Current Genetics最新文献

The wide ecological distribution of actinobacteria suggests that they have developed efficient mechanisms to adapt to extremely nutritionally deficient (oligotrophic) conditions. The impact of nutrient limitation typically observed in oligotrophic areas on bacteria remains to be assessed for many species. The non-model Rhodococcus aetherivorans L13can grow under oligotrophic conditions, even without an added carbon source. Oligotrophic cells of L13 undergo physiological and morphological changes compared to glucose-grown cells, including forming short-fragmenting cells, producing an extracellular polymeric substance, and a 26-fold decrease in respiratory activity. We conducted genome sequencing of L13 and assembled the entire genome, subsequently comparing the abundance of gene transcripts in oligotrophic cells to those of glucose-grown cells, to explore the oligotrophy-responsive mechanisms at the genetic level. The genome comprises 6,543,485 base pairs, distributed across a single chromosome and six extrachromosomal plasmids (one linear and five circular). RNA-Seq analysis revealed the significant dysregulation of 2,665 genes (44% of the total genes detected). Results suggested a profound reorganization of its carbon and energy metabolism, including the activation of (i) mechanisms for utilizing air components; (ii) various dehydrogenases involved in aldehyde and alcohol metabolism, (iii) several enzymes involved in C2 metabolism, glyoxylate shunt, and TCA bypass routes, and downregulation of several genes that encode CO₂ releasing-decarboxylase enzymes. Our results suggested that the adaptation strategy of L13 to oligotrophic conditions is supported by a combination of metabolic events, including low metabolic activity, the activation of C2 and ketoacids metabolism, and the display of a carbon conservative metabolic program.

Bacillus thuringiensis is a prominent, eco-friendly entomopathogenic bacterium used as a plant-incorporated toxin in genetically modified crops and as a stomach poison for insects in the form of spore formulations. Upon entering the alkaline environment of the insect gut, the toxin undergoes proteolytic breakdown, converting the protoxin into its activated form. The activated toxin then binds to receptors, forming pores that disrupt the ionic balance within the cell, ultimately leading to the insect's death. Alongside the four major receptors (Cadherin, ABCC, APN, and ALP), several other notable receptors are present on the Brush Border Membrane Vesicle of insects. Binding to these receptors plays a crucial role, and any mutations in these receptors can result in improper binding, leading to the development of resistant insect strains. This review explores the major receptors of insecticidal Cry toxins, the intricate interactions between toxins and receptors, receptor mutations, and strategies to overcome the resistance.

It was reported that yeast proteins Ssz1 and Upf1 can cure certain [PSI⁺] variants in wild-type cells and there is a special class of variants whose propagation requires the triple mutation of ssz1∆ upf1∆ Hsp104^T160M. Attempts to isolate variants with the exact properties from the 74-D694 strain (and tested there) are not yet successful. The effort nevertheless leads to an alternative analysis about how ssz1∆ and upf1∆ mutations can help prion propagation. The cellular propagation of the yeast prion [PSI⁺] requires appropriate activities of the Hsp104 disaggregase. Many [PSI⁺] variants isolated in wild-type strains cannot propagate in cells expressing Hsp104^T160M, which has weaker activities. Yet another group of [PSI⁺] variants shows the opposite, propagating well with Hsp104^T160M but is eliminated by the wild-type protein. Deletion of SSZ1 and UPF1 genes in Hsp104^T160M cells generates a just-right environment that supports the propagation of both types of [PSI⁺] variants. The pro-prion effect is not due to the removal of active curing by Ssz1 or Upf1-such curing activity is not observed for the variants. Rather, the double deletion causes a cellular response, which enables more efficient fragmentation of prion fibers, thus remedying the weak activity of Hsp104^T160M. The "Goldilocks" conditioning seems also applicable to other yeast prions. Two [PIN⁺] variants that propagate well with wild-type Hsp104 but poorly with Hsp104^∆N, lacking residues (2-147), can however thrive with the latter if Ssz1 and Upf1 are also deleted from the cell. In this case, the double deletion results in higher Hsp104^∆N expression, leading to improved generation of prion seeds for robust propagation.

