scholarly journals A New Pathway for Forming Acetate and Synthesizing ATP during Fermentation in Bacteria

2021 ◽  
Author(s):  
Bo Zhang ◽  
Christopher Lingga ◽  
Courtney Bowman ◽  
Timothy J. Hackmann
Keyword(s):  
Large Scale ◽  
Biochemical Pathway ◽  
Acetyl Coa ◽  
Diverse Range ◽  
Coa Transferase ◽  
Fermentative Bacteria ◽  
Substrate Level ◽  
Genes Encoding ◽  
Eukaryotic Gene ◽  
Succinyl Coa Synthetase

Many bacteria and other organisms carry out fermentations forming acetate. These fermentations have broad importance to foods, agriculture, and industry. They also are important to bacteria themselves because they often generate ATP. Here we found a biochemical pathway for forming acetate and synthesizing ATP that was unknown in fermentative bacteria. We found the bacterium Cutibacterium granulosum formed acetate during fermentation of glucose. It did not use phosphotransacetylase or acetate kinase, enzymes found in nearly all acetate-forming bacteria. Instead, it used a pathway involving two different enzymes. The first enzyme, succinyl-CoA:acetate CoA-transferase (SCACT), forms acetate from acetyl-CoA. The second enzyme, succinyl-CoA synthetase (SCS), synthesizes ATP. We identified the genes encoding these enzymes, and they were homologs of SCACT and SCS genes found in other bacteria. The pathway resembles one described in eukaryotes, but it uses bacterial, not eukaryotic, gene homologs. To find other instances of the pathway, we analyzed sequences of all biochemically-characterized homologs of SCACT and SCS (103 enzymes from 64 publications). Homologs with similar enzymatic activity had similar sequences, enabling a large-scale search for them in genomes. We searched nearly 600 genomes of bacteria known to form acetate, and we found 6% encoded homologs with SCACT and SCS activity. This included >30 species belonging to 5 different phyla, showing a diverse range of bacteria encode the SCACT/SCS pathway. This work suggests the SCACT/SCS pathway is important to forming acetate in many branches of the tree of life. Importance Pathways for forming acetate during fermentation have been studied for over 80 years. In that time, several pathways have been described in a range of organisms, from bacteria to animals. However, one pathway (involving succinyl-CoA:acetate CoA-transferase and succinyl-CoA synthetase) has not been reported in prokaryotes. Here we discovered enzymes for this pathway in the fermentative bacterium Cutibacterium granulosum. We also found >30 other fermentative bacteria that encode this pathway, demonstrating it could be common. This pathway represents a new way for bacteria to form acetate from acetyl-CoA and synthesize ATP via substrate-level phosphorylation. It could be a target for controlling yield of acetate during fermentation, with relevance to foods, agriculture, and industry.

scholarly journals A new pathway for forming acetate and synthesizing ATP during fermentation in bacteria

2020 ◽  
Author(s):  
Bo Zhang ◽  
Courtney Bowman ◽  
Timothy J. Hackmann
Keyword(s):  
High Energy ◽  
Acetate Kinase ◽  
Acetyl Phosphate ◽  
Biochemical Pathway ◽  
Common Pathway ◽  
Acetyl Coa ◽  
Enzymatic Assays ◽  
Biochemical Pathways ◽  
Coa Transferase ◽  
Fermentative Bacteria

