Characterisation of the nitrile hydratase gene clusters of Rhodococcus erythropolis strains AJ270 and AJ300 and Microbacterium sp. AJ115 indicates horizontal gene transfer and reveals an insertion of IS1166

2005 ◽  
Vol 87 (3) ◽  
pp. 221-232 ◽  
Author(s):  
Rebecca O’Mahony ◽  
John Doran ◽  
Lee Coffey ◽  
Orla J. Cahill ◽  
Gary W. Black ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Nitrile Hydratase ◽  
Rhodococcus Erythropolis ◽  
Gene Clusters

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 Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont, Basidiobolus

2020 ◽  
Vol 10 (9) ◽  
pp. 3417-3433
Author(s):  
Javier F Tabima ◽  
Ian A Trautman ◽  
Ying Chang ◽  
Yan Wang ◽  
Stephen Mondo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Secondary Metabolism ◽  
Gene Clusters ◽  
Biologically Active ◽  
Constitutive Gene Expression ◽  
Gut Symbionts ◽  
Phylogenomic Analyses ◽  
Siderophore Activity

Abstract Research into secondary metabolism (SM) production by fungi has resulted in the discovery of diverse, biologically active compounds with significant medicinal applications. The fungi rich in SM production are taxonomically concentrated in the subkingdom Dikarya, which comprises the phyla Ascomycota and Basidiomycota. Here, we explore the potential for SM production in Mucoromycota and Zoopagomycota, two phyla of nonflagellated fungi that are not members of Dikarya, by predicting and identifying core genes and gene clusters involved in SM. The majority of non-Dikarya have few genes and gene clusters involved in SM production except for the amphibian gut symbionts in the genus Basidiobolus. Basidiobolus genomes exhibit an enrichment of SM genes involved in siderophore, surfactin-like, and terpene cyclase production, all these with evidence of constitutive gene expression. Gene expression and chemical assays also confirm that Basidiobolus has significant siderophore activity. The expansion of SMs in Basidiobolus are partially due to horizontal gene transfer from bacteria, likely as a consequence of its ecology as an amphibian gut endosymbiont.

scholarly journals Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics

mBio ◽  
2019 ◽  
Vol 10 (5) ◽  
Author(s):  
Abdoul-Razak Tidjani ◽  
Jean-Noël Lorenzi ◽  
Maxime Toussaint ◽  
Erwin van Dijk ◽  
Delphine Naquin ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Public Goods ◽  
Significant Proportion ◽  
Gene Clusters ◽  
Recent Common Ancestor ◽  
Natural Soil ◽  
Gene Pools ◽  
Bacterial Gene ◽  
Integrative And Conjugative Elements

ABSTRACT In this work, by comparing genomes of closely related individuals of Streptomyces isolated at a spatial microscale (millimeters or centimeters), we investigated the extent and impact of horizontal gene transfer in the diversification of a natural Streptomyces population. We show that despite these conspecific strains sharing a recent common ancestor, all harbored significantly different gene contents, implying massive and rapid gene flux. The accessory genome of the strains was distributed across insertion/deletion events (indels) ranging from one to several hundreds of genes. Indels were preferentially located in the arms of the linear chromosomes (ca. 12 Mb) and appeared to form recombination hot spots. Some of them harbored biosynthetic gene clusters (BGCs) whose products confer an inhibitory capacity and may constitute public goods that can favor the cohesiveness of the bacterial population. Moreover, a significant proportion of these variable genes were either plasmid borne or harbored signatures of actinomycete integrative and conjugative elements (AICEs). We propose that conjugation is the main driver for the indel flux and diversity in Streptomyces populations. IMPORTANCE Horizontal gene transfer is a rapid and efficient way to diversify bacterial gene pools. Currently, little is known about this gene flux within natural soil populations. Using comparative genomics of Streptomyces strains belonging to the same species and isolated at microscale, we reveal frequent transfer of a significant fraction of the pangenome. We show that it occurs at a time scale enabling the population to diversify and to cope with its changing environment, notably, through the production of public goods.

