We are analyzing https://link.springer.com/article/10.1186/s12866-014-0276-5.

Title:
Identifying feasible metabolic routes in Mycobacterium smegmatis and possible alterations under diverse nutrient conditions | BMC Microbiology
Description:
Background Many studies on M. tuberculosis have emerged from using M. smegmatis MC 2 155 (Msm), since they share significant similarities and yet Msm is non-pathogenic and faster growing. Although several individual molecules have been studied from Msm, many questions remain open about its metabolism as a whole and its capability to be versatile. Adaptability and versatility are emergent properties of a system, warranting a molecular systems perspective to understand them. Results We identify feasible metabolic pathways in Msm in reference condition with transcriptome, phenotypic microarray, along with functional annotation of the genome. Together with transcriptome data, specific genes from a set of alternatives have been mapped onto different pathways. About 257 metabolic pathways can be considered to be feasible in Msm. Next, we probe cellular metabolism with an array of alternative carbon and nitrogen sources and identify those that are utilized and favour growth as well as those that do not support growth. In all, about 135 points in the entire metabolic map are probed. Analyzing growth patterns under these conditions, lead us to hypothesize different pathways that can become active in various conditions and possible alternate routes that may be induced, thus explaining the observed physiological adaptations. Conclusions The study provides the first detailed analysis of feasible pathways towards adaptability. We obtain mechanistic insights that explain observed phenotypic behaviour by studying gene-expression profiles and pathways inferred from the genome sequence. Comparison of transcriptome and phenome analysis of Msm and Mtb provides a rationale for understanding commonalities in metabolic adaptability.
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Keywords {🔍}

pubmed, msm, growth, article, google, scholar, central, cas, mycobacterium, expression, carbon, analysis, pathways, metabolic, smegmatis, gene, phenotypic, genome, data, genes, mtb, file, conditions, metabolism, additional, sources, figure, tuberculosis, enzymes, microarray, high, expressed, source, nutrient, reference, sequence, similar, acid, msmeg, condition, organism, profile, functional, nitrogen, proteins, feasible, plates, plate, observed, transporters,

Topics {✒️}

anupam singh & nagasuma chandra birds eye-view author information authors feasible paths nagasuma chandra alpha-methyl-d-glucoside group gene-expression profile collected integrated view author correspondence genomic view jyothi padiadpu studying gene-expression profiles article baloni article download pdf y-axis represents time gene expression profile open access license x-axis represents time curve-parameter estimation strategies peptidoglycan inhibitor d-cycloserine full size image gene expression profiles high-throughput phenotypic testing alpha-d-ribose-phosphate feasible metabolic pathways intra-array normalization deals questions remain open l-serine ammonia lyase isotopomer-assisted metabolite analysis attainable metabolic routes mycobacterium smegmatis d-alanine gene redundancy central carbon metabolism related subjects genome-wide studies increases obtain transcriptome profiles central carbon metabolites genome-scale structural analysis growth profile compared full access purine salvage pathways gene expression values privacy choices/manage cookies metabolic network illustrate expression profile average gene expression normalized gene expression connecting diverse pieces selected metabolic pathways phenotypic microarray analysis

Questions {❓}

Lopez-Marin LM, Segura E, Hermida-Escobedo C, Lemassu A, Salinas-Carmona MC: 6,6?
PM plates were inoculated with 100?
The pellet was resuspended in 100?

Schema {🗺️}

WebPage:
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         description:Many studies on M. tuberculosis have emerged from using M. smegmatis MC 2 155 (Msm), since they share significant similarities and yet Msm is non-pathogenic and faster growing. Although several individual molecules have been studied from Msm, many questions remain open about its metabolism as a whole and its capability to be versatile. Adaptability and versatility are emergent properties of a system, warranting a molecular systems perspective to understand them. We identify feasible metabolic pathways in Msm in reference condition with transcriptome, phenotypic microarray, along with functional annotation of the genome. Together with transcriptome data, specific genes from a set of alternatives have been mapped onto different pathways. About 257 metabolic pathways can be considered to be feasible in Msm. Next, we probe cellular metabolism with an array of alternative carbon and nitrogen sources and identify those that are utilized and favour growth as well as those that do not support growth. In all, about 135 points in the entire metabolic map are probed. Analyzing growth patterns under these conditions, lead us to hypothesize different pathways that can become active in various conditions and possible alternate routes that may be induced, thus explaining the observed physiological adaptations. The study provides the first detailed analysis of feasible pathways towards adaptability. We obtain mechanistic insights that explain observed phenotypic behaviour by studying gene-expression profiles and pathways inferred from the genome sequence. Comparison of transcriptome and phenome analysis of Msm and Mtb provides a rationale for understanding commonalities in metabolic adaptability.
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      headline:Identifying feasible metabolic routes in Mycobacterium smegmatis and possible alterations under diverse nutrient conditions
      description:Many studies on M. tuberculosis have emerged from using M. smegmatis MC 2 155 (Msm), since they share significant similarities and yet Msm is non-pathogenic and faster growing. Although several individual molecules have been studied from Msm, many questions remain open about its metabolism as a whole and its capability to be versatile. Adaptability and versatility are emergent properties of a system, warranting a molecular systems perspective to understand them. We identify feasible metabolic pathways in Msm in reference condition with transcriptome, phenotypic microarray, along with functional annotation of the genome. Together with transcriptome data, specific genes from a set of alternatives have been mapped onto different pathways. About 257 metabolic pathways can be considered to be feasible in Msm. Next, we probe cellular metabolism with an array of alternative carbon and nitrogen sources and identify those that are utilized and favour growth as well as those that do not support growth. In all, about 135 points in the entire metabolic map are probed. Analyzing growth patterns under these conditions, lead us to hypothesize different pathways that can become active in various conditions and possible alternate routes that may be induced, thus explaining the observed physiological adaptations. The study provides the first detailed analysis of feasible pathways towards adaptability. We obtain mechanistic insights that explain observed phenotypic behaviour by studying gene-expression profiles and pathways inferred from the genome sequence. Comparison of transcriptome and phenome analysis of Msm and Mtb provides a rationale for understanding commonalities in metabolic adaptability.
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         Mycobacterium smegmatis
         Feasible metabolic paths
         Phenotypic microarray
         Gene expression
         Gene redundancy
         Adaptation
         Microbiology
         Biological Microscopy
         Mycology
         Parasitology
         Virology
         Life Sciences
         general
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            address:
               name:Supercomputer Education and Research Centre, IISc, Bangalore, India
               type:PostalAddress
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               type:PostalAddress
            type:Organization
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            address:
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               type:PostalAddress
            type:Organization
      name:Kuldeepkumar R Gupta
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               type:PostalAddress
            type:Organization
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            address:
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      name:Molecular Biophysics Unit, IISc, Bangalore, India
      name:Department of Biochemistry, IISc, Bangalore, India

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