When Less is More: Red Algae as Models for Studying Gene Loss and Genome Evolution in Eukaryotes

Published on Jan 2, 2018in Critical Reviews in Plant Sciences 6.16
· DOI :10.1080/07352689.2018.1482364
Debashish Bhattacharya64
Estimated H-index: 64
(Rutgers University),
Huan Qiu18
Estimated H-index: 18
(Rutgers University)
+ 3 AuthorsDana C. Price19
Estimated H-index: 19
(Rutgers University)
Abstract
AbstractGenome evolution is usually viewed through the lens of growth in size and complexity over time, exemplified by plants and animals. In contrast, genome reduction is associated with a narrowing of ecological potential, such as in parasites and endosymbionts. But, can nuclear genome reduction also occur in, and potentially underpin a major radiation of free-living eukaryotes? An intriguing example of this phenomenon is provided by the red algae (Rhodophyta) that have lost many conserved pathways such as for flagellar motility, macroautophagy regulation, and phytochrome based light sensing. This anciently diverged, species-rich, and ecologically important algal lineage has undergone at least two rounds of large-scale genome reduction during its >1 billion-year evolutionary history. Here, using recent analyses of genome data, we review knowledge about the evolutionary trajectory of red algal nuclear and organelle gene inventories and plastid encoded autocatalytic introns. We compare and contrast Rhodop...
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References119
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David R. Mitchell22
Estimated H-index: 22
(State University of New York Upstate Medical University)
Eukaryotic cilia and flagella are motile organelles built on a scaffold of doublet microtubules and powered by dynein ATPase motors. Some thirty years ago, two competing views were presented to explain how the complex machinery of these motile organelles had evolved. Overwhelming evidence now refutes the hypothesis that they are the modified remnants of symbiotic spirochaete-like prokaryotes, and supports the hypothesis that they arose from a simpler cytoplasmic microtubule-based intracellular t...
109 Citations Source Cite
Published on Jun 18, 2015in PeerJ 2.12
Marie-Mathilde Perrineau9
Estimated H-index: 9
(Rutgers University),
Dana C. Price19
Estimated H-index: 19
(Rutgers University)
+ 1 AuthorsDebashish Bhattacharya64
Estimated H-index: 64
(Rutgers University)
Group II introns are closely linked to eukaryote evolution because nuclear spliceosomal introns and the small RNAs associated with the spliceosome are thought to trace their ancient origins to these mobile elements. Therefore, elucidating how group II introns move, and how they lose mobility can potentially shed light on fundamental aspects of eukaryote biology. To this end, we studied five strains of the unicellular red alga Porphyridium purpureum that surprisingly contain 42 group II introns i...
9 Citations Source Cite
Published on Aug 1, 2015in Nature Reviews Genetics 41.47
Marie-Anne Félix35
Estimated H-index: 35
,
Michalis Barkoulas15
Estimated H-index: 15
Robustness of a phenotypic trait is characterized as lack of, or low, variance in that phenotype under a particular genetic or environmental perturbation. The authors review recent studies characterizing robustness, provide guidance in reporting robust features and insights into how variation propagates across biological systems.
73 Citations Source Cite
Published on Sep 1, 2013in BioEssays 4.42
Yuri I. Wolf84
Estimated H-index: 84
(National Institutes of Health),
Eugene V. Koonin167
Estimated H-index: 167
(National Institutes of Health)
A common belief is that evolution generally proceeds towards greater complexity at both the organismal and the genomic level, numerous examples of reductive evolution of parasites and symbionts notwithstanding. However, recent evolutionary reconstructions challenge this notion. Two notable examples are the reconstruction of the complex archaeal ancestor and the intron-rich ancestor of eukaryotes. In both cases, evolution in most of the lineages was apparently dominated by extensive loss of genes...
127 Citations Source Cite
Published on Apr 3, 2015in Autophagy 11.10
Adva Shemi3
Estimated H-index: 3
(Weizmann Institute of Science),
Shifra Ben-Dor23
Estimated H-index: 23
(Weizmann Institute of Science),
Assaf Vardi28
Estimated H-index: 28
(Weizmann Institute of Science)
Aquatic photosynthetic eukaryotes represent highly diverse groups (green, red, and chromalveolate algae) derived from multiple endosymbiosis events, covering a wide spectrum of the tree of life. They are responsible for about 50% of the global photosynthesis and serve as the foundation for oceanic and fresh water food webs. Although the ecophysiology and molecular ecology of some algal species are extensively studied, some basic aspects of algal cell biology are still underexplored. The recent w...
