Biology subjects

Saha, M. S.

Publications and source records attributed to Saha, M. S..

4 recordsLinked to original sources

bioRxiv2025

A novel phage satellite class induces prophage excision in Mycolicibacterium aichiense

Phage satellites are mobile genetic elements that parasitize a helper phage to complete their life cycle. While phage satellites are widespread in diverse bacterial hosts, none have been isolated in Mycobacteriaceae. Here, we report the first phage satellites isolated and characterized in Mycobacteriaceae, Extracellular Prophage-Inducing Particles (EPIPs). EPIPs induce a helper phage--HerbertWM, a Mycolicibacterium aichiense prophage--upon infection. Genomic sequencing of thirteen isolates revealed a notably small genome size and high sequence similarity between EPIPs, suggesting they are a distinct class of phage satellite. EPIPs were categorized into groups based on Virus Intergenomic Distance Calculator similarity scores, gene content, and synteny. Gene content is largely conserved across the isolates, though EPIPs notably lack capsid proteins, tail proteins, and holins, suggesting EPIPs hijack the machinery of HerbertWM to replicate, assemble, and lyse the host. Furthermore, the unique gene content of EPIPs compared to other phage satellites, particularly the presence of a tape measure protein and absence of antirepressors, suggests they may exhibit unique mechanisms of assembly and prophage induction. Transmission electron microscopy of EPIPs reveals that they not only feature smaller capsids compared to HerbertWM, but that they feature longer tails of variable length, further suggesting a unique mechanism of tail hijacking that the tape measure protein may facilitate. Additionally, greater EPIP protein similarity to prophage proteins as opposed to free phage proteins suggests a functional or evolutionary relationship may exist. The synteny among EPIPs and the unique gene content suggest EPIPs are a distinct class of phage satellites that induce Mycobacteriaceae prophages.

microbiology↗

bioRxiv2025

Survival and Spread of Engineered Mycobacterium smegmatis and Associated Mycobacteriophage in Soil Microcosms

The inoculation of microbes into soil environments has numerous applications for improving soil quality and crop health; however, the ability of exogenous and engineered microbes to survive and spread in soil remains uncertain. To address this challenge, we assayed the survival and spread of Mycobacterium smegmatis, engineered with either plasmid transformation or genome integration, as well as its mycobacteriophage Kampy, in both sterilized and non-sterilized soil microcosms over a period of 49 days. While engineered M. smegmatis and Kampy persisted in all soil microcosms, there was minimal evidence of spread to 5 cm away from the inoculation site. There was a higher prevalence of Kampy observed in sterilized soil than non-sterilized soil, suggesting a detrimental effect of the native soil biotic and viral community on the ability of this phage to proliferate in the soil microcosm. Additionally, higher abundance of the genome-integrated bacteria relative to the plasmid-carrying bacteria as well as evidence for loss of plasmid over the duration of the experiment suggest a burden associated with bacteria harboring plasmids, although plasmids were still retained across 49 days. To our knowledge, this is the first study to simultaneously measure the persistence and spread of bacteria and their associated phage in both sterilized and non-sterilized soil microcosms, employing bacteria with plasmid-based and genome-integrated engineered circuits. As such, this study provides a novel understanding of challenges associated with the deployment of bioengineered microbes into soil environments. ImportanceHealthy soil is essential to sustain life, as it provides habitable land, enables food production, promotes biodiversity, sequesters and cycles nutrients, and filters water. Given the prevalence of soil degradation, treatment of soil with microbes that promote soil and crop health could improve global soil sustainability; furthermore, the application of bioengineering and synthetic biology to these microbes allows fine-tunable and robust control of gene-of-interest expression. These solutions require the successful deployment of bacteria into the soil, an environment in which abundant competition and often limited nutrients can result in bacterial death or dormancy. This study employs Mycobacterium smegmatis as a chassis alongside its bacteriophage Kampy in soil microcosms to assess the ability of non-native microbes to survive and spread in soil. Insights from this experiment highlight important challenges which must be overcome for successful deployment of engineered microbes in the field.

microbiology↗

bioRxiv2021

Crowdsourcing biocuration: the Community Assessment of Community Annotation with Ontologies (CACAO)

Experimental data about known gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a ten-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills. Significance StatementThe primary scientific literature catalogs the results from publicly funded scientific research about gene function in human-readable format. Information captured from those studies in a widely adopted, machine-readable standard format comes in the form of Gene Ontology annotations about gene functions from all domains of life. Manual annotations based on inferences directly from the scientific literature, including the evidence used to make such inferences, represents the best return on investment by improving data accessibility across the biological sciences. To supplement professional curation, our CACAO project enabled annotation of the scientific literature by community annotators, in this case undergraduates, which resulted in contribution of thousands of validated entries to public resources. These annotations are now being used by scientists worldwide.

bioinformatics↗

bioRxiv2018

The Genetic Insulator RiboJ Increases Expression of Insulated Genes

The self-cleaving ribozyme RiboJ is an insulator commonly used in genetic circuits to prevent unexpected interactions between neighboring parts. These interactions can compromise the modularity of the circuit, impeding the implementation of predictable genetic constructs. Despite its utility as an insulator, a quantitative assessment of the effect of RiboJ on the properties of downstream genetic parts is lacking. Here, we characterized the impact of insulation with RiboJ on expression of a reporter gene driven by a promoter from a library of 24 frequently employed constitutive promoters. We show that depending on the strength of the promoters, insulation with RiboJ increased protein abundance between twofold and tenfold and increased transcript abundance by an average of twofold. This result is the first to demonstrate that genetic insulators can impact the expression of downstream genes, potentially hindering the design of predictable genetic circuits and constructs.

synthetic biology↗