Microbial Community Analysis of Anaerobic Enrichment Cultures Supplemented with Bacterial Peptidoglycan as the Sole Substrate

Methanogenic microbial communities were enriched from rice paddy soil and anaerobic digester sludge using peptidoglycan purified from gram-negative Escherichia coli or gram-positive Micrococcus luteus as the sole substrate. Methane production data suggested the anaerobic degradation of peptidoglycan and also that peptidoglycan from E. coli had lower degradability. The community structures of enrichment cultures fed peptidoglycan from E. coli or M. luteus were similar, but distinctly different. A number of phylogenetically novel and uncultured bacteria, particularly in the phyla Bacteroidetes. WWE1. Armatimonadetes, and Verrucomicrobia, dominated the enrichment cultures, suggesting their involvement in anaerobic peptidoglycan degradation

Spatio-temporal assessment and trend analysis of surface water salinity in the coastal region of Bangladesh

The study was designed to collect water samples over two seasons-wet-monsoon season (n = 96) (March-April) and dry-monsoon season (n = 44) (September October)-to understand the seasonal variation in anion and cation hydrochemistry of the coastal rivers and estuaries contributing in the spatial trend in salinity. Hydrochemical examination of wet-monsoon season primarily revealed Ca-MgHCO3 type (66%) and followed by Na-Cl type (17.70%) water. In the dry-monsoon season, the scenario reversed with primary water being Na-Cl type (52.27%) followed by Ca-Mg-HCO3 type (31.81%). Analysis of Cl/Br molar ratio vs. Cl (mg/L) depicted sampling area affected by seawater intrusion (SWI). Spatial analysis by ordinary kriging method confirmed approximately 77% sample in the dry-monsoon, and 34% of the wet-monsoon season had shown SWI. The most saline-intruded areas in the wet-monsoon seasons were extreme south-west coastal zone of Bangladesh, lower Meghna River floodplain and Meghna estuarine floodplain and southeastern part of Chittagong coastal plains containing the districts of Chittagong and Cox's Bazar adjacent to Bay of Bengal. In addition, mid-south zone is also affected slightly in the dry-monsoon season. From the analyses of data, this study could further help to comprehend seasonal trends in the hydrochemistry and water quality of the coastal and estuarine rivers. In addition, it can help policy makers to obligate some important implications for the future initiatives taken for the management of land, water, fishery, agriculture and environment of coastal rivers and estuaries of Bangladesh

Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages

Deazaguanine modifications play multifaceted roles in the molecular biology of DNA and tRNA, shaping diverse yet essential biological processes, including the nuanced fine-tuning of translation efficiency and the intricate modulation of codon-anticodon interactions. Beyond their roles in translation, deazaguanine modifications contribute to cellular stress resistance, self-nonself discrimination mechanisms, and host evasion defenses, directly modulating the adaptability of living organisms. Deazaguanine moieties extend beyond nucleic acid modifications, manifesting in the structural diversity of biologically active natural products. Their roles in fundamental cellular processes and their presence in biologically active natural products underscore their versatility and pivotal contributions to the intricate web of molecular interactions within living organisms. Here, we discuss the current understanding of the biosynthesis and multifaceted functions of deazaguanines, shedding light on their diverse and dynamic roles in the molecular landscape of life

Mapping the tRNA modification landscape of Bartonella henselae Houston I and Bartonella quintana Toulouse

Transfer RNA (tRNA) modifications play a crucial role in maintaining translational fidelity and efficiency, and they may function as regulatory elements in stress response and virulence. Despite their pivotal roles, a comprehensive mapping of tRNA modifications and their associated synthesis genes is still limited, with a predominant focus on free-living bacteria. In this study, we employed a multidisciplinary approach, incorporating comparative genomics, mass spectrometry, and next-generation sequencing, to predict the set of tRNA modification genes responsible for tRNA maturation in two intracellular pathogens—Bartonella henselae Houston I and Bartonella quintana Toulouse, which are causative agents of cat-scratch disease and trench fever, respectively. This analysis presented challenges, particularly because of host RNA contamination, which served as a potential source of error. However, our approach predicted 26 genes responsible for synthesizing 23 distinct tRNA modifications in B. henselae and 22 genes associated with 23 modifications in B. quintana. Notably, akin to other intracellular and symbiotic bacteria, both Bartonella species have undergone substantial reductions in tRNA modification genes, mostly by simplifying the hypermodifications present at positions 34 and 37. Bartonella quintana exhibited the additional loss of four modifications and these were linked to examples of gene decay, providing snapshots of reductive evolution

Structural basis of Qng1-mediated salvage of the micronutrient queuine from queuosine-5'-monophosphate as the biological substrate

Eukaryotic life benefits from—and ofttimes critically relies upon—the de novo biosynthesis and supply of vitamins and micronutrients from bacteria. The micronutrient queuosine (Q), derived from diet and/or the gut microbiome, is used as a source of the nucleobase queuine, which once incorporated into the anticodon of tRNA contributes to translational efficiency and accuracy. Here, we report high-resolution, substrate-bound crystal structures of the Sphaerobacter thermophilus queuine salvage protein Qng1 (formerly DUF2419) and of its human ortholog QNG1 (C9orf64), which together with biochemical and genetic evidence demonstrate its function as the hydrolase releasing queuine from queuosine-5′-monophosphate as the biological substrate. We also show that QNG1 is highly expressed in the liver, with implications for Q salvage and recycling. The essential role of this family of hydrolases in supplying queuine in eukaryotes places it at the nexus of numerous (patho)physiological processes associated with queuine deficiency, including altered metabolism, proliferation, differentiation and cancer progression