PubMed · 13419213
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1957. GALACTOSE utilization in sucklings.. https://doi.org/10.1111/j.1753-4887.1957.tb00498.x
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Investigation of carbohydrate metabolism in lactic acid bacteria is essential for the rational selection of strains for fermentation processes, particularly in emerging applications involving non-conventional substrates or building of synthetic microbial consortia. However, establishing robust genotype-phenotype relationships remains challenging, as gene presence alone often fails to explain observed metabolic traits without considering the genomic context and regulatory architecture. In the present study, we combined hybrid genome assembly (Illumina and Oxford Nanopore) with high-throughput phenotype profiling (Biolog GENIII and PM2A) to investigate carbohydrate utilization in five Lacticaseibacillus strains. Phenotypic assays revealed clear intra- and inter-specific variability in substrate utilization. We therefore investigated whether such differences could be attributed to the organization and regulatory context of carbohydrate-associated loci, rather than to gene presence alone. Functional annotation based on COG and CAZyme databases revealed candidate genomic regions potentially involved in carbohydrate metabolism. Comparative analysis between predicted and experimentally observed substrate usage highlighted specific loci associated with carbohydrate utilization profile. The trehalose (tre) operon was conserved across all strains, while at least two distinct cellobiose-associated loci were detected in each genome. Despite the presence of these loci, L. paracasei strains were unable to metabolize cellobiose, a phenotype likely linked to the presence of a downstream TetR-type transcriptional repressor within the cellobiose (cel) operon. Additionally, a genomic region uniquely found in L. rhamnosus strains was associated with gentiobiose utilization, consistent with phenotypic observations. Overall, these findings highlight the importance of integrating phenotypic validation with complete genome context to support the identification of candidate structural and regulatory determinants of carbohydrate utilization in lactic acid bacteria. KEY POINTS: • Phenotype microarrays reveal metabolic traits of interest in isolated strains. • Regulatory context is key to understanding carbohydrate metabolism differences. • Basis of subspecies-dependent cellobiose metabolism in L. paracasei is provided.
Here we report the draft genome sequence of Naganishia friedmannii (formerly Cryptococcus friedmannii) isolate, a Basidiomycota yeast commonly found in some of the most extreme environments of the Earth's cryosphere. We isolated N. friedmannii strain Llullensis from soils at 6000 m above sea level on Volcán Llullaillaco, Argentina. The genome was 22.2 Mb with 6251 identified protein coding genes. Proteins known to be associated with thermal, osmotic, and radiation stress were identified in the genome. Comparative analysis with seven other Naganishia genomes revealed unique features underlying its polyextremophilic lifestyle. Naganishia friedmannii showed an expansion of genes involved in breaking down plant-derived carbohydrates, supporting the hypothesis that it survives at high elevations by metabolizing wind-deposited organic matter. Surprisingly, many genes involved in cell-cycle checkpoints and DNA repair were missing, as in several other Naganishia species. This extensive loss may be adaptive in extreme environments prone to abiotic stress, where a high mutation rate could generate advantageous traits, and reduced cell-cycle control may allow for faster reproduction that would be advantageous for rapid growth during brief periods of soil wetting following rare snow events.
BACKGROUND AND AIMS: Plants need some kind of stored resources to resprout after shoot destruction. The aim of this study was to determine the relative importance of carbohydrate and nitrogen (N) storage levels for their ability to resprout. METHODS: A shoot clipping experiment was conducted on Quercus crispula seedlings, which were grown in a factorial experimental design, with two light levels (40% and 3% of full light) and three nutrient concentrations (low, medium and high). KEY RESULTS: At the time of shoot clipping (the end of spring leaf expansion), seedlings exposed to 40% light had an average total non-structural carbohydrate (TNC) concentration of 17.0% in their roots compared with 4.9% in the roots of seedlings exposed to 3% light, and the average amount of TNC (TNC pools) in the roots was 203.8 mg and 20.0 mg at 40% light and 3% light, respectively. In contrast, root N concentration averaged 2.3% in the 3% light treatment compared with 1.2% in the 40% light treatment, and it increased with successive rises in nutrient concentrations at both light levels. Regardless of the nutrient status, at the 40% light level >80% of the seedlings resprouted after shoot clipping. Few seedlings, however, resprouted at the 3% light level, particularly in the medium- and high-nutrient treatments. Furthermore, both root TNC concentrations and TNC pools decreased after resprouting, but the amount of root N remained constant. CONCLUSIONS: These results suggest that carbohydrate storage has a stronger influence on resprouting in Quercus crispula than N storage. However, the size of the resprouting shoot was positively correlated with the amount of both N and TNC in roots. The level of N storage is, therefore, also important for the growth of resprouting shoots.