The genomes of polyextremophilic Cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions

Published on Jan 23, 2019in bioRxiv
· DOI :10.1101/526111
Alessandro W. Rossoni2
Estimated H-index: 2
(University of Düsseldorf),
Dana C. Price19
Estimated H-index: 19
(Rutgers University)
+ 4 AuthorsAndreas P. M. Weber57
Estimated H-index: 57
(University of Düsseldorf)
Abstract
The role and extent of horizontal gene transfer (HGT) in eukaryotes are hotly disputed topics that impact our understanding regarding the origin of metabolic processes and the role of organelles in cellular evolution. We addressed this issue by analyzing 10 novel Cyanidiales genomes and determined that 1% of their gene inventory is HGT-derived. Numerous HGT candidates originated from polyextremophilic prokaryotes that live in similar habitats as the Cyanidiales and encodes functions related to polyextremophily. HGT candidates differ from native genes in GC-content, number of splice sites, and gene expression. HGT candidates are more prone to loss, which may explain the nonexistence of a eukaryotic pan-genome. Therefore, absence of a pan-genome and cumulative effects fail to provide substantive arguments against our hypothesis of recurring HGT followed by differential loss in eukaryotes. The maintenance of 1% HGTs, even under selection for genome reduction underlines the importance of non-endosymbiosis related foreign gene acquisition.
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References8
Published on Feb 1, 2012in Biochemistry and Cell Biology 2.25
David J. Dilworth15
Estimated H-index: 15
,
Geoff Gudavicius4
Estimated H-index: 4
+ 1 AuthorsChristopher J. Nelson8
Estimated H-index: 8
The post-translational modification of proteins and enzymes provides a dynamic and reversible means to control protein function and transmit biological signals. While covalent modifications such as phosphorylation and acetylation have drawn much attention, in the past decade the involvement of peptidyl-proline isomerases (PPIs) in signaling and post-translational modification of protein function has become increasingly apparent. Three distinct families of PPI enzymes (parvulins, cyclophilins, an...
19 Citations Source Cite
Published on Jul 1, 2014in Molecular and Biochemical Parasitology 1.74
David Horn37
Estimated H-index: 37
(University of Dundee)
Studies on Variant Surface Glycoproteins (VSGs) and antigenic variation in the African trypanosome, Trypanosoma brucei, have yielded a remarkable range of novel and important insights. The features first identified in T. brucei extend from unique to conserved-among-trypanosomatids to conserved-among-eukaryotes. Consequently, much of what we now know about trypanosomatid biology and much of the technology available has its origin in studies related to VSGs. T. brucei is now probably the most adva...
99 Citations Source Cite
Published on Jan 1, 2010in Nucleic Acids Research 11.56
Lewis Y. Geer23
Estimated H-index: 23
,
Aron Marchler-Bauer28
Estimated H-index: 28
+ 6 AuthorsStephen H. Bryant51
Estimated H-index: 51
The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI’s Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type, without requiring time-consuming inference of biological relationship...
363 Citations Source Cite
Published on Feb 1, 2009in Cellular and Molecular Life Sciences 6.72
Angelita Simonetti7
Estimated H-index: 7
,
Stefano Marzi15
Estimated H-index: 15
+ 5 AuthorsMarat Yusupov28
Estimated H-index: 28
The assembly of the protein synthesis machinery occurs during translation initiation. In bacteria, this process involves the binding of messenger RNA(mRNA) start site and fMet-tRNAfMet to the ribosome, which results in the formation of the first codon-anticodon interaction and sets the reading frame for the decoding of the mRNA. This interaction takes place in the peptidyl site of the 30S ribosomal subunit and is controlled by the initiation factors IF1, IF2 and IF3 to form the 30S initiation co...
94 Citations Source Cite
Published on Dec 1, 2006in Biochemistry 3.00
K. Sudhindra Rao4
Estimated H-index: 4
,
Mark Albro2
Estimated H-index: 2
+ 1 AuthorsFrank E. Frerman27
Estimated H-index: 27
Glutaryl-CoA dehydrogenase (GCD) is a homotetrameric enzyme containing one noncovalently bound FAD per monomer that oxidatively decarboxylates glutaryl-CoA to crotonyl-CoA and CO2. GCD belongs to the family of acyl-CoA dehydrogenases that are evolutionarily conserved in their sequence, structure, and function. However, there are differences in the kinetic mechanisms among the different acyl-CoA dehydrogenases. One of the unanswered aspects is that of the rate-determining step in the steady-state...
11 Citations Source Cite
Published on Feb 1, 2015in Current Opinion in Microbiology 6.71
George Vernikos1
Estimated H-index: 1
(Novartis),
Duccio Medini16
Estimated H-index: 16
(Novartis)
+ 1 AuthorsHervé Tettelin47
Estimated H-index: 47
(University of Maryland, Baltimore)
Next generation sequencing technologies have engendered a genome sequence data deluge in public databases. Genome analyses have transitioned from single or few genomes to hundreds to thousands of genomes. Pan-genome analyses provide a framework for estimating the genomic diversity of the dataset at hand and predicting the number of additional whole genomes sequences that would be necessary to fully characterize that diversity. We review recent implementations of the pan-genome approach, its impa...
114 Citations Source Cite
Published on Apr 14, 2016in PLOS Genetics 5.54
W Forddoolittle58
Estimated H-index: 58
(Dalhousie University),
Tyler D.P. Brunet5
Estimated H-index: 5
(Dalhousie University)
A universal Tree of Life (TOL) has long been a goal of molecular phylogeneticists, but reticulation at the level of genes and possibly at the levels of cells and species renders any simple interpretation of such a TOL, especially as applied to prokaryotes, problematic.
14 Citations Source Cite
Published on May 1, 2018in Nature Ecology and Evolution
William Martin79
Estimated H-index: 79
(University of Düsseldorf)
5 Citations Source Cite
Cited By1
Published on Mar 4, 2019in bioRxiv
Alessandro W. Rossoni2
Estimated H-index: 2
(University of Düsseldorf),
Andreas P. M. Weber57
Estimated H-index: 57
(University of Düsseldorf)
Rapid fluctuation of environmental conditions can impose severe stress upon living organisms. Surviving such episodes of stress requires a rapid acclimation response, e.g., by transcriptional and post-transcriptional mechanisms. Persistent change of the environmental context, however, requires longer-term adaptation at the genetic level. Fast-growing unicellular aquatic eukaryotes enable analysis of adaptive responses at the genetic level in a laboratory setting. In this study, we applied contin...
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