There is great interest in establishing microalgae as new platforms for the sustainable production of high-value products such as recombinant proteins. Many human therapeutic proteins must be glycosylated, which requires their passage through the secretory pathway into the culture medium. While the low complexity of proteins in the culture medium should facilitate affinity purification of secreted recombinant proteins, this has proven challenging for proteins secreted by the unicellular green alga Chlamydomonas reinhardtii. In Leishmania tarentulae, we observed that C-terminally exposed affinity tags are frequently truncated, presumably due to proteolytic activity. We wondered whether this might also occur in Chlamydomonas and contribute to the difficulties in affinity purification of secreted proteins in this alga. Using the methionine-rich 2S albumin from Bertholletia excelsa and the ectodomain of the SARS-CoV-2 spike protein produced and secreted in Chlamydomonas, we demonstrate that they can be efficiently affinity-purified from the culture medium by Ni-NTA chromatography when the 8xHis affinity tag is internalized. This finding represents an important step towards further development of Chlamydomonas as a host for the sustainable production of high-value recombinant proteins.

The bacterial strain HT11 isolated from broad bean (Vicia faba L.) exhibited strong antifungal activity against Botrytis fabiopsis, the causative agent of red spot disease in broad bean. To gain insights into the secondary metabolites produced by HT11,its entire genome was sequenced and subjected to comprehensive analysis. The genome comprised a single circular chromosome of 6,335,588 base pairs (bp) in length. Comparative analysis of the 16 S rRNA gene and the average nucleotide identity (ANI) confirmed the HT11 strain as a new Pseudomonas strain. The complete genome encoded 5,366 predicted open reading frames (ORFs), 66 tRNA genes and 16 rRNA genes. The total length of the annotated genes accounted for 82.93% (5,254,103/6,335,588 bp) of the complete genome. Functional categorization of the predicted ORFs revealed 24 Clusters of Orthologous Groups of proteins (COG). Fourteen gene clusters were identified with in the genome, associated with the biosynthesis of pyochelin, pyocyanin, viscosin, and tolaasin I/tolaasin F. Additionally, three gene clusters were implicated in the biosynthesis of unknown metabolites. These findings establish a foundational basis for further investigations into the interactions between Pseudomonas sp. HT11 and the pathogenic fungus Botrytis fabiopsis.

The Staphylococcus genus, composed of Gram-positive bacteria, includes several pathogenic species such as Staphylococcus aureus, S. epidermidis, S. haemolyticus, and S. saprophyticus, each implicated in a range of infections. This study investigates the codon usage patterns in key virulence genes, including Autolysin (alt), Elastin Binding protein (EbpS), Lipase, Thermonuclease, Intercellular Adhesion Protein (IcaR), and V8 Protease, across four Staphylococcus species. Using metrics such as the Effective Number of Codons (ENc), Relative Synonymous Codon Usage (RSCU), Codon Adaptation Index (CAI), alongside neutrality and parity plots, we explored the codon preferences and nucleotide composition biases. Our findings revealed a pronounced AT-rich codon preference, with AT-rich genomes likely aiding in energy-efficient translation and bacterial survival in host environments. These insights provide a deeper understanding of the evolutionary adaptations and translational efficiency mechanisms that contribute to the pathogenicity of Staphylococcus species. This knowledge could pave the way for novel therapeutic interventions targeting codon usage to disrupt virulence gene expression.

Dental plaque biofilms are the primary etiologic factor for various chronic oral infectious diseases. In recent years, dental plaque shows enormous potential to know about an individual microbiota. Various microbiome studies of oral cavity from different geographical locations reveals abundance of microbial species. Although, the representation of Indian population in this respect is limited, which make us curious to undergo this study. This study investigates the dental plaque microbiota of North Indian individuals based on their age, gender, and dietary patterns; specifically, food preference and availability of water source using 16 S rRNA metagenomics analysis. The findings from this study revealed that Streptococcus levels are high across genders, age groups, and water source, highlighting its role as a predominant dental caries associated species like Streptococcus mutans, Streptococcus pyogenes, Streptococcus sobrinus and Streptococcus oralis in the studied population groups. Additionally, the abundance of Actinomyces is observed higher in young individuals and females whereas Fusobacterium and Leptotrichia were high in elderly individuals. Moreover, non-vegetarians have higher abundance of Streptococcus and Fusobacterium, whereas vegetarians show higher abundance of Prevotella and Leptotrichia. The study also highlights the influence of water type on bacterial composition of dental plaque in the studied population i.e., individuals consuming underground water has high abundance of Streptococcus, whereas individuals consuming RO water exhibit elevated Prevotella and Leptotrichia. Insights emerged from the analysis illuminates the complex dynamics of microbiota in dental plaque among North Indians. This study also highlight that this variation of microbiome is influenced by age, gender, and dietary habits (vegetarian or non-vegetarian lifestyle). These results will fill a significant knowledge gap regarding the Indian dental plaque microbiome but also offer a foundation to conduct metagenome studies and potential therapeutic implications for future personalized oral health interventions.

