scholarly journals Bakterielle Mechanismen der marinen Polysaccharidverwertung

BIOspektrum ◽  
2020 ◽  
Vol 26 (7) ◽  
pp. 800-802
Author(s):  
Thomas Schweder ◽  
Uwe Bornscheuer ◽  
Jan-Hendrik Hehemann ◽  
Rudolf Amann
Keyword(s):  
Algal Biomass ◽  
Major Part ◽  
Gene Clusters ◽  
Carbohydrate Active Enzymes ◽  
High Productivity ◽  
Rapid Turnover ◽  
Conserved Gene ◽  
Complex Polymer

AbstractThe oceans have been compared to a “global heterotrophic digester”. This is due to the high productivity of microalgae and the rapid turnover of the produced biomass by microbes. A major part of the algal biomass consists of diverse polysaccharides which belong to the most complex polymer structures in nature. These marine sugars are decomposed by specialized bacteria, mainly of the phyla Bacteroidetes and Gammaproteobacteria, which possess dedicated conserved gene clusters encoding a remarkable diversity of carbohydrate-active enzymes.

scholarly journals Conserved Gene Clusters in Bacterial Genomes Provide Further Support for the Primacy of RNA

1997 ◽  
Vol 45 (5) ◽  
pp. 467-472 ◽  
Author(s):  
Janet L. Siefert ◽  
Kirt A. Martin ◽  
Fadi Abdi ◽  
William R. Widger ◽  
George E. Fox
Keyword(s):  
Gene Clusters ◽  
Bacterial Genomes ◽  
Conserved Gene

scholarly journals Horizontal gene transfer of a unique nif island drives convergent evolution of free-living N2-fixing Bradyrhizobium

2021 ◽  
Author(s):  
Jinjin Tao ◽  
Sishuo Wang ◽  
Tianhua Liao ◽  
Haiwei Luo
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Agricultural Research ◽  
Current Knowledge ◽  
Gene Clusters ◽  
Soil Samples ◽  
Genomic Context ◽  
Free Living ◽  
Phylogenomic Analyses ◽  
Conserved Gene

SummaryThe alphaproteobacterial genus Bradyrhizobium has been best known as N2-fixing members that nodulate legumes, supported by the nif and nod gene clusters. Recent environmental surveys show that Bradyrhizobium represents one of the most abundant free-living bacterial lineages in the world’s soils. However, our understanding of Bradyrhizobium comes largely from symbiotic members, biasing the current knowledge of their ecology and evolution. Here, we report the genomes of 88 Bradyrhizobium strains derived from diverse soil samples, including both nif-carrying and non-nif-carrying free-living (nod free) members. Phylogenomic analyses of these and 252 publicly available Bradyrhizobium genomes indicate that nif-carrying free-living members independently evolved from symbiotic ancestors (carrying both nif and nod) multiple times. Intriguingly, the nif phylogeny shows that all nif-carrying free-living members comprise a cluster which branches off earlier than most symbiotic lineages. These results indicate that horizontal gene transfer (HGT) promotes nif expansion among the free-living Bradyrhizobium and that the free-living nif cluster represents a more ancestral version compared to that in symbiotic lineages. Further evidence for this rampant HGT is that the nif in free-living members consistently co-locate with several important genes involved in coping with oxygen tension which are missing from symbiotic members, and that while in free-living Bradyrhizobium nif and the co-locating genes show a highly conserved gene order, they each have distinct genomic context. Given the dominance of Bradyrhizobium in world’s soils, our findings have implications for global nitrogen cycles and agricultural research.

scholarly journals EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes

2019 ◽  
Author(s):  
Marina Marcet-Houben ◽  
Toni Gabaldón
Keyword(s):  
Secondary Metabolism ◽  
Computational Prediction ◽  
Gene Clusters ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Automated Inference ◽  
Or Gene ◽  
Conserved Gene ◽  
Genome Comparisons

Abstract Motivation The evolution and role of gene clusters in eukaryotes is poorly understood. Currently, most studies and computational prediction programs limit their focus to specific types of clusters, such as those involved in secondary metabolism. Results We present EvolClust, a python-based tool for the inference of evolutionary conserved gene clusters from genome comparisons, independently of the function or gene composition of the cluster. EvolClust predicts conserved gene clusters from pairwise genome comparisons and infers families of related clusters from multiple (all versus all) genome comparisons. Availability and implementation https://github.com/Gabaldonlab/EvolClust/. Supplementary information Supplementary data are available at Bioinformatics online.

