Biology subjects

Kopejtka, K.

Publications and source records attributed to Kopejtka, K..

3 recordsLinked to original sources

bioRxiv2025

Particle attachment drives seasonal abundance and photoheterotrophy of marine aerobic anoxygenic phototrophs

BackgroundAerobic Anoxygenic Phototrophic (AAP) bacteria are an essential component of aquatic microbial communities and play an important role in carbon cycling due to their ability to supplement their chemoorganotrophic metabolism with light-derived energy. While most of the previous studies focused on abundance, species composition and seasonal changes of AAP bacteria, their affinity for the particle-attachment did not attract much attention. Similarly, it remains unclear whether the entire AAP community is phototrophically active. This study investigated the seasonal changes in the composition of free-living and particle-attached AAP bacteria in the central Adriatic Seas coastal waters using both DNA and RNA pufM amplicon gene sequencing in the particle-attached and the free-living fractions. ResultsAAP bacterial abundance grew from 1.27 x 104 cells mL-1 in winter to 8.30 x 104 cells mL-1 in summer. The proportion of AAP bacteria was consistently higher in the particle-attached fraction, particularly in spring and summer. DNA and RNA pufM amplicon analyses revealed large differences in activity among the species forming the AAP communities. Additionally, DNA-based assessments underestimated the phototrophic activity of certain genera, demonstrating discrepancies between the gene presence and its functional activity. ConclusionsOur data demonstrated that the expression of phototrophic genes in AAP bacteria is not uniform and largely varies throughout seasons and fractions. The particle-attached fraction harboured more than twice as many active AAP bacteria as the free-living fraction, with seasonal shifts and lifestyle driving changes in the phototrophy gene expression. RNA and DNA libraries revealed discrepancies between total and active AAP bacterial communities, emphasizing the necessity of transcript-based approaches for accurately assessing photoheterotrophic activity in marine environments. The pronounced partitioning of AAP bacterial diversity and activity between free-living and particle-attached fractions indicated the ecological specialization of certain AAP lineages, which may have noteworthy implications for the consumption of particulate organic matter and, ultimately, carbon cycling in coastal waters.

microbiology↗

bioRxiv2024

On the Evolution of Chromosomal Regions with High Gene Strand Bias in Bacteria

On circular bacterial chromosomes, the majority of genes are coded on the leading strand. This gene strand bias (GSB) ranges from up to 85% in some Bacillota to little more than 50% in other phyla. The factors defining the extent of the GSB remain to be found. Here, we report that species in the phylum Gemmatimonadota share a unique chromosome architecture, distinct from neighboring phyla: In a conserved 600 kb region around the terminus of replication, almost all genes were located on the leading strands while on the remaining part of the chromosome the strand preference was more balanced. The high strand bias (HSB) region harbors the rRNA clusters, core, and highly expressed genes. Selective pressure for reduction of collisions with DNA replication to minimize detrimental mutations can explain the conservation of essential genes in this region. Repetitive and mobile elements are underrepresented, suggesting reduced recombination frequency by structural isolation from other parts of the chromosome. We propose that the HSB region forms a distinct chromosomal domain. Gemmatimonadota chromosomes evolved mainly by expansion through horizontal gene transfer and duplications outside of the ancient HSB region. In support of our hypothesis, we could further identify two Spiroplasma strains on a similar evolutionary path. ImportanceOn bacterial chromosomes, a preferred location of genes on the leading strand has evolved to reduce conflicts between replication and transcription. Despite a vast body of research, the question why bacteria show large differences in their GSB is still not solved. The discovery of hybrid chromosomes in different phyla, including Gemmatimonadota, in which a conserved high GSB is found exclusively in a region at ter, points towards a role of nucleoid structure, additional to replication, in the evolution of strand preferences. A fine-grained structural analysis of the ever-increasing number of available bacterial genomes could help to better understand the forces that shape the sequential and spatial organization of the cells information content.

evolutionary biology↗

bioRxiv2022

The development of intracytoplasmic membranes in alphaproteobacteria involves the conserved mitochondrial crista-developing Mic60 protein

Mitochondrial cristae expand the surface area of respiratory membranes and ultimately allow for the evolutionary scaling of respiration with cell volume across eukaryotes. The discovery of Mic60 homologs among alphaproteobacteria, the closest extant relatives of mitochondria, suggested that cristae might have evolved from bacterial intracytoplasmic membranes (ICMs). Here, we investigated the predicted structure and function of alphaproteobacterial Mic60, and a protein encoded by an adjacent gene Orf52, in two distantly related purple alphaproteobacteria, Rhodobacter sphaeroides and Rhodopseudomonas palustris. In addition, we assessed the potential physical interactors of Mic60 and Orf52 in R. sphaeroides. We show that the three -helices of mitochondrial Mic60s mitofilin domain, as well as its adjacent membrane-binding amphipathic helix, are present in alphaproteobacterial Mic60. The disruption of Mic60 and Orf52 caused photoheterotrophic growth defects, which are most severe under low light conditions, and both their disruption and overexpression led to enlarged ICMs in both studied alphaproteobacteria. We also found that alphaproteobacterial Mic60 physically interacts with BamA, the homolog of Sam50, one of the main physical interactors of eukaryotic Mic60. This interaction, responsible for making contact sites at mitochondrial envelopes, has been conserved in modern alphaproteobacteria despite more than a billion years of evolutionary divergence. Our results suggest a role for Mic60 in photosynthetic ICM development and contact site formation at alphaproteobacterial envelopes. Overall, we provide support for the hypothesis that mitochondrial cristae evolved from alphaproteobacterial ICMs, and therefore have improved our understanding of the nature of the mitochondrial ancestor.

evolutionary biology↗