Dataset Information

Decoding the similarities and differences among mycobacterial species.

ABSTRACT: Mycobacteriaceae comprises pathogenic species such as Mycobacterium tuberculosis, M. leprae and M. abscessus, as well as non-pathogenic species, for example, M. smegmatis and M. thermoresistibile. Genome comparison and annotation studies provide insights into genome evolutionary relatedness, identify unique and pathogenicity-related genes in each species, and explore new targets that could be used for developing new diagnostics and therapeutics. Here, we present a comparative analysis of ten-mycobacterial genomes with the objective of identifying similarities and differences between pathogenic and non-pathogenic species. We identified 1080 core orthologous clusters that were enriched in proteins involved in amino acid and purine/pyrimidine biosynthetic pathways, DNA-related processes (replication, transcription, recombination and repair), RNA-methylation and modification, and cell-wall polysaccharide biosynthetic pathways. For their pathogenicity and survival in the host cell, pathogenic species have gained specific sets of genes involved in repair and protection of their genomic DNA. M. leprae is of special interest owing to its smallest genome (1600 genes and ~1300 psuedogenes), yet poor genome annotation. More than 75% of the pseudogenes were found to have a functional ortholog in the other mycobacterial genomes and belong to protein families such as transferases, oxidoreductases and hydrolases.

SUBMITTER: Malhotra S

PROVIDER: S-EPMC5595346 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Decoding the similarities and differences among mycobacterial species.

Malhotra Sony S Vedithi Sundeep Chaitanya SC Blundell Tom L TL

PLoS neglected tropical diseases 20170830 8

Mycobacteriaceae comprises pathogenic species such as Mycobacterium tuberculosis, M. leprae and M. abscessus, as well as non-pathogenic species, for example, M. smegmatis and M. thermoresistibile. Genome comparison and annotation studies provide insights into genome evolutionary relatedness, identify unique and pathogenicity-related genes in each species, and explore new targets that could be used for developing new diagnostics and therapeutics. Here, we present a comparative analysis of ten-myc ...[more]

PMID: 28854187

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Project description:Yield losses due to cultivation in saline soils is a common problem all over the world as most crop plants are glycophytes and, hence, susceptible to salt stress. The use of halophytic crops could be an interesting alternative to cope with this issue. The Amaranthaceae family comprises by far the highest proportion of salt-tolerant halophytic species. Amaranth and quinoa belong to this family, and their seeds used as pseudo-cereal grains have received much attention in recent years because of their exceptional nutritional value. While advances in the knowledge of salt tolerance mechanisms of quinoa have been remarkable in recent years, much less attention was received by amaranth, despite evidences pointing to amaranth as a promising species to be grown under salinity. In order to advance in the understanding of strategies used by amaranth to confront salt stress, we studied the comparative responses of amaranth and quinoa to salinity (100 mM NaCl) at the physiological, anatomical, and molecular levels. Amaranth was able to exhibit salt tolerance throughout its life cycle, since grain production was not affected by the saline conditions applied. The high salt tolerance of amaranth is associated with a low basal stomatal conductance due to a low number of stomata (stomatal density) and degree of stomata aperture (in adaxial surface) of leaves, which contributes to avoid leaf water loss under salt stress in a more efficient way than in quinoa. With respect to Na+ homeostasis, amaranth showed a pattern of Na+ distribution throughout the plant similar to glycophytes, with the highest accumulation found in the roots, followed by the stem and the lowest one detected in the leaves. Contrarily, quinoa exhibited a Na+ includer character with the highest accumulation detected in the shoots. Expression levels of main genes involved in Na+ homeostasis (SOS1, HKT1s, and NHX1) showed different patterns between amaranth and quinoa, with a marked higher basal expression in amaranth roots. These results highlight the important differences in the physiological and molecular responses of amaranth and quinoa when confronted with salinity.

Dataset Information

Decoding the similarities and differences among mycobacterial species.

Publications

Decoding the similarities and differences among mycobacterial species.

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