 20 DPA fibers and roots, and low in flowers and leaves. GhCDKA protein levels in fibers increased from 5–15 DPA, peaked at 15 DPA, and decreased from 15 t0 20 DPA. The differential expression of GhCDKA suggested that the gene might play an important role in fiber development. The GhCDKA sequence data was used to develop single nucleotide polymorphism (SNP) markers specific for the CDKA gene in cotton. A primer specific to one of the SNPs was used to locate the CDKA gene to chromosome 16 by deletion analysis using a series of hypoaneuploid interspecific hybrids.

scholarly journals Isolation and Characterization of a Mutant of the Marine Bacterium Alcanivorax borkumensis SK2 Defective in Lipid Biosynthesis

2010 ◽  
Vol 76 (9) ◽  
pp. 2884-2894 ◽  
Author(s):  
Efraín Manilla-Pérez ◽  
Alvin Brian Lange ◽  
Stephan Hetzler ◽  
Marc Wältermann ◽  
Rainer Kalscheuer ◽  
...  
Keyword(s):  
Carbon Source ◽  
Sole Carbon Source ◽  
Marine Bacterium ◽  
Neutral Lipids ◽  
Nile Red ◽  
Dry Weight ◽  
Wax Ester ◽  
Gene Encoding ◽  
Isolation And Characterization ◽  
Key Enzyme

ABSTRACT In many microorganisms, the key enzyme responsible for catalyzing the last step in triacylglycerol (TAG) and wax ester (WE) biosynthesis is an unspecific acyltransferase which is also referred to as wax ester synthase/acyl coenzyme A (acyl-CoA):diacylglycerol acyltransferase (WS/DGAT; AtfA). The importance and function of two AtfA homologues (AtfA1 and AtfA2) in the biosynthesis of TAGs and WEs in the hydrocarbon-degrading marine bacterium Alcanivorax borkumensis SK2 have been described recently. However, after the disruption of both the AtfA1 and AtfA2 genes, reduced but substantial accumulation of TAGs was still observed, indicating the existence of an alternative TAG biosynthesis pathway. In this study, transposon-induced mutagenesis was applied to an atfA1 atfA2 double mutant to screen for A. borkumensis mutants totally defective in biosynthesis of neutral lipids in order to identify additional enzymes involved in the biosynthesis of these lipids. At the same time, we have searched for a totally TAG-negative mutant in order to study the function of TAGs in A. borkumensis. Thirteen fluorescence-negative mutants were identified on Nile red ONR7a agar plates and analyzed for their abilities to synthesize lipids. Among these, mutant 2 M131 was no longer able to synthesize and accumulate TAGs if pyruvate was used as the sole carbon source. The transposon insertion was localized in a gene encoding a putative cytochrome c family protein (ABO_1185). Growth and TAG accumulation experiments showed that the disruption of this gene resulted in the absence of TAGs in 2 M131 but that growth was not affected. In cells of A. borkumensis SK2 grown on pyruvate as the sole carbon source, TAGs represented about 11% of the dry weight of the cells, while in the mutant 2 M131, TAGs were not detected by thin-layer and gas chromatography analyses. Starvation and lipid mobilization experiments revealed that the lipids play an important role in the survival of the cells. The function of neutral lipids in A. borkumensis SK2 is discussed.

scholarly journals Anomalous placement of introns in a member of the intermediate filament multigene family: an evolutionary conundrum.

1986 ◽  
Vol 6 (5) ◽  
pp. 1529-1534 ◽  
Author(s):  
S A Lewis ◽  
N J Cowan
Keyword(s):  
Glial Fibrillary Acidic Protein ◽  
Intermediate Filament ◽  
Multigene Family ◽  
Protein Gene ◽  
Sequence Data ◽  
Complete Sequence ◽  
Acidic Protein ◽  
Type I ◽  
Neurofilament Protein ◽  
Gene Encoding

The origin of introns and their role (if any) in gene expression, in the evolution of the genome, and in the generation of new expressed sequences are issues that are understood poorly, if at all. Multigene families provide a favorable opportunity for examining the evolutionary history of introns because it is possible to identify changes in intron placement and content since the divergence of family members from a common ancestral sequence. Here we report the complete sequence of the gene encoding the 68-kilodalton (kDa) neurofilament protein; the gene is a member of the intermediate filament multigene family that diverged over 600 million years ago. Five other members of this family (desmin, vimentin, glial fibrillary acidic protein, and type I and type II keratins) are encoded by genes with six or more introns at homologous positions. To our surprise, the number and placement of introns in the 68-kDa neurofilament protein gene were completely anomalous, with only three introns, none of which corresponded in position to introns in any characterized intermediate filament gene. This finding was all the more unexpected because comparative amino acid sequence data suggest a closer relationship of the 68-kDa neurofilament protein to desmin, vimentin, and glial fibrillary acidic protein than between any of these three proteins and the keratins. It appears likely that an mRNA-mediated transposition event was involved in the evolution of the 68-kDa neurofilament protein gene and that subsequent events led to the acquisition of at least two of the three introns present in the contemporary sequence.