ABSTRACTMany bacteria and other organisms form acetate during fermentation. Forming acetate from high energy-precursors (acetyl-CoA or acetyl phosphate) is one of the few ways that fermentative bacteria generate ATP. Here we found a biochemical pathway for forming acetate and synthesizing ATP that was unknown in bacteria. We found the bacterium Cutibacterium granulosum formed acetate during fermentation of glucose. With enzymatic assays, we showed it formed acetate using a pathway involving two enzymes. The first enzyme, succinyl-CoA:acetate CoA-transferase (SCACT), forms acetate from acetyl-CoA. The second enzyme, succinyl-CoA synthetase (SCS), synthesizes ATP. This pathway is common in eukaryotes, but it has not been found in bacteria or other organisms. We found two related bacteria (C. acnes and Acidipropionibacterium acidipropionici) also used this pathway. None used the most common pathway for forming acetate in bacteria (involving acetate kinase and phosphotransacetylase). The SCACT/SCS pathway may be used by many bacteria, not just C. granulosum and relatives. When we searched genomes for bacteria known to form acetate, we found over 1/6 encoded this pathway. These bacteria belong to 104 different species and subspecies in 12 different phyla. With this discovery, all five pathways known to form acetate and ATP during fermentation can be found in bacteria. This discovery is important to manipulating fermentation and to the evolution of biochemical pathways.

scholarly journals Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP

2020 ◽  
Vol 287 (1934) ◽  
pp. 20201538
Author(s):  
Euki Yazaki ◽  
Keitaro Kume ◽  
Takashi Shiratori ◽  
Yana Eglit ◽  
Goro Tanifuji ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Light Microscopy ◽  
Metabolic Pathways ◽  
Large Scale ◽  
Phylogenetic Position ◽  
Acetyl Coa ◽  
Transcriptomic Data ◽  
Substrate Level Phosphorylation ◽  
Substrate Level ◽  
Phylogenomic Analyses

We here report the phylogenetic position of barthelonids, small anaerobic flagellates previously examined using light microscopy alone. Barthelona spp. were isolated from geographically distinct regions and we established five laboratory strains. Transcriptomic data generated from one Barthelona strain (PAP020) were used for large-scale, multi-gene phylogenetic (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the base of the Fornicata clade, indicating that barthelonids represent a deep-branching metamonad clade. Considering the anaerobic/microaerophilic nature of barthelonids and preliminary electron microscopy observations on strain PAP020, we suspected that barthelonids possess functionally and structurally reduced mitochondria (i.e. mitochondrion-related organelles or MROs). The metabolic pathways localized in the MRO of strain PAP020 were predicted based on its transcriptomic data and compared with those in the MROs of fornicates. We here propose that strain PAP020 is incapable of generating ATP in the MRO, as no mitochondrial/MRO enzymes involved in substrate-level phosphorylation were detected. Instead, we detected a putative cytosolic ATP-generating enzyme (acetyl-CoA synthetase), suggesting that strain PAP020 depends on ATP generated in the cytosol. We propose two separate losses of substrate-level phosphorylation from the MRO in the clade containing barthelonids and (other) fornicates.

scholarly journals Barthelonids represent a deep-branching Metamonad clade with mitochondrion-related organelles generating no ATP

2019 ◽  
Author(s):  
Euki Yazaki ◽  
Keitaro Kume ◽  
Takashi Shiratori ◽  
Yana Eglit ◽  
Goro Tanifuji ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Light Microscopy ◽  
Metabolic Pathways ◽  
Large Scale ◽  
Phylogenetic Position ◽  
Acetyl Coa ◽  
Transcriptomic Data ◽  
Substrate Level Phosphorylation ◽  
Substrate Level ◽  
Phylogenomic Analyses

AbstractWe here report the phylogenetic position of barthelonids, small anaerobic flagellates previously examined using light microscopy alone. Barthelona spp. were isolated from geographically distinct regions and we established five laboratory strains. Transcriptomic data generated from one Barthelona strain (PAP020) was used for large-scale, multi-gene phylogenetic (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the base of the Fornicata clade, indicating that barthelonids represent a deep-branching Metamonad clade. Considering the anaerobic/microaerophilic nature of barthelonids and preliminary electron microscopy observations on strain PAP020, we suspected that barthelonids possess functionally and structurally reduced mitochondria (i.e. mitochondrion-related organelles or MROs). The metabolic pathways localized in the MRO of strain PAP020 were predicted based on its transcriptomic data and compared with those in the MROs of fornicates. Strain PAP020 is most likely incapable of generating ATP in the MRO, as no mitochondrial/MRO enzymes involved in substrate-level phosphorylation were detected. Instead, we detected the putative cytosolic ATP-generating enzyme (acetyl-CoA synthetase), suggesting that strain PAP020 depends on ATP generated in the cytosol. We propose two separate losses of substrate-level phosphorylation from the MRO in the clade containing barthelonids and (other) fornicates.

