Biology subjects

Shamsuzzaman, M.

Publications and source records attributed to Shamsuzzaman, M..

6 recordsLinked to original sources

bioRxiv2024

Role of Phage-Antibiotic Combinations in Reducing ESBL-Producing and Carbapenem-Resistant Escherichia coli

The emergence of extended-spectrum {beta}-lactamase (ESBL)-producing E. coli and carbapenem-resistant E. coli (CREC) poses a significant global health concern. Here, we isolated and characterized two novel phages and studied their effectiveness with antibiotics against ESBL-producing E. coli and CREC. The isolated phages, EC.W1-9 and EC.W15-4, belonged to the Podoviridae and Myoviridae families, respectively. They are safe for bacterial control as they do not contain integrase or toxin-coding genes. The phage combination considerably enhanced lytic ability, effectively lysing 61.7% of the 60 E. coli isolates, compared to lysis in the 41.6% -55% range by individual phages. Phages EC.W1-9 and EC.W15-4 combined demonstrated 100% susceptibility against different E. coli sequence types, including ST73, ST648, ST2311, ST405, ST7962, ST131, ST13003, and ST167. Additionally, studies showed synergy between antibiotics and phage combinations against ESBL-producing E.coli, with susceptibility of 73.3% and 54% for CREC. The combined treatment of isolated phages and antibiotics significantly increased survival rates in BALB/c mice exposed to various ST types of ESBL-producing E. coli and CREC, including ST131, ST648, and ST410. Survival rates against KBN7288 (ST131) increased by approximately 75% and 50% compared to individual phages EC.W1-9 and EC.W15-4, respectively. When phages and antibiotics were combined, survival rates against E. coli isolates KBN5617 (ST410), KBN6241 (ST410), and KBN4004 (ST648) ranged from 75% - 100%. Finally, this study highlights the importance of phage and phage-antibiotic combinations to prepare phages for killing different ST types of ESBL-producing E. coli and CREC isolates. IMPORTANCEWhen combined with antibiotics, phage therapy shows promise in fighting multidrug-resistant bacteria. However, antagonism between phages and antibiotics has been reported. This research isolates and characterizes two novel phages, EC.W1-9 and EC.W15-4, from the Podoviridae and Myoviridae families, respectively, and evaluates their effectiveness against ESBL-producing E. coli and CREC. These phages, lacking integrase or toxin-coding genes, showed significant promise in bacterial control. Combined phage treatment lysed 61.7% of E. coli isolates, outperforming individual phages. The phage combination showed 100% susceptibility against different E. coli sequence types. Additionally, the synergy between phages and antibiotics increased susceptibility rates to 73.3% for ESBL-producing E. coli and 54% for CREC. In BALB/c mice, combined treatments significantly improved survival rates against various E. coli isolates. Finally. this study emphasizes the potential of phage and phage-antibiotic combinations in targeting various ST types of ESBL-producing E. coli and CREC.

microbiology↗

bioRxiv2022

Inhibiting ribosome assembly and ribosome translation have distinctly different effects on the abundance and paralogue composition of ribosomal protein mRNAs in Saccharomyces cerevisiae

Many mutations in genes for ribosomal proteins and assembly factors cause cell stress and altered cell fate resulting in congenital diseases, collectively called ribosomopathies. Even though all such mutations depress the cells protein synthesis capacity, they generate many different phenotypes, suggesting that the diseases are not due simply to insufficient protein synthesis capacity. To learn more, we have investigated how the global transcriptome in Saccharomyces cerevisiae responds to reduced protein synthesis generated in two different ways: abolishing the assembly of new ribosomes or inhibiting ribosomal function. Our results show that the mechanism by which protein synthesis is obstructed affects the ribosomal protein transcriptome differentially: ribosomal protein mRNA abundance increases during the abolition of ribosome formation but decreases during the inhibition of ribosome function. Interestingly, the ratio between mRNAs from some, but not all, paralogous genes encoding slightly different versions of a given r-protein change differently during the two types of stress, suggesting that specific ribosomal protein paralogues may contribute to the stress response. Unexpectedly, the abundance of transcripts for ribosome assembly factors and translation factors remains relatively unaffected by the stresses. On the other hand, the state of the translation apparatus does affect cell physiology: mRNA levels for some other proteins not directly related to the translation apparatus also change differentially, though not coordinately with the r-protein genes, in response to the stresses. ImportanceMutations in genes for ribosomal proteins or assembly factors cause a variety of diseases called ribosomopathies. These diseases are typically ascribed to a reduction in the cells capacity for protein synthesis. Paradoxically, ribosomal mutations result in a wide variety of disease phenotypes, even though they all reduce protein synthesis. Here we show that the transcriptome changes differently depending on how the protein synthesis capacity is reduced. Most strikingly, inhibiting ribosome formation and ribosome function have opposite effects on the abundance of mRNA for ribosomal proteins, while genes for ribosome translation and assembly factors show no systematic responses. Thus, the process by which the protein synthesis capacity is reduced contributes decisively to global mRNA composition. This emphasis on process is a new concept in understanding ribosomopathies and other stress responses.

