scholarly journals Plant P450s as versatile drivers for evolution of species-specific chemical diversity

2013 ◽  
Vol 368 (1612) ◽  
pp. 20120426 ◽  
Author(s):  
Björn Hamberger ◽  
Søren Bak
Keyword(s):  
Metabolic Pathways ◽  
Gene Families ◽  
Plant Evolution ◽  
Chemical Diversity ◽  
Raw Material ◽  
Divergent Evolution ◽  
Substantial Contribution ◽  
Functional Diversification ◽  
Specific Chemical ◽  
Member Gene

The irreversible nature of reactions catalysed by P450s makes these enzymes landmarks in the evolution of plant metabolic pathways. Founding members of P450 families are often associated with general (i.e. primary) metabolic pathways, restricted to single copy or very few representatives, indicative of purifying selection. Recruitment of those and subsequent blooms into multi-member gene families generates genetic raw material for functional diversification, which is an inherent characteristic of specialized (i.e. secondary) metabolism. However, a growing number of highly specialized P450s from not only the CYP71 clan indicate substantial contribution of convergent and divergent evolution to the observed general and specialized metabolite diversity. We will discuss examples of how the genetic and functional diversification of plant P450s drives chemical diversity in light of plant evolution. Even though it is difficult to predict the function or substrate of a P450 based on sequence similarity, grouping with a family or subfamily in phylogenetic trees can indicate association with metabolism of particular classes of compounds. Examples will be given that focus on multi-member gene families of P450s involved in the metabolic routes of four classes of specialized metabolites: cyanogenic glucosides, glucosinolates, mono- to triterpenoids and phenylpropanoids.

scholarly journals Long-term Diet Quality and Gut Microbiome Functionality: A Prospective, Shotgun Metagenomic Study among Urban Chinese Adults

2021 ◽  
Vol 5 (4) ◽  
Author(s):  
Danxia Yu ◽  
Yaohua Yang ◽  
Jirong Long ◽  
Wanghong Xu ◽  
Qiuyin Cai ◽  
...  
Keyword(s):  
Diet Quality ◽  
Gut Microbiome ◽  
Metabolic Pathways ◽  
Gene Families ◽  
Diet Group ◽  
Healthy Diet ◽  
Chinese Adults ◽  
Α Diversity ◽  
Unhealthy Diet

ABSTRACT Background Diet is known to affect human gut microbiome composition; yet, how diet affects gut microbiome functionality remains unclear. Objective We compared the diversity and abundance/presence of fecal microbiome metabolic pathways among individuals according to their long-term diet quality. Methods In 2 longitudinal cohorts, we assessed participants’ usual diets via repeated surveys during 1996–2011 and collected a stool sample in 2015–2018. Participants who maintained a healthy or unhealthy diet (i.e., stayed in the highest or lowest quintile of a healthy diet score throughout follow-up) were selected. Participants were excluded if they reported a history of cancer, cardiovascular disease, diabetes, or hypertension; had diarrhea or constipation in the last 7 d; or used antibiotics in the last 6 mo before stool collection. Functional profiling of shotgun metagenomics was performed using HUMAnN2. Associations of dietary variables and 420 microbial metabolic pathways were evaluated via multivariable-adjusted linear or logistic regression models. Results We included 144 adults (mean age = 64 y; 55% female); 66 had an unhealthy diet and 78 maintained a healthy diet. The healthy diet group had higher Shannon α-diversity indexes of microbial gene families and metabolic pathways (both P < 0.02), whereas β-diversity, as evaluated by Bray-Curtis distance, did not differ between groups (both P > 0.50). At P < 0.01 [false discovery rate (FDR) <0.15], the healthy diet group showed enriched pathways for vitamin and carrier biosynthesis (e.g., tetrahydrofolate, acetyl-CoA, and l-methionine) and tricarboxylic acid (TCA) cycle, and increased degradation (or reduced biosynthesis) of certain sugars [e.g., cytidine monophosphate (CMP)-legionaminate, deoxythymidine diphosphate (dTDP)-l-rhamnose, and sucrose], nucleotides, 4-aminobutanoate, methylglyoxal, sulfate, and aromatic compounds (e.g., catechol and toluene). Meanwhile, several food groups were associated with the CMP-legionaminate biosynthesis pathway at FDR <0.05. Conclusions In a small longitudinal study of generally healthy, older Chinese adults, we found long-term healthy eating was associated with increased α-diversity of microbial gene families and metabolic pathways and altered symbiotic functions relevant to human nutrition and health.

scholarly journals Expansion, retention and loss in the Acyl-CoA Synthetase “Bubblegum” (Acsbg) gene family in vertebrate history

