Biology Reference
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of the Calvin cycle genes returned to the initial levels while transcription
of the oxidative pentose phosphate pathway genes remained high, which is
consistent with known metabolic aspects of vegetative cells and heterocysts,
respectively.
3.5.2. Directional RNA sequencing in
Anabaena
sp. strain PCC 7120
The study by
Flaherty et al. (2011)
was performed using directional RNA-
Seq to analyse the
Anabaena
transcriptome during nitrogen stepdown. By
using this technique, they obtained information on transcript abundance
and boundaries, including detection of operons, and on the length of the
untranslated region (UTR) of each transcript. The results, represented in
RPKM (reads per kilobase of coding sequence model per million mapped
reads in the sample), showed that most of the genes differentially transcribed
upon nitrogen deprivation were activated. The fact that genes known to
be regulated early after nitrogen deprivation, such as
amt4
and
amt1
(
Paz-
Yepes, Merino-Puerto, Herrero, & Flores, 2008
) or the
urt
operon (
Val-
ladares, Montesinos, Herrero, & Flores, 2002
), were not yet differentially
expressed at 6 h in this analysis suggests that the acclimation to nitrogen-
depleted medium in this work was delayed with respect to previous analy-
ses (hence, we have chosen not to include this time point in
Table 8.1
).
On the chromosome, 434 genes were substantially upregulated at 12 h and
396 genes were upregulated at 21 h. In contrast, only 32 and 35 genes were
downregulated at 12 h and 21 h, respectively. Among the genes showing
the highest induction 12 h after nitrogen stepdown, there were those in the
Hep island, a number encoding glycosyl transferases (probably involved in
the formation of the heterocyst envelope too), and several encoding regula-
tors (including NtcA and PatS). The genes activated at both 12 and 21 h
included those encoding some enzymes expressed in the mature heterocyst,
such as
ald
(
Pernil et al., 2010
),
cphB1
(
Picossi et al., 2004
),
glnA
(
Valladares
et al., 2004
), and
invB
(
López-Igual et al., 2010
). The genes showing highest
induction at 21 h were involved in the function of the heterocyst, includ-
ing the
nifHDK
gene cluster, the
cox3
operon,
hupLS
(encoding an uptake
hydrogenase), etc., and in the formation of the Hgl layer.
3.5.3. Transcription start point mapping in
Anabaena
sp.
strain PCC 7120
The transcriptomic analysis carried out by
Mitschke, Vioque, Haas, Hess,
and Muro-Pastor (2011)
addressed the differential use of transcriptional start
points (TSPs) in ammonium-grown cells and in cells incubated for 8 h in