A UNIVERSAL OPERON PREDICTOR FOR PROKARYOTIC GENOMES

2009 ◽  
Vol 07 (01) ◽  
pp. 19-38 ◽  
Author(s):  
GUOJUN LI ◽  
DONGSHENG CHE ◽  
YING XU
Keyword(s):  
Structural Information ◽  
Prokaryotic Genome ◽  
Prediction Method ◽  
Gene Clusters ◽  
Specific Information ◽  
Theoretic Approach ◽  
Graph Theoretic ◽  
Prokaryotic Genomes ◽  
Conserved Gene ◽  
Two Kingdoms

Identification of operons at the genome scale of prokaryotic organisms represents a key step in deciphering of their transcriptional regulation machinery, biological pathways, and networks. While numerous computational methods have been shown to be effective in predicting operons for well-studied organisms such as Escherichia coli K12 and Bacillus subtilis 168, these methods generally do not generalize well to genomes other than the ones used to train the methods, or closely related genomes because they rely on organism–specific information. Several methods have been explored to address this problem through utilizing only genomic structural information conserved across multiple organisms, but they all suffer from the issue of low prediction sensitivity. In this paper, we report a novel operon prediction method that is applicable to any prokaryotic genome with high prediction accuracy. The key idea of the method is to predict operons through identification of conserved gene clusters across multiple genomes and through deriving a key parameter relevant to the distribution of intergenic distances in genomes. We have implemented this method using a graph-theoretic approach, to calculate a set of maximum gene clusters in the target genome that are conserved across multiple reference genomes. Our computational results have shown that this method has higher prediction sensitivity as well as specificity than most of the published methods. We have carried out a preliminary study on operons unique to archaea and bacteria, respectively, and derived a number of interesting new insights about operons between these two kingdoms. The software and predicted operons of 365 prokaryotic genomes are available at .

scholarly journals Evolclust: automated inference of evolutionary conserved gene clusters in eukaryotes

2019 ◽  
Author(s):  
Marina Marcet-Houben ◽  
Toni Gabaldón
Keyword(s):  
Secondary Metabolism ◽  
Computational Prediction ◽  
Gene Clusters ◽  
Link Type ◽  
Automated Inference ◽  
Or Gene ◽  
Conserved Gene ◽  
Genome Comparisons

AbstractMotivationThe evolution and role of gene clusters in eukaryotes is poorly understood. Currently, most studies and computational prediction programs limit their focus to specific types of clusters, such as those involved in secondary metabolism.ResultsWe present Evolclust, a python-based tool for the inference of evolutionary conserved gene clusters from genome comparisons, independently of the function or gene composition of the cluster. Evolclust predicts conserved gene clusters from pairwise genome comparisons and infers families of related clusters from multiple (all vs all) genome comparisons.Availabilityhttps://github.com/Gabaldonlab/EvolClust/[email protected]

Gene Discovery in Gelsemium Highlights Conserved Gene Clusters in Monoterpene Indole Alkaloid Biosynthesis

ChemBioChem ◽  
2018 ◽  
Vol 20 (1) ◽  
pp. 83-87 ◽  
Author(s):  
Jakob Franke ◽  
Jeongwoon Kim ◽  
John P. Hamilton ◽  
Dongyan Zhao ◽  
Gina M. Pham ◽  
...  
Keyword(s):  
Gene Discovery ◽  
Indole Alkaloid ◽  
Gene Clusters ◽  
Alkaloid Biosynthesis ◽  
Conserved Gene ◽  
Indole Alkaloid Biosynthesis

scholarly journals Reservoir water in Singapore contains ESBL-producing and carbapenem-resistant bacteria with conjugatable conserved gene cluster transfer between different species.

2021 ◽  
Author(s):  
Yang Zhong ◽  
Siyao Guo ◽  
Joergen Schlundt
Keyword(s):  
One Health ◽  
Gene Clusters ◽  
Resistant Bacteria ◽  
Klebsiella Pneumonia ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Beta Lactamase ◽  
Reservoir Water ◽  
The One ◽  
Conserved Gene

