More Like this

1. Genetic Diversity of Potassium Ion Channel Proteins Encoded by Chloroviruses That Infect Chlorella heliozoae

   https://doi.org/10.3390/v12060678  

   Murry, Carter R.; Agarkova, Irina V.; Ghosh, Jayadri S.; Fitzgerald, Fiona C.; Carlson, Roger M.; Hertel, Brigitte; Kukovetz, Kerri; Rauh, Oliver; Thiel, Gerhard; Van Etten, James L. (June 2020, Viruses)

   null (Ed.)

   Chloroviruses are large, plaque-forming, dsDNA viruses that infect chlorella-like green algae that live in a symbiotic relationship with protists. Chloroviruses have genomes from 290 to 370 kb, and they encode as many as 400 proteins. One interesting feature of chloroviruses is that they encode a potassium ion (K+) channel protein named Kcv. The Kcv protein encoded by SAG chlorovirus ATCV-1 is one of the smallest known functional K+ channel proteins consisting of 82 amino acids. The KcvATCV-1 protein has similarities to the family of two transmembrane domain K+ channel proteins; it consists of two transmembrane α-helixes with a pore region in the middle, making it an ideal model for studying K+ channels. To assess their genetic diversity, kcv genes were sequenced from 103 geographically distinct SAG chlorovirus isolates. Of the 103 kcv genes, there were 42 unique DNA sequences that translated into 26 new Kcv channels. The new predicted Kcv proteins differed from KcvATCV-1 by 1 to 55 amino acids. The most conserved region of the Kcv protein was the filter, the turret and the pore helix were fairly well conserved, and the outer and the inner transmembrane domains of the protein were the most variable. Two of the new predicted channels were shown to be functional K+ channels. 

   more » « less
2. Selecting genes for analysis using historically contingent progress: from RNA changes to protein-protein interactions

   https://doi.org/10.1101/2024.05.01.592119  

   Lalit, Farhaan; Jose, Antony M (May 2024, bioRxiv)

   SUMMARY Progress in biology has generated numerous lists of genes that share some property. But, advancing from these lists of genes to understanding their roles is slow and unsystematic. Here we use RNA silencing inC. elegansto illustrate an approach for prioritizing genes for detailed study given limited resources. The partially subjective relationships between genes forged by both deduced functional relatedness and biased progress in the field was captured as mutual information and used to cluster genes that were frequently identified yet remain understudied. Studied genes in these clusters suggest regulatory links connecting RNA silencing with other processes like the cell cycle. Many proteins encoded by the understudied genes are predicted to physically interact with known regulators of RNA silencing. These predicted influencers of RNA-regulated expression could be used for feedback regulation, which is essential for the homeostasis observed in all living systems. Thus, among the gene products altered when a process is perturbed are regulators of that process, providing a way to use RNA sequencing to identify candidate protein-protein interactions. Together, the analysis of perturbed transcripts and potential interactions of the proteins they encode could help prioritize candidate regulators of any process. 

   more » « less
3. Evolutionary Analysis of the Zinc Finger and Homeoboxes Family of Proteins Identifies Multiple Conserved Domains and a Common Early Chordate Ancestor

   https://doi.org/10.1093/gbe/evaa039  

   Nail, Alexandra N; Smith, Jeramiah J; Peterson, Martha L; Spear, Brett T; Das, Sabyasachi (March 2020, Genome Biology and Evolution)

   Abstract The Zinc Fingers and Homeoboxes (Zhx) proteins, Zhx1, Zhx2, and Zhx3, comprise a small family of proteins containing two amino-terminal C2–H2 zinc fingers and four or five carboxy-terminal homeodomains. These multiple homeodomains make Zhx proteins unusual because the majority of homeodomain-containing proteins contain a single homeodomain. Studies in cultured cells and mice suggest that Zhx proteins can function as positive or negative transcriptional regulators. Zhx2 regulates numerous hepatic genes, and all three Zhx proteins have been implicated in different cancers. Because Zhx proteins contain multiple predicted homeodomains, are associated with interesting physiological traits, and seem to be only present in the vertebrate lineage, we investigated the evolutionary history of this small family by comparing Zhx homologs from a wide range of chordates. This analysis indicates that the zinc finger motifs and homeodomains are highly similar among all Zhx proteins and also identifies additional Zhx-specific conserved regions, including a 13 amino acid amino-terminal motif that is nearly identical among all gnathostome Zhx proteins. We found single Zhx proteins in the sea lamprey (Petromyzon marinus) and in the nonvertebrate chordates sea squirt (Ciona intestinalis) and lancelet (Branchiostoma floridae); these Zhx proteins are most similar to gnathostome Zhx3. Based on our analyses, we propose that a duplication of the primordial Zhx gene gave rise to Zhx3 and the precursor to Zhx1 and Zhx2. A subsequent tandem duplication of this precursor generated Zhx1 and Zhx2 found in gnathostomes. 