scholarly journals The Bacillus subtilis yqjI Gene Encodes the NADP+-Dependent 6-P-Gluconate Dehydrogenase in the Pentose Phosphate Pathway

2004 ◽  
Vol 186 (14) ◽  
pp. 4528-4534 ◽  
Author(s):  
Nicola Zamboni ◽  
Eliane Fischer ◽  
Dietmar Laudert ◽  
Stéphane Aymerich ◽  
Hans-Peter Hohmann ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Glucose Dehydrogenase ◽  
Reducing Power ◽  
Pentose Phosphate ◽  
Gene Encoding ◽  
Metabolic Intermediates ◽  
The Third ◽  
Key Enzyme ◽  
Sequence Similarities

ABSTRACT Despite the importance of the oxidative pentose phosphate (PP) pathway as a major source of reducing power and metabolic intermediates for biosynthetic processes, almost no direct genetic or biochemical evidence is available for Bacillus subtilis. Using a combination of knockout mutations in known and putative genes of the oxidative PP pathway and 13C-labeling experiments, we demonstrated that yqjI encodes the NADP+-dependent 6-P-gluconate dehydrogenase, as was hypothesized previously from sequence similarities. Moreover, YqjI was the predominant isoenzyme during glucose and gluconate catabolism, and its role in the oxidative PP pathway could not be played by either of two homologues, GntZ and YqeC. This conclusion is in contrast to the generally held view that GntZ is the relevant isoform; hence, we propose a new designation for yqjI, gndA, the monocistronic gene encoding the principal 6-P-gluconate dehydrogenase. Although we demonstrated the NAD+-dependent 6-P-gluconate dehydrogenase activity of GntZ, gntZ mutants exhibited no detectable phenotype on glucose, and GntZ did not contribute to PP pathway fluxes during growth on glucose. Since gntZ mutants grew normally on gluconate, the functional role of GntZ remains obscure, as does the role of the third homologue, YqeC. Knockout of the glucose-6-P dehydrogenase-encoding zwf gene was primarily compensated for by increased glycolytic fluxes, but about 5% of the catabolic flux was rerouted through the gluconate bypass with glucose dehydrogenase as the key enzyme.

Abstract 5455: A Novel Haplotype on GCH1 Gene, Encoding GTP Cyclohydrolase 1, Regulates Vascular Biopterin Synthesis, eNOS Coupling and Vascular Redox in Human Vessels

Circulation ◽  
2008 ◽  
Vol 118 (suppl_18) ◽  
Author(s):  
Charalambos Antoniades ◽  
Cheerag Shirodaria ◽  
Thomasz Guzik ◽  
Tim Van-Assche ◽  
Ravi Pillai ◽  
...  
Keyword(s):  
Vascular Endothelium ◽  
Inflammatory Cells ◽  
Gtp Cyclohydrolase ◽  
Gene Encoding ◽  
Enos Uncoupling ◽  
Key Enzyme ◽  
Biopterin Synthesis ◽  
No Bioavailability ◽  
Gch1 Gene ◽  
O2 Production

Background: GTP cyclohydrolase (GTPCH) is a key enzyme in biopterins synthesis, while tetrahydrobiopterin (BH4) is a regulator of eNOS coupling in vascular endothelium. A novel haplotype in GCH1 gene, combining dbSNPs: rs8007267G/A, rs3783641A/T and rs10483639C/G, affects GTPCH activity and biopterins levels in inflammatory cells. We examined the effect of this haplotype on vascular biopterins, eNOS coupling and redox state in human vessels from patients with coronary atherosclerosis. Methods: Samples of saphenous veins (SV) were obtained from 347 patients undergoing CABG. Vasorelaxations of SV to acetylcholine (ACh) and vascular O2- (± eNOS inhibitor LNAME) were determined. Biopterins were measured by HPLC. The haplotypes were defined as X (rs8007267A+ rs3783641T+ rs10483639G) or O (all other haplotypes). Results: The haplotype distribution was OO:245(71%), OX:95(27%) and XX:7(2%). Carriers of the X haplotype had lower plasma (Fig. a ) and vascular (Fig. b ) BH4. The X haplotype was associated with higher vascular O2- (XX+XO: 2.97±0.44 vs OO:1.90±0.10 RLU/Sec/mg, p<0.01), greater LNAME-inhibitable O2- (Fig. c ) suggesting eNOS uncoupling) and lower NO bioavailability (Fig. d ) in human vessels. The X haplotype was also associated with higher plasma ox-LDL (51.0±2.2 in XX+XO vs 44.2±1.4 U/L in OO p<0.05) and lower BH4:total biopterins ratio (43.1±3.2 in XX+XO vs 51.7±2.1% in OO, p<0.05). Conclusions: This novel haplotype on GCH1 gene regulates biopterins biosynthesis in both plasma and vascular endothelium. This haplotype also regulates eNOS coupling, O2- production and NO bioavailability in human vessels, and may play a role in atherogenesis.

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