eukaryotic evolution
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2021 ◽  
Author(s):  
Ang Li ◽  
Xuemeng Sun ◽  
A Emilia Arguello ◽  
Ralph E Kleiner

Epitranscriptomic RNA modifications can regulate biological processes, but there remains a major gap in our ability to identify and measure individual modifications at nucleotide resolution. Here we present Mal-Seq, a chemical method to sequence 5-formylcytosine (f5C) modifications on RNA based upon selective and efficient malononitrile-mediated labeling of f5C residues to generate adducts that are read as C-to-T mutations upon reverse transcription and PCR amplification. We apply Mal-Seq to characterize the prevalence of f5C at the wobble position of mt-tRNA(Met) in different organisms and tissue types and find that high-level f5C modification is present in mammals but lacking in lower eukaryotes. Our work sheds light on mitochondrial tRNA modifications throughout eukaryotic evolution and provides a general platform for characterizing the f5C epitranscriptome.


2021 ◽  
Author(s):  
Daniel Tamarit ◽  
Sarah Teakel ◽  
Michealla Marama ◽  
David Aragão ◽  
Svetlana Y. Gerdes ◽  
...  

The multiple functions of PGRMC1, the archetypal heme-binding eukaryotic MAPR family member, include steroidogenic regulation, membrane trafficking, and steroid responsiveness. The interrelationships between these functions are currently poorly understood. Previous work has shown that different MAPR subclasses were present early in eukaryotic evolution, and that tyrosine phosphorylated residues appeared in the eumetazoan ancestor, coincident with a gastrulation organizer. Here we show that MAPR proteins are related to a newly recognized class of prokaryotic cytochrome-b5 domain proteins. Our first solved structure of this new class exhibits shared MAPR-like folded architecture and heme-binding orientation. We also report that a protein subgroup from Candidate Phyla Radiation (CPR) bacteria shares MAPR-like heme-interacting tyrosines. Our results support bacterial origins for both PGRMC1 and CYP51A, that catalyze the meiosis-associated 14-demethylation of the first sterol lanosterol from yeast to humans. We propose that eukaryotic acquisition of a membrane-trafficking function related to sterol metabolism was associated with the appearance of MAPR genes early in eukaryotic evolution.


2021 ◽  
Author(s):  
Mahwash Jamy ◽  
Charlie Biwer ◽  
Daniel Vaulot ◽  
Aleix Obiol ◽  
Hongmei Jing ◽  
...  

The successful colonisation of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and terrestrial (including both freshwater and soil) communities. Although microbes represent by far the vast majority of eukaryote diversity, the role of the salt barrier in shaping the diversity across the eukaryotic tree is poorly known. Traditional views suggest rare and ancient marine-terrestrial transitions, but this view is being challenged by the discovery of several recently transitioned lineages. Here, we investigate habitat evolution across the tree of eukaryotes using a unique set of taxon-rich environmental phylogenies inferred from a combination of long-read and short-read metabarcoding data spanning the ribosomal DNA operon. Our results show that overall marine and terrestrial microbial communities are phylogenetically distinct, but transitions have occurred in both directions in almost all major eukaryotic lineages, with at least 350 transition events detected. Some groups have experienced relatively high rates of transitions, most notably fungi for which crossing the salt barrier has most likely been an important aspect of their successful diversification. At the deepest phylogenetic levels, ancestral habitat reconstruction analyses suggest that eukaryotes may have first evolved in non-saline habitats, and that the two largest known eukaryotic assemblages (TSAR and Amorphea) arose in different habitats. Overall, our findings indicate that crossing the salt barrier has played an important role in eukaryotic evolution by providing new ecological niches to fill.


Author(s):  
Luke W. Thomas ◽  
Margaret Ashcroft

Mitochondria are key organelles in eukaryotic evolution that perform crucial roles as metabolic and cellular signaling hubs. Mitochondrial function and dysfunction are associated with a range of diseases, including cancer. Mitochondria support cancer cell proliferation through biosynthetic reactions and their role in signaling, and can also promote tumorigenesis via processes such as the production of reactive oxygen species (ROS). The advent of (nuclear) genome-wide CRISPR-Cas9 deletion screens has provided gene-level resolution of the requirement of nuclear-encoded mitochondrial genes (NEMGs) for cancer cell viability (essentiality). More recently, it has become apparent that the essentiality of NEMGs is highly dependent on the cancer cell context. In particular, key tumor microenvironmental factors such as hypoxia, and changes in nutrient (e.g., glucose) availability, significantly influence the essentiality of NEMGs. In this mini-review we will discuss recent advances in our understanding of the contribution of NEMGs to cancer from CRISPR-Cas9 deletion screens, and discuss emerging concepts surrounding the context-dependent nature of mitochondrial gene essentiality.


mBio ◽  
2021 ◽  
Author(s):  
Antonio de Jesús López-Fuentes ◽  
Karime Naid Nachón-Garduño ◽  
Fernando Suaste-Olmos ◽  
Ariadna Mendieta-Romero ◽  
Leonardo Peraza-Reyes

Meiosis consists of a reductional cell division, which allows ploidy maintenance during sexual reproduction and which provides the potential for genetic recombination, producing genetic variation. Meiosis constitutes a process of foremost importance for eukaryotic evolution.