   more » « less
4. Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family Asfarviridae

   https://doi.org/10.3389/fmicb.2021.657471  

   Karki, Sangita; Moniruzzaman, Mohammad; Aylward, Frank O. (March 2021, Frontiers in Microbiology)

   null (Ed.)

   The family Asfarviridae is a group of nucleo-cytoplasmic large DNA viruses (NCLDVs) of which African swine fever virus (ASFV) is well-characterized. Recently the discovery of several Asfarviridae members other than ASFV has suggested that this family represents a diverse and cosmopolitan group of viruses, but the genomics and distribution of this family have not been studied in detail. To this end we analyzed five complete genomes and 35 metagenome-assembled genomes (MAGs) of viruses from this family to shed light on their evolutionary relationships and environmental distribution. The Asfarvirus MAGs derive from diverse marine, freshwater, and terrestrial habitats, underscoring the broad environmental distribution of this family. We present phylogenetic analyses using conserved marker genes and whole-genome comparison of pairwise average amino acid identity (AAI) values, revealing a high level of genomic divergence across disparate Asfarviruses. Further, we found that Asfarviridae genomes encode genes with diverse predicted metabolic roles and detectable sequence homology to proteins in bacteria, archaea, and eukaryotes, highlighting the genomic chimerism that is a salient feature of NCLDV. Our read mapping from Tara oceans metagenomic data also revealed that three Asfarviridae MAGs were present in multiple marine samples, indicating that they are widespread in the ocean. In one of these MAGs we identified four marker genes with > 95% AAI to genes sequenced from a virus that infects the dinoflagellate Heterocapsa circularisquama (HcDNAV). This suggests a potential host for this MAG, which would thereby represent a reference genome of a dinoflagellate-infecting giant virus. Together, these results show that Asfarviridae are ubiquitous, comprise similar sequence divergence as other NCLDV families, and include several members that are widespread in the ocean and potentially infect ecologically important protists. 

   more » « less
5. Productivity and photophysiology in a large, oligotrophic lake

   Evans, Kate A.; Tappenbeck, Tyler; Peoples, Logan; Church, Matthew (June 2023, Association for the Sciences of Limnology and Oceanography)

   We used a combination of approaches to measure primary production and plankton photophysiology in oligotrophic Flathead Lake, Montana (USA). Estimates of net ecosystem production (NEP) based on measurements of O2 to Ar ratios, together with radiocarbon (14C) assimilation incubations, revealed seasonal patterns in NEP and 14C-primary production. NEP was elevated during the summer, becoming negative during the winter. Rates of 14C-primary production were similarly seasonal, with peak rates in the summer and lower rates in the winter. Photosynthesis-irradiance curves indicated that plankton productivity in the subsurface chlorophyll maximum was light-limited year-round, while plankton production in the near-surface waters was light-saturated during the summer. We found that, despite physiological evidence of photoinhibition during the summer, this process appears to play a minor role in constraining primary production in Flathead Lake. Finally, use of metagenomic sequencing provided insight into photophysiological potential among the abundant cyanobacteria in the lake. Cyanobacteria belonging to Synechococcus/Cyanobium were well represented, some of which demonstrated seasonality while others appeared to be present year-round. Analyses of the metagenomic assembled genomes (MAGs) from these cyanobacteria revealed genes involved in phycoerythrin and phycoerythrobilin syntheses, with one MAG also possessing genes that encode phycourobilin. Such results point to flexibility in pigmentation as central to the physiology and competitive success of cyanobacteria in this lake. 

   more » « less