Building a Culture of Ethical, Comparable, Authentic Assessment

2019 ◽  
pp. 463-481
Author(s):  
Andrew Reid ◽  
Julie Ballantyne
Keyword(s):  
Teaching And Learning ◽  
Large Scale ◽  
Authentic Assessment ◽  
Subject Area ◽  
Music Educators ◽  
System Level ◽  
Diverse Range ◽  
Effective Learning ◽  
School Based ◽  
The Subject

In an ideal world, assessment should be synonymous with effective learning and reflect the intricacies of the subject area. It should also be aligned with the ideals of education: to provide equitable opportunities for all students to achieve and to allow both appropriate differentiation for varied contexts and students and comparability across various contexts and students. This challenge is made more difficult in circumstances in which the contexts are highly heterogeneous, for example in the state of Queensland, Australia. Assessment in music challenges schooling systems in unique ways because teaching and learning in music are often naturally differentiated and diverse, yet assessment often calls for standardization. While each student and teacher has individual, evolving musical pathways in life, the syllabus and the system require consistency and uniformity. The challenge, then, is to provide diverse, equitable, and quality opportunities for all children to learn and achieve to the best of their abilities. This chapter discusses the designing and implementation of large-scale curriculum as experienced in secondary schools in Queensland, Australia. The experiences detailed explore the possibilities offered through externally moderated school-based assessment. Also discussed is the centrality of system-level clarity of purpose, principles and processes, and the provision of supportive networks and mechanisms to foster autonomy for a diverse range of music educators and contexts. Implications for education systems that desire diversity, equity, and quality are discussed, and the conclusion provokes further conceptualization and action on behalf of students, teachers, and the subject area of music.

scholarly journals Flavonoid-Modifying Capabilities of the Human Gut Microbiome—An In Silico Study

Nutrients ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 2688
Author(s):  
Tobias Goris ◽  
Rafael R. C. Cuadrat ◽  
Annett Braune
Keyword(s):  
Gut Microbiome ◽  
Large Scale ◽  
Health Impact ◽  
Gut Bacteria ◽  
Human Gut ◽  
Positive Health ◽  
Human Gut Microbiome ◽  
Nutritional Recommendations ◽  
Genes Encoding ◽  
A Minor

Flavonoids are a major group of dietary plant polyphenols and have a positive health impact, but their modification and degradation in the human gut is still widely unknown. Due to the rise of metagenome data of the human gut microbiome and the assembly of hundreds of thousands of bacterial metagenome-assembled genomes (MAGs), large-scale screening for potential flavonoid-modifying enzymes of human gut bacteria is now feasible. With sequences of characterized flavonoid-transforming enzymes as queries, the Unified Human Gastrointestinal Protein catalog was analyzed and genes encoding putative flavonoid-modifying enzymes were quantified. The results revealed that flavonoid-modifying enzymes are often encoded in gut bacteria hitherto not considered to modify flavonoids. The enzymes for the physiologically important daidzein-to-equol conversion, well studied in Slackiaisoflavoniconvertens, were encoded only to a minor extent in Slackia MAGs, but were more abundant in Adlercreutzia equolifaciens and an uncharacterized Eggerthellaceae species. In addition, enzymes with a sequence identity of about 35% were encoded in highly abundant MAGs of uncultivated Collinsella species, which suggests a hitherto uncharacterized daidzein-to-equol potential in these bacteria. Of all potential flavonoid modification steps, O-deglycosylation (including derhamnosylation) was by far the most abundant in this analysis. In contrast, enzymes putatively involved in C-deglycosylation were detected less often in human gut bacteria and mainly found in Agathobacter faecis (formerly Roseburia faecis). Homologs to phloretin hydrolase, flavanonol/flavanone-cleaving reductase and flavone reductase were of intermediate abundance (several hundred MAGs) and mainly prevalent in Flavonifractor plautii. This first comprehensive insight into the black box of flavonoid modification in the human gut highlights many hitherto overlooked and uncultured bacterial genera and species as potential key organisms in flavonoid modification. This could lead to a significant contribution to future biochemical-microbiological investigations on gut bacterial flavonoid transformation. In addition, our results are important for individual nutritional recommendations and for biotechnological applications that rely on novel enzymes catalyzing potentially useful flavonoid modification reactions.