cell biology↗

bioRxiv2020

Mosaic changes to the global transcriptome in response to inhibiting ribosome formation versus inhibition of ribosome function

Cell fate is susceptible to several internal and external stresses. Stress resulting from mutations in genes for ribosomal proteins and assembly factors leads to many congenital diseases, collectively called ribosomopathies. Even though such mutations all depress the cells protein synthesis capacity, they are manifested in many different phenotypes. This prompted us to use Saccharomyces cerevisiae to explore whether reducing the protein synthesis capacity by different mechanisms result in the same or different changes to the global transcriptome. We have compared the transcriptome after abolishing the assembly of new ribosomes and inhibiting the translocation of ribosomes on the mRNA. Our results show that these alternate obstructions generate different mosaics of expression for several classes of genes, including genes for ribosomal proteins, mitotic cell cycle, cell wall synthesis, and protein transport.

genomics↗

bioRxiv2019

Interaction between the assembly of the ribosomal subunits: Disruption of 40S ribosomal assembly causes accumulation of extra-ribosomal 60S ribosomal protein uL18/L5

Inhibition of the synthesis of a ribosomal protein (r-protein) abrogates the assembly of its cognate subunit, while assembly of the other subunit continues. Ribosomal components that are not stably incorporated into ribosomal particles due to the disrupted assembly are rapidly degraded. The 60S protein uL18/L5 is an exception, because this protein accumulates extra-ribosomally during inhibition of 60S assembly. Since the r-proteins in each ribosomal subunit are essential only for formation of their own subunit, it would be predicted that accumulation of extra-ribosomal uL18/5 only occurs during restriction of 60S assembly, and not during abolition of 40S assembly. Contrary to this prediction, we report here that repression of 40S r-protein genes does in fact lead to accumulation of uL18/L5 does outside the ribosome due modified 60S assembly. Furthermore, the effect varies depending on which 40S ribosomal protein is repressed. We propose that disruption of early steps in the 40S subunit assembly changes the kinetics of 60S subunit assembly resulting in a buildup of extra-ribosomal uL18/L5, even though 60S formation continues. Finally, our results show that maintenance of the pool of extra-ribosomal uL18/L5 requires continual protein synthesis showing that extra-ribosomal protein is not stable, but is slowly \"consumed\" by incorporation into 60S subunits and/or turnover.

molecular biology↗

bioRxiv2018

The small and large ribosomal subunits depend on each other for stability and accumulation

The 1:1 balance between the numbers of large and small ribosomal subunits can be disturbed by mutations that inhibit the assembly of one of the subunits. We have investigated if the cell has mechanisms to counteract an imbalance of subunits. We show that accumulation of 40S subunits stops after abrogating 60S assembly. In contrast, cessation of the 40S pathways does not prevent 60S accumulation, but does, however, lead to fragmentation of the 25S rRNA in 60S subunits. Even though 40S subunits do not accumulate in the absence of 60S assembly, 40S assembly continues, indicating that excess 40S is degraded after assembly. Thus, the cell expends substantial resources in a futile attempt to increase the number of functional 80S ribosomes. We propose that a mechanism for preventing the accumulation of 40S subunits in excess over 60S subunits may have evolved to prevent mRNAs from being tied up in 40S-mRNA translation initiation complexes that cannot be turned into productive translation complexes because of the deficit of 60S subunits.

molecular biology↗

bioRxiv2017

Transcriptome analysis reveals the differences between cellular response to ribosomal stress and translational stress

Ribosome biogenesis is an essential metabolic process of a growing cell. Cells need to continuously synthesize new ribosomes in order to make new proteins than can support building biomass and cell division. It is obvious that in the absence of ribosome biogenesis, cell growth will stop and cell division will stall. However, it is not clear whether cell growth stops due to reduced protein synthesis capacity (translational stress) or due to activation of signaling specific to ribosome biogenesis abnormalities (ribosomal stress). To understand the signaling pathways leading to cell cycle arrest under ribosomal and translational stress conditions, we performed time series RNA-seq experiments of cells at different time of ribosomal and translational stress. We found that expression of ribosomal protein genes follow different course over the time of these two stress types. In addition, ribosomal stress is sensed early in the cell, as early as 2hr. Up-regulation of genes responsive to oxidative stress and over representation of mRNAs for transcription factors responsive to stress was detected in cell at 2hr of ribosomal protein depletion. Even though, we detected phenotypic similarities in terms of cell separation and accumulation in G1 phase cells during inhibition of ribosome formation and ribosome function, different gene expression patterns underlie these phenotypes, indicating a difference in causalities of these phenotypes. Both ribosomal and translational stress show common increased expression of stress responsive gene expression, like Crz1 target gene expression, signature of oxidative stress response and finally membrane or cell wall instability. We speculate that cell membrane and cell wall acts as major stress sensor in the cell and adjust cellular metabolism accordingly. Any change in membrane lipid composition, or membrane protein oxidation, or decrease or increase in intracellular turgor pressure causes stress in cell membrane. Cell membrane or cell wall stress activates and/or inactivates specific signaling pathway which triggers stress responsive gene expression and adaptation of cellular behavior accordingly.

genomics↗