2018 ◽  
Author(s):  
Mónica Lopes-Marques ◽  
André M. Machado ◽  
Raquel Ruivo ◽  
Elza Fonseca ◽  
Estela Carvalho ◽  
...  
Keyword(s):  
Gene Family ◽  
Metabolic Pathways ◽  
Evolutionary History ◽  
Gene Families ◽  
Gene Repertoire ◽  
Physiological Processes ◽  
Complex Lipid ◽  
History Of ◽  
Enzyme Families ◽  
Rate Limiting

AbstractFatty acids (FAs) constitute a considerable fraction of all lipid molecules with a fundamental role in numerous physiological processes. In animals, the majority of complex lipid molecules are derived from the transformation of FAs through several biochemical pathways. Yet, for FAs to enroll in these pathways they require an activation step. FA activation is catalyzed by the rate limiting action of Acyl-CoA synthases. Several Acyl-CoA enzyme families have been previously described and classified according to the chain length of FA they process. Here, we address the evolutionary history of the ACSBG gene family which activates, FA with more than 16 carbons. Currently, two different ACSBG gene families, ACSBG1 and ACSBG2, are recognized in vertebrates. We provide evidence that a wider and unequal ACSBG gene repertoire is present in vertebrate lineages. We identify a novel ACSBG-like gene lineage which occurs specifically in amphibians, ray finned fish, coelacanths and chondrichthyes named ACSBG3. Also, we show that the ACSBG2 gene lineage duplicated in the Theria ancestor. Our findings, thus offer a far richer understanding on FA activation in vertebrates and provide key insights into the relevance of comparative and functional analysis to perceive physiological differences, namely those related with lipid metabolic pathways.

scholarly journals Lotus japonicus NF-YA1 Plays an Essential Role During Nodule Differentiation and Targets Members of the SHI/STY Gene Family

2016 ◽  
Vol 29 (12) ◽  
pp. 950-964 ◽  
Author(s):  
Md Shakhawat Hossain ◽  
Arina Shrestha ◽  
Sihui Zhong ◽  
Mandana Miri ◽  
Ryan S. Austin ◽  
...  
Keyword(s):  
Gene Family ◽  
Lotus Japonicus ◽  
Cortical Cell ◽  
Plant Evolution ◽  
Nodule Formation ◽  
Functional Diversification ◽  
Nuclear Factor Y ◽  
Functional Analyses ◽  
Transcription Factor Gene Family ◽  
Selection Of

Legume plants engage in intimate relationships with rhizobial bacteria to form nitrogen-fixing nodules, root-derived organs that accommodate the microsymbiont. Members of the Nuclear Factor Y (NF-Y) gene family, which have undergone significant expansion and functional diversification during plant evolution, are essential for this symbiotic liaison. Acting in a partially redundant manner, NF-Y proteins were shown, previously, to regulate bacterial infection, including selection of a superior rhizobial strain, and to mediate nodule structure formation. However, the exact mechanism by which these transcriptional factors exert their symbiotic functions has remained elusive. By carrying out detailed functional analyses of Lotus japonicus mutants, we demonstrate that LjNF-YA1 becomes indispensable downstream from the initial cortical cell divisions but prior to nodule differentiation, including cell enlargement and vascular bundle formation. Three affiliates of the SHORT INTERNODES/STYLISH transcription factor gene family, called STY1, STY2, and STY3, are demonstrated to be among likely direct targets of LjNF-YA1, and our results point to their involvement in nodule formation.

scholarly journals Sedolisins, a New Class of Secreted Proteases from Aspergillus fumigatus with Endoprotease or Tripeptidyl-Peptidase Activity at Acidic pHs

2006 ◽  
Vol 72 (3) ◽  
pp. 1739-1748 ◽  
Author(s):  
Utz Reichard ◽  
Barbara Léchenne ◽  
Abdul R. Asif ◽  
Frank Streit ◽  
Eric Grouzmann ◽  
...  
Keyword(s):  
Aspergillus Fumigatus ◽  
Signal Sequence ◽  
Gene Families ◽  
Peptidase Activity ◽  
New Class ◽  
Tripeptidyl Peptidase ◽  
Genes Encoding ◽  
Member Gene ◽  
Culture Supernatants ◽  
Hydrolysis Of

