Biology subjects

Avramov, A.

Publications and source records attributed to Avramov, A..

3 recordsLinked to original sources

bioRxiv2025

Molecular insights into phycobilisome assembly pathway reveal crystalline bodies in cyanobacteria

In oxygenic photosynthetic organisms, light energy is converted to chemical energy to drive CO2 fixation reactions and sustain life on Earth. Cyanobacteria contain phycobilisome (PBS) complexes that play critical roles in light harvesting and directing light energy to the photosystem I and II reaction centers. The proper assembly of PBS components is an intricate process that is required for their activity and association with photosystem I and II. To understand the complex mechanisms regulating the PBS assembly, we knocked out the terminal emitter apcE, which forms the structural scaffold for the PBS core. ApcE knockout led to growth and pigment defects, including elevated levels of photosystem II and abnormal emission spectra. Light microscopy experiments revealed the accumulation of highly fluorescent puncta localized to the pole of apcE knockout cells. Further investigation using electron cryo-tomography identified highly repetitive crystalline arrays of densely packed PBS cylinders. Together, these data indicate that cyanobacteria may accumulate PBS components in the form of highly organized crystalline bodies as intermediates during PBS assembly.

microbiology↗

bioRxiv2024

Machine Learning Models for Segmentation and Classification of Cyanobacterial Cells

Timelapse microscopy has recently been employed to study the metabolism and physiology of cyanobacteria at the single-cell level. However, the identification of individual cells in brightfield images remains a significant challenge. Traditional intensity-based segmentation algorithms perform poorly when identifying individual cells in dense colonies due to a lack of contrast between neighboring cells. Here, we describe a newly developed software package called Cypose which uses machine learning (ML) models to solve two specific tasks: segmentation of individual cyanobacterial cells, and classification of cellular phenotypes. The segmentation models are based on the Cellpose framework, while classification is performed using a convolutional neural network named Cyclass. To our knowledge, these are the first developed ML-based models for cyanobacteria segmentation and classification. When compared to other methods, our segmentation models showed improved performance and were able to segment cells with varied morphological phenotypes, as well as differentiate between live and lysed cells. We also found that our models were robust to imaging artifacts, such as dust and cell debris. Additionally, the classification model was able to identify different cellular phenotypes using only images as input. Together, these models improve cell segmentation accuracy and enable high-throughput analysis of dense cyanobacterial colonies and filamentous cyanobacteria.

microbiology↗

bioRxiv2024

Cyanobacteria form a procarboxysome-like structure in response to high CO2

Fixing 25% of CO2 globally, cyanobacteria are integral to climate change efforts. The cyanobacterial CO2 concentrating mechanism (CCM) features the carboxysome, a bacterial microcompartment which houses their CO2 fixing machinery. The proteinaceous shell of the carboxysome restricts diffusion of CO2, both inward and outward. While necessary for CCM function in air (0.04% CO2), when grown in high CO2 levels (3% CO2) representative of early earth, the shell would harmfully limit CO2 fixation. To understand how carboxysomes change form and function in response to increased CO2 conditions, we used a Grx1-roGFP2 redox sensor and single cell timelapse fluorescence microscopy to track subcellular redox states of Synechococcus sp. PCC 7002 grown in air or 3% CO2. Comparing different levels of compartmentalization, we targeted the cytosol, a shell-less carboxysomal assembly intermediate called the procarboxysome, and the carboxysome. The carboxysome redox state was dynamic and, under 3% CO2, procarboxysome-like structures formed and mirrored cytosolic redox states, indicating that a more permeable shell architecture may be favorable when [CO2] is high. This work represents a step in understanding how cyanobacteria respond to changing CO2 concentrations and the selective forces driving carboxysome evolution.

biochemistry↗