27 Citations Source Cite
Published on Sep 1, 2011in Fems Microbiology Reviews 11.39
Jane Wiedenbeck2
Estimated H-index: 2
(Wesleyan University),
Frederick M. Cohan38
Estimated H-index: 38
(Wesleyan University)
Horizontal genetic transfer (HGT) has played an important role in bacterial evolution at least since the origins of the bacterial divisions, and HGT still facilitates the origins of bacterial diversity, including diversity based on antibiotic resistance. Adaptive HGT is aided by unique features of genetic exchange in bacteria such as the promiscuity of genetic exchange and the shortness of segments transferred. Genetic exchange rates are limited by the genetic and ecological similarity of organi...
287 Citations Source Cite
Published on Aug 1, 2011in Current protocols in immunology
Leslie B. Poole47
Estimated H-index: 47
(Wake Forest University),
Andrea Hall9
Estimated H-index: 9
(Oregon State University),
Kimberly J. Nelson19
Estimated H-index: 19
(Wake Forest University)
Peroxiredoxins are important hydroperoxide detoxification enzymes, yet have only come to the fore in recent years relative to the other major players in peroxide detoxification, heme-containing catalases and peroxidases, and glutathione peroxidases. These cysteine-dependent peroxidases exhibit high reactivity with hydrogen peroxide, organic hydroperoxides and peroxynitrite and play major roles not only in peroxide defense, but also in regulating peroxide-mediated cell signaling. This overview fo...
50 Citations Source Cite
Published on May 1, 2015in Nature 41.58
Anja Spang17
Estimated H-index: 17
,
Jimmy H. Saw16
Estimated H-index: 16
+ 7 AuthorsThijs J. G. Ettema31
Estimated H-index: 31
The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an ...
366 Citations Source Cite
Published on Dec 1, 2009in Current Biology 9.25
Yael T. Aminetzach1
Estimated H-index: 1
(Harvard University),
John R. Srouji5
Estimated H-index: 5
(Harvard University)
+ 1 AuthorsHopi E. Hoekstra41
Estimated H-index: 41
(Harvard University)
Summary How do proteins evolve novel functions? To address this question, we are studying the evolution of a mammalian toxin, the serine protease BLTX [1], from the salivary glands of the North American shrew Blarina brevicauda . Here, we examine the molecular changes responsible for promoting BLTX toxicity. First, we show that regulatory loops surrounding the BLTX active site have evolved adaptively via acquisition of small insertions and subsequent accelerated sequence evolution. Second, these...
39 Citations Source Cite
Published on Oct 1, 2013in Current Biology 9.25
Huan Qiu18
Estimated H-index: 18
(Rutgers University),
Dana C. Price19
Estimated H-index: 19
(Rutgers University)
+ 6 AuthorsDebashish Bhattacharya64
Estimated H-index: 64
(Rutgers University)
Summary Thriving in the hot, acidic, and metal-rich environments associated with geothermal areas is possible for only a few eukaryotes, with the Cyanidiophytina red algae ( Cyanidium , Galdieria , and Cyanidioschyzon ) being a famous example. These unicellular taxa can live in pH 0–4 and temperatures reaching up to 56°C [1,2]. Because Cyanidiophytina is sister to a vast array of mesophilic red algae (the Rhodophytina), such as the unicellular Porphyridium and the seaweed Chondrus [3], the genet...
32 Citations Source Cite
Cited By3
Published on Feb 1, 2019in Plant Physiology 5.95
Guo Wei1
Estimated H-index: 1
(University of Tennessee),
Qidong Jia6
Estimated H-index: 6
(University of Tennessee)
+ 5 AuthorsFeng Chen29
Estimated H-index: 29
(University of Tennessee)
Red algae (Rhodophyta) and land plants belong to the monophyletic clade Archaeplastida, and taxa of both groups are rich producers of terpene secondary metabolites. The terpene carbon skeletons of land plants are made by two types of terpene synthases: typical plant terpene synthases and microbial-type terpene synthases (MTPSLs); however, terpene biosynthesis in red algae is poorly understood. By systematic sequence analysis of seven genomes and 34 transcriptomes of red algae, MTPSL homologs wer...
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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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