Highlighted articles published by İTÜ Molecular Biology and Genetics Department in 2024

1. The study entitled “PIN1 is a novel interaction partner and a negative upstream regulator of the transcription factor NFIB”, first authored by PhD candidate Sinem Sarıtaş Erdoğan, from the research group of Assoc. Prof. Dr. Aslı Kumbasar, was published in the FEBS Letters (ranked as a Q1 journal in the Scopus index) as a research article. 

NFIB is a transcription factor of the Nuclear Factor One (NFI) family that is essential for embryonic development and is implicated in various pathologies, including cancer, when dysregulated. Despite its importance, the mechanisms of NFIB’s post-translational regulation and upstream modulators remain poorly understood. This study identified PIN1 as a novel interaction partner of NFIB and demonstrated its ability to suppress NFIB’s transcriptional activity. Surprisingly, this repression does not depend on PIN1’s enzymatic activity, even though the interaction is phosphorylation-dependent. Intriguingly, PIN1 stabilizes NFIB, suggesting that it modulates NFIB function through conformational changes rather than altering its abundance. These findings unveil a previously unrecognized post-translational regulation for NFIB and potentially other NFI members.

For more information:  https://doi.org/10.1002/1873-3468.15010

2. The interdisciplinary study entitled “Transcriptomic and Physiological Meta-Analysis of Multiple Stress-Resistant Saccharomyces cerevisiae Strains”, conducted by the  research groups of Prof. Dr. Zeynep Petek Çakar (ITU Molecular Biology and Genetics Department) and Assoc. Prof. Dr. Mehmet Baysan (ITU Computer Engineering Department) was published in the international journal “Stresses” (ranked as a Q1 journal in the Scopus index), as an invited article.

The research focused on re-evaluating diverse stress-resistant S. cerevisiae strains developed through adaptive laboratory evolution, to reveal the correlated stress/stressor clusters based on their transcriptomic and stress–cross-resistance data. Using principal component analysis (PCA) and k-means clustering, the team identified common genes and pathways linked to stress resistance. These findings were further analyzed using the KEGG database to associate key pathways with stress responses.

Notably, the study demonstrated that caffeine and coniferyl aldehyde stressors show distinct physiological and transcriptomic profiles compared to other stress factors. Pathway analysis results indicated common downregulation in ribosome biogenesis and upregulation of starch and sucrose metabolism across clusters. Various genes impacting distinct pathways were identified as significant for each cluster and their associations with stress factors were established. Several of the highlighted genes are pivotal for further exploration and could potentially clarify new aspects of stress response mechanisms and multiple stress-resistance in yeast.

For more information: https://doi.org/10.3390/stresses4040046

3. Evolutionary engineering and molecular characterization of cobalt-resistant Rhodobacter sphaeroides

Prof. Dr. Zeynep Petek Çakar's research group at İTÜ has been successfully improving resistance of microbial cells to various industrial stress types. For this purpose, the research group has been employing the highly effective inverse metabolic engineering approach known as adaptive laboratory evolution or evolutionary engineering. The stress responses and resistance exhibited by microbial cells during the evolutionary engineering process alter their typical physiological behavior. It is imperative to identify the metabolic and molecular differences between the original and evolved microbial cells to develop microorganisms that exhibit improved characteristics relevant to industrial applications.

In this recent international collaborative study resulting from the COST Action CM0902 (with Dr. Massimo Trotta from IPCF-CNR Bari, Italy) published by the prestigious international journal Frontiers in Microbiology (a Q1 journal according to Scopus index), Prof. Çakar’s group and her collaborators developed a cobalt-resistant Rhodobacter sphaeroides strain by evolutionary engineering and characterized the evolved strain at the genomic and physiological levels.

R. sphaeroides is an important photosynthetic purple non-sulfur bacterium, as it has a high adaptation ability that allows it to grow in diverse nutritional and environmental conditions, including heavy-metal-polluted environments. R. sphaeroides is able to fix CO₂ and N₂, and produce H₂ and polyhydroxybutyrate (PHB). It has a significant biotechnological potential regarding bio-based production of chemicals and fuels and bioremediation. Cobalt is an industrially important element with magnetic properties and a variety of applications, including refining of alloys, production of gas turbines, jet engines, electrochemical materials and permanent magnets as well as its use in the cathodes of lithium-ions batteries of highly demanded electric vehicles, to tackle the global warming issue. However, as a transition metal, cobalt is toxic to living organisms at high concentrations. The highly cobalt-resistant and genetically stable evolved R. sphaeroides strain developed in this study was unaffected from toxic levels of cobalt, and higher levels of cobalt ions were associated with the evolved strain than the reference strain. This may imply that cobalt ions accumulated in or on the evolved strain, indicating the potential of the evolved strain for cobalt bioremediation. Whole genome sequencing of the evolved strain identified 23 single nucleotide polymorphisms in various genes that are associated with transcriptional regulators, NifB family-FeMo cofactor biosynthesis, putative virulence factors, TRAP-T family transporter, sodium/proton antiporter, and also in genes with unknown functions, which may have a potential role in the cobalt resistance of R. sphaeroides.

For more information: https://doi.org/10.3389/fmicb.2024.1412294

4. Within the scope of Aycan Kayrav's MSc thesis, the article “Revealing the role of the X25 domains through the characterization of truncated variants of amylopullulanase enzyme from Thermoanaerobacter brockii brockii” supervised by Prof. Dr. Nevin Gül Karagüler in the Department of Molecular Biology & Genetics was published in the International Journal of Biological Macromolecules.

Today, more than 3.000 enzymes are used in industrial fields. However, the usage of enzymes in the industry is limited because of the loss of the stability of enzymes under harsh industrial process conditions. The discovery of extremophilic organisms and their extremozymes, together with protein engineering studies, helps to overcome this problem. In our previous study, the amylopullulanase (apu) enzyme from the thermophilic, anaerobic bacterium Thermoanaerobacter brockii brockii (tbb), and its two truncated variants were recombinantly produced and characterized to be used in the starch industry (Mumcu et al. 2023). In this paper, for the first time, the role of the X25 domains of the tbbapu enzyme was revealed by the construction of four more truncated variants using protein engineering studies. Sequence alignment, characterization, and structural studies of these six truncated variants of the Tbbapu enzyme all prove that the X25 domains are a strong carbohydrate-binding domain candidate. It was also represented that, the X25 domains play an important role in the stability of the enzyme against thermal, detergent, inhibitors, and organic solvents in industrial applications. 

For further information:

DOI: 10.1016/j.ijbiomac.2024.132404

DOI: 10.1016/j.enzmictec.2022.110176