scholarly journals Arabidopsis Genes Essential for Seedling Viability: Isolation of Insertional Mutants and Molecular Cloning

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1765-1778
Author(s):  
Gregory J Budziszewski ◽  
Sharon Potter Lewis ◽  
Lyn Wegrich Glover ◽  
Jennifer Reineke ◽  
Gary Jones ◽  
...  
Keyword(s):  
Large Scale ◽  
Protein Translocation ◽  
Gene Families ◽  
Mutant Phenotype ◽  
Lethal Mutant ◽  
A Genome ◽  
Genes Encoding ◽  
High Level ◽  
Mutant Lines ◽  
Genome Scale

Abstract We have undertaken a large-scale genetic screen to identify genes with a seedling-lethal mutant phenotype. From screening ~38,000 insertional mutant lines, we identified >500 seedling-lethal mutants, completed cosegregation analysis of the insertion and the lethal phenotype for >200 mutants, molecularly characterized 54 mutants, and provided a detailed description for 22 of them. Most of the seedling-lethal mutants seem to affect chloroplast function because they display altered pigmentation and affect genes encoding proteins predicted to have chloroplast localization. Although a high level of functional redundancy in Arabidopsis might be expected because 65% of genes are members of gene families, we found that 41% of the essential genes found in this study are members of Arabidopsis gene families. In addition, we isolated several interesting classes of mutants and genes. We found three mutants in the recently discovered nonmevalonate isoprenoid biosynthetic pathway and mutants disrupting genes similar to Tic40 and tatC, which are likely to be involved in chloroplast protein translocation. Finally, we directly compared T-DNA and Ac/Ds transposon mutagenesis methods in Arabidopsis on a genome scale. In each population, we found only about one-third of the insertion mutations cosegregated with a mutant phenotype.

scholarly journals Alterations of mesenchymal stromal cells in cerebrospinal fluid: insights from transcriptomics and an ALS clinical trial

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ashley A. Krull ◽  
Deborah O. Setter ◽  
Tania F. Gendron ◽  
Sybil C. L. Hrstka ◽  
Michael J. Polzin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cerebrospinal Fluid ◽  
Growth Factors ◽  
Mesenchymal Stromal Cells ◽  
Stromal Cells ◽  
Large Scale ◽  
Therapeutic Benefit ◽  
Protein Levels ◽  
Genes Encoding ◽  
Intrathecal Space

Abstract Background Mesenchymal stromal cells (MSCs) have been studied with increasing intensity as clinicians and researchers strive to understand the ability of MSCs to modulate disease progression and promote tissue regeneration. As MSCs are used for diverse applications, it is important to appreciate how specific physiological environments may stimulate changes that alter the phenotype of the cells. One need for neuroregenerative applications is to characterize the spectrum of MSC responses to the cerebrospinal fluid (CSF) environment after their injection into the intrathecal space. Mechanistic understanding of cellular biology in response to the CSF environment may predict the ability of MSCs to promote injury repair or provide neuroprotection in neurodegenerative diseases. Methods In this study, we characterized changes in morphology, metabolism, and gene expression occurring in human adipose-derived MSCs cultured in human (hCSF) or artificial CSF (aCSF) as well as examined relevant protein levels in the CSF of subjects treated with MSCs for amyotrophic lateral sclerosis (ALS). Results Our results demonstrated that, under intrathecal-like conditions, MSCs retained their morphology, though they became quiescent. Large-scale transcriptomic analysis of MSCs revealed a distinct gene expression profile for cells cultured in aCSF. The aCSF culture environment induced expression of genes related to angiogenesis and immunomodulation. In addition, MSCs in aCSF expressed genes encoding nutritional growth factors to expression levels at or above those of control cells. Furthermore, we observed a dose-dependent increase in growth factors and immunomodulatory cytokines in CSF from subjects with ALS treated intrathecally with autologous MSCs. Conclusions Overall, our results suggest that MSCs injected into the intrathecal space in ongoing clinical trials remain viable and may provide a therapeutic benefit to patients.

