The Role of the Horizontal Gene Pool and Lateral Gene Transfer in Enhancing Microbial Activities in Marine Sediments

2006 ◽  
Author(s):  
Patricia A. Sobecky
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Marine Sediments ◽  
Gene Pool ◽  
Microbial Activities

scholarly journals Origin and Evolution of Polycyclic Triterpene Synthesis

2020 ◽  
Vol 37 (7) ◽  
pp. 1925-1941 ◽  
Author(s):  
Carlos Santana-Molina ◽  
Elena Rivas-Marin ◽  
Ana M Rojas ◽  
Damien P Devos
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Carotenoid Biosynthesis ◽  
Sterol Biosynthesis ◽  
Origin And Evolution ◽  
Eukaryotic Genes ◽  
Triterpene Synthesis ◽  
Phylogenetic Profiling ◽  
Fossil Records

Abstract Polycyclic triterpenes are members of the terpene family produced by the cyclization of squalene. The most representative polycyclic triterpenes are hopanoids and sterols, the former are mostly found in bacteria, whereas the latter are largely limited to eukaryotes, albeit with a growing number of bacterial exceptions. Given their important role and omnipresence in most eukaryotes, contrasting with their scant representation in bacteria, sterol biosynthesis was long thought to be a eukaryotic innovation. Thus, their presence in some bacteria was deemed to be the result of lateral gene transfer from eukaryotes. Elucidating the origin and evolution of the polycyclic triterpene synthetic pathways is important to understand the role of these compounds in eukaryogenesis and their geobiological value as biomarkers in fossil records. Here, we have revisited the phylogenies of the main enzymes involved in triterpene synthesis, performing gene neighborhood analysis and phylogenetic profiling. Squalene can be biosynthesized by two different pathways containing the HpnCDE or Sqs proteins. Our results suggest that the HpnCDE enzymes are derived from carotenoid biosynthesis ones and that they assembled in an ancestral squalene pathway in bacteria, while remaining metabolically versatile. Conversely, the Sqs enzyme is prone to be involved in lateral gene transfer, and its emergence is possibly related to the specialization of squalene biosynthesis. The biosynthesis of hopanoids seems to be ancestral in the Bacteria domain. Moreover, no triterpene cyclases are found in Archaea, invoking a potential scenario in which eukaryotic genes for sterol biosynthesis assembled from ancestral bacterial contributions in early eukaryotic lineages.

scholarly journals Metabolic and Evolutionary Relationships among Pyrococcus Species: Genetic Exchange within a Hydrothermal Vent Environment

2005 ◽  
Vol 187 (21) ◽  
pp. 7492-7499 ◽  
Author(s):  
Scott D. Hamilton-Brehm ◽  
Gerrit J. Schut ◽  
Michael W. W. Adams
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Tandem Repeats ◽  
Pyrococcus Furiosus ◽  
Open Reading Frames ◽  
Pcr Analysis ◽  
Pulsed Field Electrophoresis ◽  
Replicative Transposition ◽  
Reading Frames

ABSTRACT Pyrococcus furiosus and Pyrococcus woesei grow optimally at temperatures near 100°C and were isolated from the same shallow marine volcanic vent system. Hybridization of genomic DNA from P. woesei to a DNA microarray containing all 2,065 open reading frames (ORFs) annotated in the P. furiosus genome, in combination with PCR analysis, indicated that homologs of 105 ORFs present in P. furiosus are absent from the uncharacterized genome of P. woesei. Pulsed-field electrophoresis indicated that the sizes of the two genomes are comparable, and the results were consistent with the hypothesis that P. woesei lacks the 105 ORFs found in P. furiosus. The missing ORFs are present in P. furiosus mainly in clusters. These clusters include one cluster (Mal I, PF1737 to PF1751) involved in maltose metabolism and another cluster (PF0691 to PF0695) whose products are thought to remove toxic reactive nitrogen species. Accordingly, it was found that P. woesei, in contrast to P. furiosus, is unable to utilize maltose as a carbon source for growth, and the growth of P. woesei on starch was inhibited by addition of a nitric oxide generator. In P. furiosus the ORF clusters not present in P. woesei are bracketed by or are in the vicinity of insertion sequences or long clusters of tandem repeats (LCTRs). While the role of LCTRs in lateral gene transfer is not known, the Mal I cluster in P. furiosus is a composite transposon that undergoes replicative transposition. The same locus in P. woesei lacks any evidence of insertion activity, indicating that P. woesei is a sister or even the parent of P. furiosus. P. woesei may have acquired by lateral gene transfer more than 100 ORFs from other organisms living in the same thermophilic environment to produce the type strain of P. furiosus.

scholarly journals Widespread lateral gene transfer among grasses

2020 ◽  
Author(s):  
Samuel G. S. Hibdige ◽  
Pauline Raimondeau ◽  
Pascal-Antoine Christin ◽  
Luke T. Dunning
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Grass Species ◽  
List Type ◽  
Phylogenetic Distance ◽  
Protein Coding ◽  
Widespread Phenomenon ◽  
Close Relatives ◽  
Additional Role

SummaryLateral gene transfer (LGT) has been documented in a broad range of prokaryotes and eukaryotes, and it can promote adaptation. LGT of functional nuclear genes has been reported among some plants, but systematic studies are needed to assess the frequency and facilitators of LGT in the group.We scan the genomes of a diverse set of 17 grass species that span more than 50 million years of divergence and include major crops to identify grass-to-grass protein-coding LGT.We identify LGT in 13 species, with significant variation in the amount each received. Rhizomatous species acquired statistically more genes, probably because this growth habit boosts opportunities for transfer into the germline. In addition, the amount of LGT increases with phylogenetic relatedness, which might reflect genomic compatibility amongst close relatives facilitating successful transfers. However, genetic exchanges among highly divergent species with overlapping distributions also occur, pointing to an additional role of biogeography.Overall, we show that LGT is a widespread phenomenon in grasses, which has moved functional genes across the entire grass family into domesticated and wild species alike. The dynamics of successful LGT appears to be dependent on both opportunity (co-occurrence and rhizomes) and compatibility (phylogenetic distance).

scholarly journals Comparative genomics and the role of lateral gene transfer in the evolution of bovine adapted Streptococcus agalactiae

2011 ◽  
Vol 11 (6) ◽  
pp. 1263-1275 ◽  
Author(s):  
Vincent P. Richards ◽  
Ping Lang ◽  
Paulina D. Pavinski Bitar ◽  
Tristan Lefébure ◽  
Ynte H. Schukken ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Streptococcus Agalactiae

scholarly journals How big is the iceberg of which organellar genes in nuclear genomes are but the tip?

2003 ◽  
Vol 358 (1429) ◽  
pp. 39-58 ◽  
Author(s):  
W. F. Doolittle ◽  
Y. Boucher ◽  
C. L. NesbØ ◽  
C. J. Douady ◽  
J. O. Andersson ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Archaeal Genome ◽  
Genome Sequences ◽  
History Of ◽  
Nuclear Genomes

As more and more complete bacterial and archaeal genome sequences become available, the role of lateral gene transfer (LGT) in shaping them becomes more and more clear. Over the long term, it may be the dominant force, affecting most genes in most prokaryotes. We review the history of LGT, suggesting reasons why its prevalence and impact were so long dismissed. We discuss various methods purporting to measure the extent of LGT, and evidence for and against the notion that there is a core of never–exchanged genes shared by all genomes, from which we can deduce the ‘true’ organismal tree. We also consider evidence for, and implications of, LGT between prokaryotes and phagocytic eukaryotes.

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