As the role of the aquatic environment in the One-Health approach has called increasing attention, the studies of Antimicrobial resistance (AMR) spreading in the water bodies have been reported worldwide. However, there are still limited studies on the AMR carrier in the reservoir water in Singapore. Since 2018, our group has collect water samples from six reservoirs in Singapore and isolated the beta-lactam-resistant bacteria from them. We then characterized the isolates with Whole-genome sequencing (WGS) and successfully identified ESBL-producing bacteria from three sampling reservoirs, and confirmed their resistance with both phenotypic and sequencing methods. To better understand the AMR spreading locally, we compared our isolates with isolates from other WGS studies in Singapore covered humans, food, and the enviroment. From there, we noticed the same sequence type (ST) as ST10, ST23, and ST38 has been shared among the environment, food, and humans, as well as the same beta-lactamase genes, are widely distributed among multiple sources. Further genetic environment comparison of beta-lactamase has suggested their spreading as conserved gene clusters among different species and sources. And this hypothesis has been supported by the successful conjugation of blaCTX-M-15 from Klebsiella pneumonia to Escherichia coli (E .coli). We also applied the shotgun metagenomic sequencing to understand the community of bacteria in reservoir water and detect the AMR genes. The composition of bacteria has shown different diversity among different samples. Besides, different beta-lactamase genes have been identified compared to culture depended methods. Here, we suggest that sequencing analysis has great potential in understanding AMR spreading in the One-Health approach. A genetic-based AMR risk assessment is in urgent need in Singapore.

scholarly journals Characterization of L-Carnitine Metabolism inSinorhizobium meliloti

2019 ◽  
Vol 201 (7) ◽  
Author(s):  
Pascal Bazire ◽  
Nadia Perchat ◽  
Ekaterina Darii ◽  
Christophe Lechaplais ◽  
Marcel Salanoubat ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Sinorhizobium Meliloti ◽  
Gene Clusters ◽  
Fatty Acid Transport ◽  
Context Analysis ◽  
Content Type ◽  
Carnitine Metabolism ◽  
Conserved Gene

ABSTRACTl-Carnitine is a trimethylammonium compound mostly known for its contribution to fatty acid transport into mitochondria. In bacteria, it is synthesized from γ-butyrobetaine (GBB) and can be used as a carbon source.l-Carnitine can be formed directly by GBB hydroxylation or synthesized via a biosynthetic route analogous to fatty acid degradation. However, this multistep pathway has not been experimentally characterized. In this work, we identified by gene context analysis a cluster ofl-carnitine anabolic genes next to those involved in its catabolism and proceeded to the completein vitrocharacterization ofl-carnitine biosynthesis and degradation inSinorhizobium meliloti. The five enzymes catalyzing the seven steps that convert GBB to glycine betaine are described. Metabolomic analysis confirmed the multistage synthesis ofl-carnitine in GBB-grown cells but also revealed that GBB is synthesized byS. meliloti. To our knowledge, this is the first report of aerobic GBB synthesis in bacteria. The conservation ofl-carnitine metabolism genes in different bacterial taxonomic classes underscores the role ofl-carnitine as a ubiquitous nutrient.IMPORTANCEThe experimental characterization of novel metabolic pathways is essential for realizing the value of genome sequences and improving our knowledge of the enzymatic capabilities of the bacterial world. However, 30% to 40% of genes of a typical genome remain unannotated or associated with a putative function. We used enzyme kinetics, liquid chromatography-mass spectroscopy (LC-MS)-based metabolomics, and mutant phenotyping for the characterization of the metabolism ofl-carnitine inSinorhizobium melilotito provide an accurate annotation of the corresponding genes. The occurrence of conserved gene clusters for carnitine metabolism in soil, plant-associated, and marine bacteria underlines the environmental abundance of carnitine and suggests this molecule might make a significant contribution to ecosystem nitrogen and carbon cycling.

scholarly journals Complete Genome Sequence of the Lignocellulose-Degrading Actinomycete Streptomyces albus CAS922

2020 ◽  
Vol 9 (21) ◽  
Author(s):  
Anna Tippelt ◽  
Markus Nett ◽  
M. Soledad Vela Gurovic
Keyword(s):  
Secondary Metabolites ◽  
Complete Genome Sequence ◽  
Sunflower Seed ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Carbohydrate Active Enzymes ◽  
Content Type ◽  
Bioactive Secondary Metabolites ◽  
Streptomyces Albus

ABSTRACT Streptomyces albus CAS922 was isolated from sunflower seed hulls. Its fully sequenced genome harbors a multitude of genes for carbohydrate-active enzymes, which likely facilitate growth on lignocellulosic biomass. Furthermore, the presence of 27 predicted biosynthetic gene clusters indicates a significant potential for the production of bioactive secondary metabolites.

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