ABSTRACT The secreted proteolytic activity of Aspergillus fumigatus is of potential importance as a virulence factor and in the industrial hydrolysis of protein sources. The A. fumigatus genome contains sequences that could encode a five-member gene family that produces proteases in the sedolisin family (MEROPS S53). Four putative secreted sedolisins with a predicted 17- to 20-amino-acid signal sequence were identified and termed SedA to SedD. SedA produced heterologously in Pichia pastoris was an acidic endoprotease. Heterologously produced SedB, SedC, and SedD were tripeptidyl-peptidases (TPP) with a common specificity for tripeptide-p-nitroanilide substrates at acidic pHs. Purified SedB hydrolyzed the peptide Ala-Pro-Gly-Asp-Arg-Ile-Tyr-Val-His-Pro-Phe to Arg-Pro-Gly, Asp-Arg-Ile, and Tyr-Val-His-Pro-Phe, thereby confirming TPP activity of the enzyme. SedB, SedC, and SedD were detected by Western blotting in culture supernatants of A. fumigatus grown in a medium containing hemoglobin as the sole nitrogen source. A degradation product of SedA also was observed. A search for genes encoding sedolisin homologues in other fungal genomes indicates that sedolisin gene families are widespread among filamentous ascomycetes.

scholarly journals Integrated Bioprocessing for the pH-Dependent Production of 4-Valerolactone from Levulinate in Pseudomonas putida KT2440

2009 ◽  
Vol 76 (2) ◽  
pp. 417-424 ◽  
Author(s):  
Collin H. Martin ◽  
Danyi Wu ◽  
Kristala L. Jones Prather
Keyword(s):  
Pseudomonas Putida ◽  
Metabolic Pathways ◽  
Acidic Medium ◽  
High Titer ◽  
Chemical Transformations ◽  
Terminal Sequence ◽  
Pseudomonas Putida Kt2440 ◽  
Specific Chemical ◽  
Mild Conditions ◽  
Ph Dependent

ABSTRACT Enzymes are powerful biocatalysts capable of performing specific chemical transformations under mild conditions, yet as catalysts they remain subject to the laws of thermodynamics, namely, that they cannot catalyze chemical reactions beyond equilibrium. Here we report the phenomenon and application of using extracytosolic enzymes and medium conditions, such as pH, to catalyze metabolic pathways beyond their intracellular catalytic limitations. This methodology, termed “integrated bioprocessing” because it integrates intracellular and extracytosolic catalysis, was applied to a lactonization reaction in Pseudomonas putida for the economical and high-titer biosynthesis of 4-valerolactone from the inexpensive and renewable source levulinic acid. Mutant paraoxonase I (PON1) was expressed in P. putida, shown to export from the cytosol in Escherichia coli and P. putida using an N-terminal sequence, and demonstrated to catalyze the extracytosolic and pH-dependent lactonization of 4-hydroxyvalerate to 4-valerolactone. With this production system, the titer of 4-valerolactone was enhanced substantially in acidic medium using extracytosolically expressed lactonase versus an intracellular lactonase: from <0.2 g liter−1 to 2.1 ± 0.4 g liter−1 at the shake flask scale. Based on these results, the production of 4-hydroxyvalerate and 4-valerolactone was examined in a 2-liter bioreactor, and titers of 27.1 g liter−1 and 8.2 g liter−1 for the two respective compounds were achieved. These results illustrate the utility of integrated bioprocessing as a strategy for enabling production from novel metabolic pathways and enhancing product titers.

Enhanced function annotations for Drosophila serine proteases: A case study for systematic annotation of multi-member gene families

Gene ◽  
2008 ◽  
Vol 407 (1-2) ◽  
pp. 199-215 ◽  
Author(s):  
Parantu K. Shah ◽  
Lokesh P. Tripathi ◽  
Lars Juhl Jensen ◽  
Murad Gahnim ◽  
Christopher Mason ◽  
...  
Keyword(s):  
Serine Proteases ◽  
Gene Families ◽  
Member Gene

scholarly journals Expansion and innovation in auxin signaling: where do we grow from here?

Development ◽  
2021 ◽  
Vol 148 (5) ◽  
pp. dev187120
Author(s):  
Román Ramos Báez ◽  
Jennifer L. Nemhauser
Keyword(s):  
Transcription Factors ◽  
Gene Families ◽  
Flowering Plants ◽  
Auxin Signaling ◽  
Regulation Of Transcription ◽  
Functional Diversification ◽  
Auxin Action ◽  
Primary Mechanism ◽  
Almost All ◽  
Developmental Responses

ABSTRACTThe phytohormone auxin plays a role in almost all growth and developmental responses. The primary mechanism of auxin action involves the regulation of transcription via a core signaling pathway comprising proteins belonging to three classes: receptors, co-receptor/co-repressors and transcription factors. Recent studies have revealed that auxin signaling can be traced back at least as far as the transition to land. Moreover, studies in flowering plants have highlighted how expansion of the gene families encoding auxin components is tied to functional diversification. As we review here, these studies paint a picture of auxin signaling evolution as a driver of innovation.