Carbapenem-resistant Acinetobacter baumannii (CRAB) is an emerging threat to healthcare settings in many countries, principally in South Asia. The current study was aimed to identify, evaluate whole-genome and characterize the prophages in genome of CRAB strain, recovered from patients of Lahore General Hospital, Lahore. More than 200 samples were collected and identified by morphological and biochemical tests. These strains were also subjected to a comprehensive antimicrobial susceptibility evaluation using Kirby-Bauer method and further confirmed as CRAB strains by exploring bla_OXA-51. In addition, the whole-genome evaluation of a Acinetobacter baumannii UOL-KIMZ-24-2 was carried out using various Bioinformatics tools. A total of 150 strains of A. baumannii were recovered and identified in the current study. Among them, 49% strains were found resistant to carbapenem. The bla_OXA-51 was found prevalent in the genome of A. baumannii recovered from medical ICU (38%). In addition, the UOL-KIMZ-24-2 genome analysis based on multilocus sequence typing (MLST) highlighted that UOL-KIMZ-24-2 belonged to ST2 (Pasteur scheme) sequence type. A total of 29 antimicrobial resistance (AMR) genes were present, importantly, bla_OXA-66, bla_OXA-23 and bla_OXA-25. The mobile genetic elements (MGEs) were identified as transposases and belonged to four classes e.g. IS15d1, ISAba24, ISEc29, and ISEc35. A total of 14 virulence factors encoded by 58 different genes were detected in UOL-KIMZ-24-2. In addition, the phage sequences were identified in genome of UOL-KIMZ-24-2, divided into 3 regions. In conclusion, UOL-KIMZ-24-2 contained a mixture of AMR genes, MGEs. prophages sequences and virulence genes.

Basic helix-loop-helix domains in yeast regulatory proteins Ino2 and Ino4 mediate formation of a heterodimer which binds to and activates expression of phospholipid biosynthetic genes. The human proto-oncoprotein c-Myc (Myc) and its binding partner Max activate genes important for cellular proliferation and contain functional domains structure and position of which strongly resembles Ino2 and Ino4. Since Ino2-Myc and Ino4-Max may be considered as orthologs we performed functional comparisons in yeast. We demonstrate that Myc and Max could be stably synthesized in S. cerevisiae and together significantly activated a target gene of Ino2/Ino4 but nevertheless were unable to functionally complement an ino2 ino4 double mutant. We also map two efficient transcriptional activation domains in the N-terminus of Myc (TAD1: aa 1-41 and TAD2: aa 91-140), corresponding to TAD positions in Ino2. We finally show that coactivators such as TFIID subunits Taf1, Taf4, Taf6, Taf10 and Taf12 as well as ATPase subunits of chromatin remodelling complexes Swi2, Sth1 and Ino80 previously shown to interact with TADs of Ino2 were also able to bind TADs of Myc, supporting the view that heterodimers Ino2/Ino4 and Myc/Max are evolutionary related but have undergone transcriptional rewiring of target genes.

Wastewater is a reservoir of pathogens and hotspots for disseminating antibiotic resistance genes across species. The metagenomic surveillance of wastewater provides insight into the native microbial community, antibiotic-resistance genes (ARGs) and mobile genetic elements. t. The COVID-19 pandemic has caused wider dissemination of ARGs and resistant bacteria in wastewater. Although immensely significant, no research has been performed on the Malaysian wastewater microbial community and ARGs or their correlation with COVID-19 infections. This study utilised a 16S metagenomics approach to characterise the microbial community in Malaysian wastewater during high and low-case phases of the pandemic. Bacteria belonging to Bacteriodales, Bacillales, Actinomycetales and opportunistic pathogens-Arcobacters, Flavobacteria, and Campylobacterales, Neisseriales, were enriched during higher COVID-19 pandemic (active cases). Additionally, copy number profiling of ARGs in water samples showed the prevalence of elements conferring resistance to antibiotics like sulphonamides, cephalosporins, and colistin. The high prevalence of intI1 and other ion-based transporters in samples highlights an extensive risk of horizontal gene transfer to previously susceptible species. Our study emphasises the importance of wastewater surveillance in understanding microbial community dynamics and ARG dissemination, particularly during public health crises like the COVID-19 pandemic.