July 2021 archive

Jul 29

Shifts in amino acid preferences as proteins evolve: a synthesis of experimental and theoretical work

Protein Sci. 2021 Jul 28. doi: 10.1002/pro.4161. Online ahead of print. ABSTRACT Amino acid preferences vary across sites and time. While variation across sites is widely accepted, the extent and frequency of temporal shifts are contentious. Our understanding of the drivers of amino acid preference change is incomplete: To what extent are temporal shifts driven …

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Jul 27

Identification of a Metacaspase Gene in the Bloom-Forming Dinoflagellate Prorocentrum minimum and its Putative Function Involved in Programmed Cell Death

Programmed cell death (PCD) in dinoflagellates has been introduced as a new concept that facilitates the demise of harmful algal blooms. Metacaspases (MCAs) play a role in PCD, but their function in dinoflagellates is unclear. Here, we cloned a novel MCA gene (PmMCA) from the harmful dinoflagellate Prorocentrum minimum and examined its molecular characteristics and gene expression during cell death. The gene was encoded in the nuclear genome with two introns. The putative protein contained 288…

Jul 27

Identification of a Metacaspase Gene in the Bloom-Forming Dinoflagellate Prorocentrum minimum and its Putative Function Involved in Programmed Cell Death

Programmed cell death (PCD) in dinoflagellates has been introduced as a new concept that facilitates the demise of harmful algal blooms. Metacaspases (MCAs) play a role in PCD, but their function in dinoflagellates is unclear. Here, we cloned a novel MCA gene (PmMCA) from the harmful dinoflagellate Prorocentrum minimum and examined its molecular characteristics and gene expression during cell death. The gene was encoded in the nuclear genome with two introns. The putative protein contained 288…

Jul 26

Coral symbionts evolved a functional polycistronic flavodiiron gene

Photosynthesis in cyanobacteria, green algae, and basal land plants is protected against excess reducing pressure on the photosynthetic chain by flavodiiron proteins (FLV) that dissipate photosynthetic electrons by reducing O(2). In these organisms, the genes encoding FLV are always conserved in the form of a pair of two-type isozymes (FLVA and FLVB) that are believed to function in O(2) photo-reduction as a heterodimer. While coral symbionts (dinoflagellates of the family Symbiodiniaceae) are…

Jul 26

Coral symbionts evolved a functional polycistronic flavodiiron gene

Photosynthesis in cyanobacteria, green algae, and basal land plants is protected against excess reducing pressure on the photosynthetic chain by flavodiiron proteins (FLV) that dissipate photosynthetic electrons by reducing O(2). In these organisms, the genes encoding FLV are always conserved in the form of a pair of two-type isozymes (FLVA and FLVB) that are believed to function in O(2) photo-reduction as a heterodimer. While coral symbionts (dinoflagellates of the family Symbiodiniaceae) are…

Jul 23

Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri

CONCLUSIONS: In-depth analysis of Naegleria genomes and transcriptomes provides a model of cellular systems involved in opportunistic pathogenicity, uncovering new angles to understanding the biology of a rare but highly fatal pathogen.

Jul 23

Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri

CONCLUSIONS: In-depth analysis of Naegleria genomes and transcriptomes provides a model of cellular systems involved in opportunistic pathogenicity, uncovering new angles to understanding the biology of a rare but highly fatal pathogen.

Jul 22

The complete mitochondrial genome of the photosymbiotic sea slug Berghia stephanieae (Valdes, 2005) (Gastropoda, Nudibranchia)

Berghia stephanieae (Nudibranchia, Cladobranchia) is a photosymbiotic sea slug that feeds exclusively on sea anemones from the genus Exaiptasia. It then specifically incorporates dinoflagellates belonging to the Symbiodiniaceae obtained from their prey. Here, we present the complete mitochondrial genome sequence of B. stephanieae combining Oxford Nanopore long read and Illumina short-read sequencing data. The mitochondrial genome has a total length of 14,786 bp, it contains the 13…

Jul 22

The complete mitochondrial genome of the photosymbiotic sea slug Berghia stephanieae (Valdes, 2005) (Gastropoda, Nudibranchia)

Berghia stephanieae (Nudibranchia, Cladobranchia) is a photosymbiotic sea slug that feeds exclusively on sea anemones from the genus Exaiptasia. It then specifically incorporates dinoflagellates belonging to the Symbiodiniaceae obtained from their prey. Here, we present the complete mitochondrial genome sequence of B. stephanieae combining Oxford Nanopore long read and Illumina short-read sequencing data. The mitochondrial genome has a total length of 14,786 bp, it contains the 13…

Jul 20

Cation and Anion Channelrhodopsins: Sequence Motifs and Taxonomic Distribution

Cation and anion channelrhodopsins (CCRs and ACRs, respectively) primarily from two algal species, Chlamydomonas reinhardtii and Guillardia theta, have become widely used as optogenetic tools to control cell membrane potential with light. We mined algal and other protist polynucleotide sequencing projects and metagenomic samples to identify 75 channelrhodopsin homologs from four channelrhodopsin families, including one revealed in dinoflagellates in this study. We carried out…