scholarly journals Combining Targeted Metabolite Analyses and Transcriptomics to Reveal Specific Chemical Composition and Associated Genes in Resistant Soybean Infected with Soybean Cyst Nematode

2020 ◽  
Author(s):  
Xue Shi ◽  
Qiansi Chen ◽  
Shiming Liu ◽  
Jiajun Wang ◽  
Deliang Peng ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Soybean Cyst Nematode ◽  
Yield Loss ◽  
Cyst Nematode ◽  
Sphingolipid Metabolism ◽  
Resistant Variety ◽  
Biological Processes ◽  
Specific Chemical ◽  
Kegg Pathways ◽  
Before And After

Abstract Background: Soybean cyst nematode Heterodera glycines is one of the most devastating pathogens on soybean and causes severe annual yield loss worldwide. Different soybean varieties exhibit different responses to soybean cyst nematode infection at various levels, such as genomic, transcriptional, proteomic, and metabolomic levels. However, there were not yet any reports on the differential responses of resistant and susceptible soybeans infected with soybean cyst nematode by combining the metabolomic analyses and transcriptomics.Results: In this study, a highly-resistant variety PI 437654 and three susceptible varieties Williams 82, Zhonghuang 13 and Hefeng 47 were used as the test materials to clarify the differences in metabolites and transcriptomics between resistant and susceptible soybeans before and after SCN infection. A local metabolite-calibrated database was used to identify potential differential metabolites, and the differences of metabolites and metabolic pathways were compared between the resistant and susceptible soybean varieties after inoculation with SCN. Totally, 37 differential metabolites and 20 KEGG metabolic pathways were identified, which were divided into three categories including the metabolites/pathways overlapped among resistant and susceptible soybeans, specific in susceptible or resistant soybeans, respectively. Twelve differential metabolites were found to be involved in predicted KEGG metabolite pathways. Moreover, 14 specifically differential metabolites such as significantly up-regulated nicotine and down-regulated D-aspartic acid, and their involved KEGG pathways such as tropane, piperidine and pyridine alkaloid biosynthesis, alanine, aspartate and glutamate metabolisms, sphingolipid metabolism and arginine biosynthesis were significantly changed and abundantly enriched in the resistant soybean, and likely played pivotal roles in defensing against SCN infection. Three key metabolites including N-acetyltranexamic acid, nicotine, and D, L-typotophan, which were found to be significantly up-regulated in the resistant soybean PI437654 infected by SCN, classified into two types and used for combination analyses with the transcriptomic expression profiling. Associated genes were predicted, and suggested their likely biological processes, cellular component, molecular function and involved pathways. Conclusions: Our results not only found out the potential novel metabolites and associated genes in the resistant response of soybean to soybean cyst nematode, but also provided new insights into the interactions between soybean and soybean cyst nematode.

scholarly journals Multivariate Analysis of Seed Chemical Diversity among Jatropha curcas in Botswana

Agronomy ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1570
Author(s):  
Shota Tadano ◽  
Gwafila Chiyapo ◽  
Yudai Ishimoto ◽  
Takafumi Konaka ◽  
Charles Mazereku ◽  
...  
Keyword(s):  
Jatropha Curcas ◽  
Seed Weight ◽  
Phorbol Esters ◽  
Chemical Properties ◽  
Principal Component ◽  
Chemical Diversity ◽  
Chemical Compositions ◽  
Severe Drought ◽  
Bioenergy Feedstock ◽  
Specific Chemical

Jatropha (Jatropha curcas L.) has been identified as a potential bioenergy feedstock in arid regions, but knowledge of the diversity of its chemical characteristics is limited. In this study, 61 Jatropha accessions growing in Botswana, where both severe drought and winter frosts frequently occur, were analyzed for their seed chemical properties. Histogram analyses and meta-analysis comparisons with seeds from other countries/continents showed that the median/mean dry seed weight, toxic compound phorbol esters, and C18:0 fatty acid levels in the Botswanan accessions were lower than those from other countries/continents. A clustered heat map analysis indicated five clades for the Botswanan accessions, and their physicochemical traits were also categorized into five groups. Many positive and negative correlations were observed among the chemical traits, including negative correlations between the C18:3 (linolenic acid) content and yield-related traits (lipid content and dry seed weight). Principal component analysis highlighted the existence of accessions with highly deviated seed chemical compositions, such as those enriched in C18:0/C18:1 and C16:0/C16:1/C18:3 fatty acids. Overall, the present study suggests considerable diversity in the seed chemical compositions of Botswanan Jatropha accessions. Various accessions could be useful as feedstock for specific industrial products, as well as for breeding materials for the fortification of specific chemical ingredients.

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