scholarly journals From Green to Red: Horizontal Gene Transfer of the Phycoerythrin Gene Cluster between Planktothrix Strains

2013 ◽  
Vol 79 (21) ◽  
pp. 6803-6812 ◽  
Author(s):  
Ave Tooming-Klunderud ◽  
Hanne Sogge ◽  
Trine Ballestad Rounge ◽  
Alexander J. Nederbragt ◽  
Karin Lagesen ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Homologous Recombination ◽  
Gene Cluster ◽  
Gene Clusters ◽  
Sequence Comparisons ◽  
Content Type ◽  
Large Gene ◽  
Dna Fragment

ABSTRACTHorizontal gene transfer is common in cyanobacteria, and transfer of large gene clusters may lead to acquisition of new functions and conceivably niche adaption. In the present study, we demonstrate that horizontal gene transfer between closely relatedPlanktothrixstrains can explain the production of the same oligopeptide isoforms by strains of different colors. Comparison of the genomes of eightPlanktothrixstrains revealed that strains producing the same oligopeptide isoforms are closely related, regardless of color. We have investigated genes involved in the synthesis of the photosynthetic pigments phycocyanin and phycoerythrin, which are responsible for green and red appearance, respectively. Sequence comparisons suggest the transfer of a functional phycoerythrin gene cluster generating a red phenotype in a strain that is otherwise more closely related to green strains. Our data show that the insertion of a DNA fragment containing the 19.7-kb phycoerythrin gene cluster has been facilitated by homologous recombination, also replacing a region of the phycocyanin operon. These findings demonstrate that large DNA fragments spanning entire functional gene clusters can be effectively transferred between closely related cyanobacterial strains and result in a changed phenotype. Further, the results shed new light on the discussion of the role of horizontal gene transfer in the sporadic distribution of large gene clusters in cyanobacteria, as well as the appearance of red and green strains.

scholarly journals Exploring tRNA gene cluster in archaea

2018 ◽  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Cluster ◽  
Trna Gene ◽  
Gene Clusters ◽  
Gene Organization ◽  
Trna Genes ◽  
Genomic Analyses ◽  
Living Organisms

AbstractShared traits between prokaryotes and eukaryotes are helpful in the understanding of the tree of life evolution. In bacteria and eukaryotes, it has been shown a particular organization of tRNA genes as clusters, but this trait has not been explored in archaea domain. Here, based on analyses of complete and draft archaeal genomes, we demonstrated the prevalence of tRNA gene clusters in archaea. tRNA gene cluster was identified at least in three Archaea class, Halobacteria, Methanobacteria and Methanomicrobia from Euryarchaeota supergroup. Genomic analyses also revealed evidence of tRNA gene cluster associated with mobile genetic elements and horizontal gene transfer inter/intra-domain. The presence of tRNA gene clusters in the three domain of life suggests a role of this type of tRNA gene organization in the biology of the living organisms.

scholarly journals Isolation of a Novel Microcystin-Degrading Bacterium and the Evolutionary Origin of mlr Gene Cluster

Toxins ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 269 ◽  
Author(s):  
Lian Qin ◽  
Xiaoxing Zhang ◽  
Xiaoguo Chen ◽  
Ke Wang ◽  
Yitian Shen ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Cluster ◽  
Genomic Island ◽  
Phylogenetic Analyses ◽  
Gene Clusters ◽  
Freshwater Ecosystems ◽  
Evolutionary Origin ◽  
Transfer Event ◽  
Degrading Bacterium

