Strand-specific RNA-seq analysis of the Lactobacillus delbrueckii subsp. bulgaricus transcriptome

Abstract

Lactobacillus delbrueckii subsp. bulgaricus 2038 (Lb. bulgaricus 2038) is an industrial bacterium that is used as a starter for dairy products. We proposed several hypotheses concerning its industrial features previously. Here, we utilized RNA-seq to explore the transcriptome of Lb. bulgaricus 2038 from four different growth phases under whey conditions. The most abundantly expressed genes in the four stages were mainly involved in translation (for the logarithmic stage), glycolysis (for control/lag stages), lactic acid production (all the four stages), and 10-formyl tetrahydrofolate production (for the stationary stage). The high expression of genes like d-lactate dehydrogenase was thought as a result of energy production, and consistent expression of EPS synthesis genes, the restriction-modification (RM) system and the CRISPR/Cas system were validated for explaining the advantage of this strain in yoghurt production. Several postulations, like NADPH production through GapN bypass, converting aspartate into carbon-skeleton intermediates, and formate production through degrading GTP, were proved not working under these culture conditions. The high expression of helicase genes and co-expressed amino acids/oligopeptides transporting proteins indicated that the helicase might mediate the strain obtaining nitrogen source from the environment. The transport system of Lb. bulgaricus 2038 was found to be regulated by antisense RNA, hinting the potential application of non-coding RNA in regulating lactic acid bacteria (LAB) gene expression. Our study has primarily uncovered Lb. bulgaricus 2038 transcriptome, which could gain a better understanding of the regulation system in Lb. bulgaricus and promote its industrial application.

Multi-omics Analysis Sheds Light on the Evolution and the Intracellular Lifestyle Strategies of Spotted Fever Group Rickettsia spp.

“…Although Rickettsia genomes evolved by reductive evolution, 1–2% of the genes, either split or fragments, may still be active, thus corroborating previous studies that demonstrated transcription of several split/fragment genes in R. conorii (Ogata et al, 2001), Mycobacterium leprae (Akama et al, 2009) and Lactobacillus delbrueckii (Zheng et al, 2016). The expressed split genes were thought to conserve functional domains, or proposed to function as a class of non-coding RNAs and act as riboregulators at both the transcriptional and post-transcriptional levels (Erdmann et al, 2001; Zheng et al, 2016). However, the remaining altered genes were not expressed, suggesting that they may have lost their functions (i.e., by becoming pseudogenes).…”

A long and abundant non-coding RNA in Lactobacillus salivarius

“…RNA-seq studies are additionally informative, because they provide enhancement of the accuracy of existing genome annotations, for example in Bacillus anthracis [ 43 ]. A few RNA-seq studies have been recently described in Lactobacillus species [ 44–49 ]. The study by Zheng et al on Lactobacillus delbrueckii subsp.…”

Proteomes of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5 Incubated in Milk at Optimal and Low Temperatures

“…This result was consistent with higher quantities of ManM in L. casei Zhang when cultured in soymilk ( 29 ) and increased transcripts for the glucose/mannose-specific PTS during L. delbrueckii subsp. bulgaricus 2038 incubation in whey ( 18 ). Taken together, these findings indicate that L. delbrueckii subsp.…”

“…The need for purine biosynthesis and salvage proteins in milk is supported by transcriptome analyses of L. delbrueckii subsp. bulgaricus 2038 and ATCC BAA-365 in whey and skim milk, respectively ( 4 , 18 ). The production of purine biosynthetic proteins was also elevated in other LAB (e.g., Lactobacillus helveticus , L. casei , and Lactococcus lactis ) when grown in milk ( 29 – 31 ).…”

“…However, identification of the precise and specialized adaptations of L. delbrueckii subsp. bulgaricus to milk have been limited to measuring its transcriptome when grown in whey ( 18 ) or in reconstituted skim milk together with S. salivarius subsp. thermophilus ( 4 ).…”