Biology subjects

Howe, C.

Publications and source records attributed to Howe, C..

5 recordsLinked to original sources

bioRxiv2024

A paleogenomic approach to reconstruct historical responses of coral reefs to anthropogenic change

Coral reefs are declining worldwide due to anthropogenic environmental change. The foundation and health of these ecosystems rely on the harmonious functioning of all members of coral holobionts, i.e., cnidarian host, symbiotic microalgae, and associated microbiome. Coral stress responses often involve shifts in the taxonomic identity of their symbionts and microbiomes. Tracing back changes in coral holobiont composition over prolonged time periods can help us reconstruct health history of reefs and gain a better understanding of coral response to current stressors. Here, we focused on a major Caribbean reef-builder coral, Orbicella faveolata, from Varadero Reef, Colombia. This reef has undergone extensive freshwater sediment discharge and pollution for decades as result of urbanization. We show, for the first time, that paleogenomic and paleoclimatic approaches can be combined to reconstruct historical coral holobiont dynamics potentially associated with anthropogenic disturbances.

molecular biology↗

bioRxiv2022

Establishment of a novel set of vectors for transformation of the dinoflagellate Amphidinium carterae

Peridinin-containing dinoflagellate algae have a chloroplast genome formed from plasmid-like minicircles. This fragmented genome has allowed us to develop a genetic modification methodology involving the use of biolistics to introduce artificial minicircles in Amphidinium carterae (Nimmo et al., 2019). The previously reported artificial minicircles were based on native minicircles containing either the psbA or atpB gene. Each artificial minicircle allowed expression of a single selectable marker instead of psbA or atpB. Here, we present two further artificial minicircles for use in transformation of A. carterae. One is based on the petD minicircle, allowing the expression of a single selectable marker. The second is based on the two-gene minicircle originally containing atpA and petB, and allows the dual expression of a selectable marker and a gene of interest. Our research suggest that all of the 20 or so minicircles in A. carterae are suitable for adaptation as artificial minicircles, allowing for the simultaneous introduction of multiple genes.

plant biology↗

bioRxiv2019

Cytochrome cM downscales photosynthesis under photomixotrophy in Synechocystis sp. PCC 6803

Photomixotrophy is a metabolic state, which enables photosynthetic microorganisms to simultaneously perform photosynthesis and metabolism of imported organic carbon substrates. This process is complicated in cyanobacteria, since many, including Synechocystis sp. PCC 6803, conduct photosynthesis and respiration in an interlinked thylakoid membrane electron transport chain. Under photomixotrophy, the cell must therefore tightly regulate electron fluxes from photosynthetic and respiratory complexes. In this study, we show via characterization of photosynthetic apparatus and the proteome, that photomixotrophic growth results in a gradual reduction of the plastoquinone pool in wild-type Synechocystis, which fully downscales photosynthesis over three days of growth. This process is circumvented by deleting the gene encoding cytochrome cM (CytM), a cryptic c-type heme protein widespread in cyanobacteria. {Delta}CytM maintained active photosynthesis over the three day period, demonstrated by high photosynthetic O2 and CO2 fluxes and effective yields of Photosystem II and Photosystem I. Overall, this resulted in a higher growth rate than wild-type, which was maintained by accumulation of proteins involved in phosphate and metal uptake, and cofactor biosynthetic enzymes. While the exact role of CytM has not been determined, a mutant deficient in the thylakoid-localised respiratory terminal oxidases and CytM ({Delta}Cox/Cyd/CytM) displayed a similar phenotype under photomixotrophy to {Delta}CytM, demonstrating that CytM is not transferring electrons to these complexes, which has previously been suggested. In summary, the obtained data suggests that CytM may have a regulatory role in photomixotrophy by reducing the photosynthetic capacity of cells. One sentence summaryThe cryptic, highly conserved cytochrome cM completely blocks photosynthesis in Synechocystis under three days of photomixotrophy, possibly by suppressing CO2 assimilation.

plant biology↗

bioRxiv2019

The Dps4 from Nostoc punctiforme ATCC 29133 is a member of His-type FOC containing Dps protein class that can be broadly found among cyanobacteria

Dps proteins (DNA-binding proteins from starved cells) have been found to detoxify H2O2. At their catalytic centers, the ferroxidase center (FOC), Dps proteins utilize Fe2+ to reduce H2O2 and therefore play an essential role in the protection against oxidative stress and maintaining iron homeostasis. Whereas most bacteria accommodate one or two Dps, there are five different Dps proteins in Nostoc punctiforme, a phototrophic and filamentous cyanobacterium. This uncommonly high number of Dps proteins implies a sophisticated machinery for maintaining complex iron homeostasis and for protection against oxidative stress. Functional analyses and structural information on cyanobacterial Dps proteins are rare, but essential for understanding the function of each of the NpDps proteins. In this study, we present the crystal structure of NpDps4 in its metal-free, iron- and zinc-bound forms. The FOC coordinates either two iron atoms or one zinc atom. Spectroscopic analyses revealed that NpDps4 could oxidize Fe2+ utilizing O2, but no evidence for its use of the oxidant H2O2 could be found. We identified Zn2+ to be an effective inhibitor of the O2-mediated Fe2+ oxidation in NpDps4. NpDps4 exhibits a FOC that is very different from canonical Dps, but structurally similar to the atypical one from DpsA of Thermosynechococcus elongatus. Sequence comparisons among Dps protein homologs to NpDps4 within the cyanobacterial phylum led us to classify a novel FOC class: the His-type FOC. The features of this special FOC have not been identified in Dps proteins from other bacterial phyla and it might be unique to cyanobacterial Dps proteins.

biochemistry↗

bioRxiv2018

A Pentatricopeptide Repeat Protein in the Plasmodium apicoplast is essential and shows sequence-specific RNA binding

The malaria parasite Plasmodium and other apicomplexans such as Toxoplasma evolved from photosynthetic organisms and contain an essential, remnant plastid termed the apicoplast. Transcription of the apicoplast genome is polycistronic with extensive RNA processing. Little is known about the mechanism of post-transcriptional processing. In plant chloroplasts, post-transcriptional RNA processing is controlled by multiple pentatricopeptide repeat (PPR) proteins. Here, we present the biochemical characterisation of the single apicoplast-targeted PPR protein. Apicoplast PPR1 is essential, and binds specific RNA sequences corresponding with previously characterized RNA processing sites. We identify the specific binding motif of PPR1. In RNAse protection assays, PPR1 shields apicoplast transcripts from ribonuclease degradation. Our results show that apicoplast RNA processing is under the control of a single protein, thus presenting an Achilles heel for the development of new anti-malarial drugs.

microbiology↗