The mlr-dependent biodegradation plays an essential role in the natural attenuation of microcystins (MCs) in eutrophic freshwater ecosystems. However, their evolutionary origin is still unclear due to the lack of mlr gene cluster sequences. In this study, a Sphingopyxis sp. strain X20 with high MC-degrading ability was isolated, and the mlrA gene activity was verified by heterologous expression. The whole sequence of the mlr gene cluster in strain X20 was obtained through PCR and thermal asymmetric interlaced (TAIL)-PCR, and then used for evolutionary origin analyses together with the sequences available in GenBank. Phylogenetic analyses of mlr gene clusters suggested that the four mlr genes had the same origin and evolutionary history. Genomic island analyses showed that there is a genomic island on the genome of sphingomonads that is capable of degrading MCs, on which the mlr gene cluster anchors. The concentrated distribution of the mlr gene cluster in sphingomonads implied that these genes have likely been present in the sphingomonads gene pool for a considerable time. Therefore, the mlr gene cluster may have initially entered into the genome of sphingomonads together with the genomic island by a horizontal gene transfer event, and then become inherited by some sphingomonads. The species other than sphingomonads have likely acquired mlr genes from sphingomonads by recently horizontal gene transfer due to the sporadic distribution of MC-degrading species and the mlr genes in them. Our results shed new light on the evolutionary origin of the mlr cluster and thus facilitate the interpretation of characteristic distribution of the mlr gene in bacteria and the understanding of whole mlr pathway.

scholarly journals Phylogenomic analyses of non-Dikarya fungi supports horizontal gene transfer driving diversification of secondary metabolism in the amphibian gastrointestinal symbiont, Basidiobolus

2020 ◽  
Author(s):  
Javier Felipe Tabima ◽  
Ian A. Trautman ◽  
Ying Chang ◽  
Yan Wang ◽  
Stephen J. Mondo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Secondary Metabolism ◽  
Gene Clusters ◽  
Biologically Active ◽  
Constitutive Gene Expression ◽  
Gut Symbionts ◽  
Phylogenomic Analyses ◽  
Siderophore Activity

Research into secondary metabolism (SM) production by fungi has resulted in the discovery of diverse, biologically active compounds with significant medicinal applications. However, the fungi rich in SM production are taxonomically restricted to Dikarya, two phyla of Kingdom Fungi, Ascomycota and Basidiomycota. Here, we explore the potential for SM production in Mucoromycota and Zoopagomycota, two phyla of nonflagellated fungi that are not members of Dikarya, by predicting and identifying core genes and gene clusters involved in SM. The majority of non-Dikarya have few genes and gene clusters involved in SM production except for the amphibian gut symbionts in the genus Basidiobolus. Basidiobolus genomes exhibit an enrichment of SM genes involved in siderophore, surfactin-like, and terpene cyclase production, all these with evidence of constitutive gene expression. Gene expression and chemical assays confirm that Basidiobolus has significant siderophore activity. The expansion of SMs in Basidiobolus are partially due to horizontal gene transfer from bacteria, likely as a consequence of its ecology as an amphibian gut endosymbiont.

Metabolic Gene Clusters in Eukaryotes

2018 ◽  
Vol 52 (1) ◽  
pp. 159-183 ◽  
Author(s):  
Hans-Wilhelm Nützmann ◽  
Claudio Scazzocchio ◽  
Anne Osbourn
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Experimental Evolution ◽  
Metabolic Pathways ◽  
Large Scale ◽  
Gene Clusters ◽  
Future Research ◽  
Coordinate Regulation ◽  
Metabolic Gene ◽  
Pathway Function

In bacteria, more than half of the genes in the genome are organized in operons. In contrast, in eukaryotes, functionally related genes are usually dispersed across the genome. There are, however, numerous examples of functional clusters of nonhomologous genes for metabolic pathways in fungi and plants. Despite superficial similarities with operons (physical clustering, coordinate regulation), these clusters have not usually originated by horizontal gene transfer from bacteria, and (unlike operons) the genes are typically transcribed separately rather than as a single polycistronic message. This clustering phenomenon raises intriguing questions about the origins of clustered metabolic pathways in eukaryotes and the significance of clustering for pathway function. Here we review metabolic gene clusters from fungi and plants, highlight commonalities and differences, and consider how these clusters form and are regulated. We also identify opportunities for future research in the areas of large-scale genomics, synthetic biology, and experimental evolution.

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