A widespread pathway for substitution of adenine by diaminopurine in phage genomes

Science ◽  
2021 ◽  
Vol 372 (6541) ◽  
pp. 512-516
Author(s):  
Yan Zhou ◽  
Xuexia Xu ◽  
Yifeng Wei ◽  
Yu Cheng ◽  
Yu Guo ◽  
...  
Keyword(s):  
Large Scale ◽  
Restriction Enzymes ◽  
Diverse Range ◽  
Host Restriction ◽  
Form And Function ◽  
Multienzyme System ◽  
Dna Modifications ◽  
Dna Production ◽  
And Function

DNA modifications vary in form and function but generally do not alter Watson-Crick base pairing. Diaminopurine (Z) is an exception because it completely replaces adenine and forms three hydrogen bonds with thymine in cyanophage S-2L genomic DNA. However, the biosynthesis, prevalence, and importance of Z genomes remain unexplored. Here, we report a multienzyme system that supports Z-genome synthesis. We identified dozens of globally widespread phages harboring such enzymes, and we further verified the Z genome in one of these phages, Acinetobacter phage SH-Ab 15497, by using liquid chromatography with ultraviolet and mass spectrometry. The Z genome endows phages with evolutionary advantages for evading the attack of host restriction enzymes, and the characterization of its biosynthetic pathway enables Z-DNA production on a large scale for a diverse range of applications.

Situating and Abandoning Geoengineering: A Typology of Five Responses to Dangerous Climate Change

2013 ◽  
Vol 46 (01) ◽  
pp. 23-27 ◽  
Author(s):  
Clare Heyward
Keyword(s):  
Climate Change ◽  
Large Scale ◽  
Solar Radiation Management ◽  
Diverse Range ◽  
Political Issues ◽  
Government Organizations ◽  
Mitigation And Adaptation ◽  
Potential Strategy ◽  
Dangerous Climate Change ◽  
Radiation Management

Geoengineering, the “deliberate, large-scale manipulation of the planetary environment in order to counteract anthropogenic climate change” (Shepherd et al. 2009, 1), is attracting increasing interest. As well as the Royal Society, various scientific and government organizations have produced reports on the potential and challenge of geoengineering as a potential strategy, alongside mitigation and adaptation, to avoid the vast human and environmental costs that climate change is thought to bring (Blackstock et al. 2009; GAO 2010; Long et al. 2011; Rickels et al. 2011). “Geoengineering” covers a diverse range of proposals conventionally divided into carbon dioxide removal (CDR) proposals and solar radiation management (SRM) proposals. This article argues that “geoengineering” should not be regarded as a third category of response to climate change, but should be disaggregated. Technically, CDR and SRM are quite different and discussing them together under the rubric of geoengineering can give the impression that all the technologies in the two categories of response always raise similar challenges and political issues when this is not necessarily the case. However, CDR and SRM should not be completely subsumed into the preexisting categories of mitigation and adaptation. Instead, they can be regarded as two parts of a five-part continuum of responses to climate change. To make this case, the first section of this article discusses whether geoengineering is distinctive, and the second situates CDR and SRM in relation to other responses to climate change.

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