2021 ◽  
Author(s):  
Mathilde Dupeyron ◽  
Tobias Baril ◽  
Alex Hayward

DDE transposons are widespread selfish genetic elements, often comprising a large proportion of eukaryotic genomic content. DDE transposons have also made important contributions to varied host functions during eukaryotic evolution, and their transposases may be the most abundant and ubiquitous genes in nature. Yet much remains unknown about their basic biology. We employ a broadscale screen of DDE transposase diversity to characterise major evolutionary patterns for all 19 DDE transposon superfamilies. We identify considerable variation in DDE transposon superfamily size, and find a dominant association with animal hosts. While few DDE transposon superfamilies specialise in plants or fungi, the four largest superfamilies contain major plant-associated clades, at least partially underlying their relative success. We recover a pattern of host conservation among DDE transposon lineages, punctuated by occasional horizontal transfer to distantly related hosts. Host range and horizontal transfer are strongly positively correlated with DDE transposon superfamily size, arguing against variation in the capacity for generalism. We find that rates of horizontal transfer decrease sharply with increasing levels of host taxonomy, supporting the existence of host-associated barriers to DDE transposon spread. Overall, despite their relatively simple genetic structure, our results imply that trade-offs in host adaptation are important in defining DDE transposon-host relationships and evolution. In addition, our study provides a phylogenetic framework to facilitate the identification and further analysis of DDE transposons.


2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Toni Gabaldón

The origin of eukaryotes has been defined as the major evolutionary transition since the origin of life itself. Most hallmark traits of eukaryotes, such as their intricate intracellular organization, can be traced back to a putative common ancestor that predated the broad diversity of extant eukaryotes. However, little is known about the nature and relative order of events that occurred in the path from preexisting prokaryotes to this already sophisticated ancestor. The origin of mitochondria from the endosymbiosis of an alphaproteobacterium is one of the few robustly established events to which most hypotheses on the origin of eukaryotes are anchored, but the debate is still open regarding the time of this acquisition, the nature of the host, and the ecological and metabolic interactions between the symbiotic partners. After the acquisition of mitochondria, eukaryotes underwent a fast radiation into several major clades whose phylogenetic relationships have been largely elusive. Recent progress in the comparative analyses of a growing number of genomes is shedding light on the early events of eukaryotic evolution as well as on the root and branching patterns of the tree of eukaryotes. Here I discuss current knowledge and debates on the origin and early evolution of eukaryotes. I focus particularly on how phylogenomic analyses have challenged some of the early assumptions about eukaryotic evolution, including the widespread idea that mitochondrial symbiosis in an archaeal host was the earliest event in eukaryogenesis. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yuma Ishigami ◽  
Takayuki Ohira ◽  
Yui Isokawa ◽  
Yutaka Suzuki ◽  
Tsutomu Suzuki

AbstractN6-methyladenosine (m6A) is a modification that plays pivotal roles in RNA metabolism and function, although its functions in spliceosomal U6 snRNA remain unknown. To elucidate its role, we conduct a large-scale transcriptome analysis of a Schizosaccharomyces pombe strain lacking this modification and found a global change of pre-mRNA splicing. The most significantly impacted introns are enriched for adenosine at the fourth position pairing the m6A in U6 snRNA, and exon sequences weakly recognized by U5 snRNA. This suggests cooperative recognition of 5’ splice site by U6 and U5 snRNPs, and also a role of m6A facilitating efficient recognition of the splice sites weakly interacting with U5 snRNA, indicating that U6 snRNA m6A relaxes the 5’ exon constraint and allows protein sequence diversity along with explosively increasing number of introns over the course of eukaryotic evolution.


Science ◽  
2021 ◽  
Vol 372 (6545) ◽  
pp. 984-989
Author(s):  
Claire Hoencamp ◽  
Olga Dudchenko ◽  
Ahmed M. O. Elbatsh ◽  
Sumitabha Brahmachari ◽  
Jonne A. Raaijmakers ◽  
...  

We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.


2021 ◽  
Author(s):  
Mari Yoshinaga ◽  
Yuji Inagaki

Structural maintenance of chromosomes (SMC) protein complexes are common in Bacteria, Archaea, and Eukaryota. SMC proteins, together with the proteins related to SMC (SMC-related proteins), constitute a superfamily of ATPases. Bacteria/Archaea and Eukaryotes are distinctive from one another in terms of the repertory of SMC proteins. A single type of SMC protein is dimerized in the bacterial and archaeal complexes, whereas eukaryotes possess six distinct SMC subfamilies (SMC1-6), constituting three heterodimeric complexes, namely cohesin, condensin, and SMC5/6 complex. Thus, to bridge the homodimeric SMC complexes in Bacteria and Archaea to the heterodimeric SMC complexes in Eukaryota, we need to invoke multiple duplications of a SMC gene followed by functional divergence. However, to our knowledge, the evolution of the SMC proteins in Eukaryota had not been examined for more than a decade. In this study, we reexamined the ubiquity of SMC1-6 in phylogenetically diverse eukaryotes that cover the major eukaryotic taxonomic groups recognized to date (101 species in total) and provide two novel insights into the SMC evolution in eukaryotes. First, multiple secondary losses of SMC5 and SMC6 occurred in the eukaryotic evolution. Second, the SMC proteins constituting cohesin and condensin (i.e., SMC1-4), and SMC5 and SMC6 were derived from closely related but distinct ancestral proteins. Finally, we discuss how SMC1-4 were evolved from the ancestral SMC protein(s) in the very early stage of eukaryotic evolution.


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