APPLIED MICROBIAL AND CELL PHYSIOLOGY
The novel sRNA s015 improves nisin yield by increasing acid
tolerance of Lactococcus lactis F44
Ya nni L i
Received: 12 April 2017 /Revised: 16 June 2017 / Accepted: 19 June 2017 / Published online: 9 July 2017
Springer-Verlag GmbH Germany 2017
Abstract Nisin, a polycyclic antibacterial peptide produced by
Lactococcus lactis, is stable at low pH. Improving the acid tol-
erance of L. lactis could thus enhance nisin yield. Small non-
coding RNAs (sRNAs) play essential roles in acid tolerance by
regulating their target mRNAs at the post-transcriptional level.
In this study, a novel sRNA, s015, was identified in L. lactis F44
via the use of RNA sequencing, qRT-PCR analysis, and
Northern blotting. s015 improved the acid tolerance of
L. lactis and boosted nisin yield at low pH. In silico predictions
enabled us to construct a library of possible s015 target mRNAs.
Statistical analysis and validation suggested that s015 contains a
highly conserved region (5′-GAAAAAAAC-3′)thatlikelyen-
compasses the regulatory core of the sRNA. atpG, busAB, cysD,
ilvB, tcsR, ung, yudD,andywdA were verified as direct targets of
s015, and the interactions between s015 and its target genes
were elucidated. This work provided new insight into the adap-
tation mechanism of L. lactis under acid stress.
Keywords L. lactis
Bacteria are subjected to various kinds of environmental stress-
es, including heat/cold shock, oxidative stress, osmotic stress,
and low pH conditions (Romeo et al. 2007; Wang et al. 2015,
2016b;Zereetal.2015). In order to cope with enormous en-
vironmental fluctuations, microorganisms have evolved vari-
ous mechanisms to maintain the intracellular homeostasis.
Small non-coding RNAs (sRNAs) play essential roles in reg-
ulating the growth and survival via post-transcriptional control
of gene expression in both eukaryotic and prokaryotic cells
(Wagner and Romby 2015). Furthermore, sRNAs can be in-
duced by environmental changes (Siqueira et al. 2016) and act
as crucial regulators for stress responses (Wang et al. 2015,
2016b;Zereetal.2015) and virulence (Bardill et al. 2011).
For example, the sRNAs ArcZ, DsrA,andRprA contribute to
acid tolerance in Escherichia coli, and DsrA and RprA are
induced under acid stress (Bak et al. 2014). Located between
and on the opposite strand of genes encoding two acid re-
sponse transcriptional regulators called gadX and gadW,the
sRNA gadY can form base pairs with the 3′-untranslated region
of the gadX mRNA, thereby conferring increased stability and
allowing for accumulation of gadX mRNA and increased ex-
pression of downstream acid resistance genes (Opdyke et al.
2004). Additionally, in Synechocystis, the expression of the
sRNA NsiR4 was induced by nitrogen limitation (Klahn et al.
2015), as was NrsZ (nitrogen-regulated sRNA) (Wenner et al.
Although small non-coding RNAs represent a very re-
cent discovery, examples of sRNAs in Gram-positive bac-
teria are still plentiful. In Lactococcus lactis MG1363, a
recently published transcriptome landscape revealed novel
hypothetical small regulatory RNAs involved in carbon up-
take and metabolism. Although analysis indicated some
previously undescribed small RNAs that could have a
J.Q. and Q.C. contributed equally to this work.
Electronic supplementary material The online version of this article
(doi:10.1007/s00253-017-8399-x) contains supplementary material,
which is available to authorized users.
* Jianjun Qiao
Department of Pharmaceutical Engineering, School of Chemical
Engineering and Technology, Tianjin University, Tianjin, China
Key Laboratory of Systems Bioengineering, Ministry of Education,
SynBio Research Platform, Collaborative Innovation Center of
Chemical Science and Engineering, Tianjin, China
Appl Microbiol Biotechnol (2017) 101:6483–6493