Biology subjects

Meza-Padilla, I.

Publications and source records attributed to Meza-Padilla, I..

3 recordsLinked to original sources

bioRxiv2024

AlphaFold 3 proteomic modelling reveals multiple photosystem structural homologs in freshwater cyanophages

Accurate protein structure prediction followed by structural homology detection enable the functional annotation of large numbers of otherwise obscure viral protein-coding genes. Here we employ AlphaFold 3 modeling and DALI structural homology search to predict the structures and functions of all 219 cryptic open reading frames in two representative freshwater cyanophages. We discover 28 previously unknown structural homologs, including three putative PsaD proteins in the same cyanophage, several viral structural proteins, and (to our knowledge) the first reported virus-encoded cyanobacteriochrome (DALI Z-score > 4.2 in all cases). Our results suggest that photosystem proteins may be more widespread in freshwater cyanophages than previously thought and emphasize the importance of applying structural homology detection methods when annotating viral genomes.

bioinformatics↗

bioRxiv2024

Structural models predict a significantly higher binding affinity between the NblA protein of cyanophage Ma-LMM01 and the phycocyanin of Microcystis aeruginosa NIES-298 compared to the host homolog

Horizontal gene transfer events between viruses and hosts are widespread across the virosphere. In cyanophage-host systems, such events often involve the transfer of genes involved in photosynthetic processes. The genome of the lytic cyanomyovirus Ma-LMM01 infecting the toxic, bloom-forming, freshwater Microcystis aeruginosa NIES-298 contains a homolog of the non-bleaching A (nblA) gene, which was probably acquired from its host. The function of the NblA protein is to disassemble phycobilisomes, cyanobacterial light harvesting complexes that can comprise up to half of the cellular soluble protein content. NblA thus plays an essential dual role in cyanobacteria: it protects the cell from high light intensities and increases the intracellular nitrogen pool under nutrient limitation. NblA has previously been shown to interact with phycocyanin, one of the main components of phycobilisomes. Using structural modeling and protein-protein docking, we show that the NblA dimer of Ma-LMM01 is predicted to have a significantly higher binding affinity for M. aeruginosa NIES-298 phycocyanin ({beta})6 hexamers, compared to the host homolog. Protein-protein docking suggests that the viral NblA structural model is able to bind deeper into the phycocyanin groove. The main structural difference between the virus and host NblA appears to be an additional -helix near the N-terminus of the viral NblA, which could be partly responsible for the deeper binding into phycocyanin. This unique helical region, absent in the cellular NblA, would be expected to constitute a viral evolutionary innovation. We propose that a higher binding affinity of NblA to the host phycocyanin may represent a selective advantage for the virus, whose rapid infection cycle requires an increased phycobilisome degradation rate that is not fulfilled by the NblA of the host.

microbiology↗

bioRxiv2023

The curious case of cyanobacteria: a tale of light and darkness

Toxic algal bloom-forming cyanobacteria are a persistent problem globally for many aquatic environments. Their occurrence is attributed to eutrophication and rising temperatures due to climate change. The result of these blooms is often loss in biodiversity, economic impacts on tourism and fisheries, and risks to human and animal health. Of particular concern is the poorly understood interplay between viruses and toxic species that form blooms because viruses may exacerbate their harmful effects. Concurrently, cyanobacteria are also a source of bioactive compounds other than toxins, which makes them good candidates for drug discovery. We show that virus infection of the cyanobacterium Microcystis aeruginosa, results in as high as a 40-fold increase in the toxin microcystin two days post virus infection (dpi), and predict that microcystin levels may remain high in a body of water up to 7 dpi, long after water discoloration and cell lysis. This implicates viruses as major contributors to toxin release from cyanobacteria and emphasizes the importance of taking them into account in predictive models and in the assessment of water safety. We also show that bioactive compounds of M. aeruginosa inhibit and delay infection of single stranded DNA and single stranded RNA viruses. This highlights the potential of cyanobacteria as an excellent source for the discovery of novel antiviral compounds, and the ease with which screening for cyanobacterial antivirals can be achieved.

microbiology↗